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GIT Logs

This is a list of recent commits to git.bioconductor.org, the devel(development) branch of the Bioconductor GIT repository.

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Package: AlphaMissenseR
Commit: 89b2f95728f82ec2fc4ccadf254c3138815c5d40
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2024-10-16 12:36:31 -0400
Commit message:

 version bump
Package: AlphaMissenseR
Commit: 01c9a13ca6246a6cd9c3c17a7d56eb5eac23420d
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2024-10-16 12:36:07 -0400
Commit message:

 Merge branch 'ccb-hms-add_orcid' into devel

- closes #9
Package: AlphaMissenseR
Commit: a2e5f39d41e17f5234bad18af76a2c89f796409b
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2024-10-16 15:43:06 +0000
Commit message:

 wording suggestion to reflect ClinVar's clinical classes
Package: AlphaMissenseR
Commit: c5090a09b663d5dd2f07e0661d8eb15aac1b8755
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2024-10-16 15:39:03 +0000
Commit message:

 orcid for @tram-nguyen-n
Package: PolySTest
Commit: b3a3fe4e3304cb8f4b0eaaa0592de95e0ceba0ee
Author: veitveit <veits@bmb.sdu.dk>
Date: 2024-10-16 18:16:34 +0200
Commit message:

 some minor final fixes
Package: PolySTest
Commit: d3a586874c6ffc8283b62014d51943d398970bcd
Author: veitveit <veits@bmb.sdu.dk>
Date: 2024-08-19 17:55:14 +0200
Commit message:

 corrected metadata call
Package: PolySTest
Commit: 137440006dbed640b61888cee05afd86b0ea515e
Author: veitveit <veits@bmb.sdu.dk>
Date: 2024-08-09 09:43:06 +0200
Commit message:

 small fixes
Package: SingleMoleculeFootprinting
Commit: f6149e11e1fea22b73e1908b28eb387d87e49a6f
Author: GuidoBarzaghi <guidobarzaghi@gmail.com>
Date: 2024-10-16 18:14:23 +0200
Commit message:

 round of devtools check
Package: RAIDS
Commit: 6667021a261d158a677faec4eabe3affc36e40df
Author: belleau <belleau@GENESDEV10.cshl.edu>
Date: 2024-10-16 11:26:03 -0400
Commit message:

 Update Description
Package: RAIDS
Commit: 7bceec5fdc525eb83b92b88c711ac6f907d2644f
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2024-10-16 11:01:02 -0400
Commit message:

 Merge pull request #564 from belleau/main

Update to parse the plink output for LD blocks.
Package: RAIDS
Commit: 6c886385d8358b074e66c7af2548736695d91d20
Author: belleau <belleau@GENESDEV10.cshl.edu>
Date: 2024-10-16 10:58:10 -0400
Commit message:

 Correct example for addGDS1KGLDBlock
Package: RAIDS
Commit: 841e6a9820163f33f5e333ac875a25040824f29e
Author: belleau <belleau@GENESDEV10.cshl.edu>
Date: 2024-10-16 10:54:23 -0400
Commit message:

 Merge branch 'main' of https://github.com/belleau/RAIDS
Package: RAIDS
Commit: 18056f22fcb6ee35d4824ded097611acc82a6284
Author: belleau <belleau@GENESDEV10.cshl.edu>
Date: 2024-10-16 10:47:30 -0400
Commit message:

 Update to parse the plink output for LD blocks.
Package: RAIDS
Commit: 6bbb29af97da20a7f7a6a7fb1b0ea51fd48dda91
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2024-10-16 10:24:58 -0400
Commit message:

 Merge pull request #563 from adeschen/main

Update main vignette
Package: RAIDS
Commit: bc8ec34d5c56fa4bbb805f11a050e0290b0d0057
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-10-16 10:14:56 -0400
Commit message:

 Update main vignette
Package: RAIDS
Commit: b4a3551bb05ab808b8f6799a8e60aedd8e95bdd9
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2024-10-16 02:28:13 -0400
Commit message:

 Merge pull request #562 from adeschen/main

Update main vignette
Package: RAIDS
Commit: e93f53647ad88d213572924b556e48c9d8bb33a3
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-10-16 00:42:34 -0400
Commit message:

 Merge branch 'main' of https://github.com/adeschen/RAIDS
Package: RAIDS
Commit: 4762a5b156506b138ea6e741e60be843462102d1
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-10-16 00:42:24 -0400
Commit message:

 Update main vignette
Package: RAIDS
Commit: 5aeea96938ffd8403028d5343289655e66d4e12e
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2024-10-16 00:42:02 -0400
Commit message:

 Merge pull request #561 from adeschen/main

Remove old image for main steps section
Package: RAIDS
Commit: 4008f4fd4a749a6b80868e568a67a1e51a8adf04
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2024-10-16 00:20:52 -0400
Commit message:

 Merge branch 'KrasnitzLab:main' into main
Package: RAIDS
Commit: 6256b604bdea01aecb94fabd877c2ffd5c95bb11
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2024-10-15 23:54:38 -0400
Commit message:

 Merge pull request #560 from adeschen/main

Update vignettes
Package: RAIDS
Commit: d3a2b96c9a9dc89067eac9687910738c7383be98
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-10-15 23:54:29 -0400
Commit message:

 Merge branch 'main' of https://github.com/adeschen/RAIDS
Package: RAIDS
Commit: 31cae4f58f2e3279425092a42976f9f8b64b7ff9
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-10-15 23:54:20 -0400
Commit message:

 Remove old image for main steps section
Package: RAIDS
Commit: e92a07aa1e8c3a64d757d82c66d8c66e4289187b
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2024-10-15 23:08:00 -0400
Commit message:

 Merge branch 'KrasnitzLab:main' into main
Package: RAIDS
Commit: 2af94c5eb535a7c2174b4348487d8cf32d6b188a
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-10-15 23:07:30 -0400
Commit message:

 Merge branch 'main' of https://github.com/adeschen/RAIDS
Package: RAIDS
Commit: b82f880c661368365618c680570dcce8ab65ed0d
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-10-15 23:07:19 -0400
Commit message:

 Warning in red about new functions available
Package: RAIDS
Commit: 540e3fb443948b2b2f1bb1cb9624458c2e56538c
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2024-10-15 23:02:42 -0400
Commit message:

 Merge pull request #559 from adeschen/main

Move old vignette
Package: RAIDS
Commit: f2aab1910d0ce019f1c0ae79dd5044ad4a4c323d
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2024-10-15 19:15:45 -0400
Commit message:

 Merge branch 'KrasnitzLab:main' into main
Package: RAIDS
Commit: bb4fbde76c2aae01ac7caeba6db4d1016e5fbc59
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2024-10-15 19:14:41 -0400
Commit message:

 Merge pull request #558 from belleau/main

Add function processBlockChr and correct some importFrom
Package: RAIDS
Commit: b6c173d111179073552a06a0640313a412d7f3a7
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-10-15 19:11:12 -0400
Commit message:

 Adding wrapper vignette
Package: RAIDS
Commit: 79692f8446fe15cb25e8c4552414fe936a507a17
Author: belleau <belleau@belleauMBP.cshl.edu>
Date: 2024-10-15 19:00:22 -0400
Commit message:

 Add function addGeneBlockRefAnnot wrapper of addGeneBlockGDSRefAnnot
Package: RAIDS
Commit: b0e3eab2b78418c57aa3e851b4a351bc0af6a631
Author: belleau <belleau@belleauMBP.cshl.edu>
Date: 2024-10-15 18:02:56 -0400
Commit message:

 Add function processBlockChr and correct some importFrom
Package: RAIDS
Commit: a5d072f124fb2c00c1a5ccc9684068b7033d96d2
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-10-15 18:02:14 -0400
Commit message:

 Update main steps figure
Package: RAIDS
Commit: ca39ffd9cae4f79456b0c714c2dc809fc8c57844
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2024-10-15 17:27:38 -0400
Commit message:

 Merge pull request #557 from adeschen/main

update github action check-bioc
Package: RAIDS
Commit: 4073172c7a45efd6dab48b99073ab6810a569564
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2024-10-15 16:44:49 -0400
Commit message:

 Merge branch 'KrasnitzLab:main' into main
Package: RAIDS
Commit: f09f3734550c917ec97a8987210769512564805e
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2024-10-15 16:44:37 -0400
Commit message:

 Merge pull request #556 from belleau/main

Update generatePhase1KG2GDS and add wrapper generatePhaseRef
Package: RAIDS
Commit: 7a0f03c4a53c63fd64afd3391a1d57055a20ffc5
Author: belleau <belleau@belleauMBP.cshl.edu>
Date: 2024-10-15 16:25:51 -0400
Commit message:

 Update generatePhase1KG2GDS and add wrapper generatePhaseRef
Package: RAIDS
Commit: d0178e67e96d7e4602c464e900082382d62f37e4
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2024-10-15 16:08:59 -0400
Commit message:

 Update check-bioc.yaml
Package: RAIDS
Commit: 20bfad8ffff6a3262d1bbe4eb58de8d84a089766
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2024-10-15 14:42:36 -0400
Commit message:

 Merge pull request #555 from adeschen/main

Update github action checkbioc
Package: RAIDS
Commit: 0a49b99ab6a01e25796a0d911552a9f02e74ff35
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2024-10-15 11:54:01 -0400
Commit message:

 Update check-bioc.yaml
Package: RAIDS
Commit: cf062dd85bd3df1ca73bf54951c2d9f78cc87d09
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2024-10-15 11:13:58 -0400
Commit message:

 Update check-bioc.yaml
Package: RAIDS
Commit: 3fab12bb011d6e18279591b17440333c7e4230a1
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2024-10-15 11:09:40 -0400
Commit message:

 Merge pull request #554 from belleau/main

Update
Package: RAIDS
Commit: 2856a66f7f6f8609a9bb5897faab5512ba67c1fd
Author: belleau <belleau@belleauMBP.local>
Date: 2024-10-15 08:24:09 -0400
Commit message:

 Add the function identifyRelativeRef wrapper of identifyRelative
Package: RAIDS
Commit: d33eb477af08d27f1247ee021d5973547fecf042
Author: belleau <belleau@belleauMBP.cshl.edu>
Date: 2024-10-11 19:16:50 -0400
Commit message:

 Add the function getRefSuperPop
Package: RAIDS
Commit: 5e45004923a0b760971dd7667264198445ce7c52
Author: belleau <belleau@belleauMBP.cshl.edu>
Date: 2024-10-11 17:43:19 -0400
Commit message:

 Add a test for createStudy2GDS1KG.
Package: RAIDS
Commit: e5154266325087b15e911e5b02de1110361b4dbf
Author: belleau <belleau@WIGMAPLE.cshl.edu>
Date: 2024-10-11 13:14:39 -0400
Commit message:

 Don't allow createStudy2GDS1KG when the gds exists.
Package: RAIDS
Commit: 5831d42fe6754e8f376a83fcc666fe38ffa0e1b1
Author: belleau <belleau@belleauMBP.cshl.edu>
Date: 2024-10-10 17:37:31 -0400
Commit message:

 Solve a variable problem in profileAncestry and add some comments
Package: RAIDS
Commit: a656ac9a91d9969d74fec5104c7b82c5a3bcc45f
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2024-09-11 14:22:19 -0400
Commit message:

 Merge pull request #553 from belleau/main

Update chapter
Package: RAIDS
Commit: 8f57ec6e2f670e22b2c088766075836004b27384
Author: belleau <belleau@belleauMBP.home>
Date: 2024-09-11 12:31:47 -0400
Commit message:

 Add function createAUROCGraph
Package: RAIDS
Commit: 98cc871e4553f2bbbe65d6b02186d2958113e054
Author: belleau <belleau@belleauMBP.home>
Date: 2024-09-11 12:00:19 -0400
Commit message:

 Update function inferAncestry and inferAncestryGeneAware
Package: RAIDS
Commit: 33ac4f216f79b3cdb31b5a07db1306a6e10991f3
Author: belleau <belleau@belleauMBP.home>
Date: 2024-09-11 11:08:41 -0400
Commit message:

 Add function wrapperAncestry
Package: RAIDS
Commit: 3938d28750a8421adad96dda3fed0811eac56853
Author: belleau <belleau@belleauMBP.home>
Date: 2024-09-11 10:35:48 -0400
Commit message:

 Changed the man of profileAncestry
Package: RAIDS
Commit: d24b7cdbcec599973220879c2e2cd5f3135b3c2a
Author: belleau <belleau@belleauMBP.home>
Date: 2024-09-11 10:12:49 -0400
Commit message:

 Add function profileAncestry
Package: RAIDS
Commit: dd43808389edb863c13991e40d31646b5595c97c
Author: belleau <belleau@belleauMBP.home>
Date: 2024-09-11 08:03:18 -0400
Commit message:

 Add computeAncestryFromSynthetic
Package: RAIDS
Commit: f4787cc5aa1ccf0e3273f037f2ff2ee7da4d28dd
Author: belleau <belleau@belleauMBP.cshl.edu>
Date: 2024-09-10 19:21:09 -0400
Commit message:

 Rename functions runDNAAncestryProfile to inferAncestry.Rd and runRNAAncestryProfile to inferAncestryGeneAware
Package: RAIDS
Commit: dd5daa9d89283702a6a4430e1a8ac1028d7d578c
Author: belleau <belleau@belleauMBP.cshl.edu>
Date: 2024-09-09 20:04:06 -0400
Commit message:

 Add functions runDNAAncestryProfile and runRNAAncestryProfile
Package: RAIDS
Commit: 6069e9c868980a8854e6bcde3060f64784e13f84
Author: belleau <belleau@LW28OSP01.cshl.edu>
Date: 2024-09-09 09:45:38 -0400
Commit message:

 add function select1KGPopForSynthetic in synthetic.R
Package: RAIDS
Commit: 1e18e879b526674108315cae88e1e225420f3c0c
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2024-09-05 19:29:38 -0400
Commit message:

 Merge pull request #552 from adeschen/main

Update createAccuracyGraph() to show y lab values
Package: RAIDS
Commit: 72f70d9f0858b39a448cf9b0bdce1a9d834e5ca9
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-09-05 18:49:35 -0400
Commit message:

 Update action test-coverage
Package: RAIDS
Commit: b70d066180fdff99fd1c34230172ecb0253bcb65
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-09-05 18:38:21 -0400
Commit message:

 Merge branch 'main' of https://github.com/adeschen/RAIDS
Package: RAIDS
Commit: 645f796c0bdcbebc4560545418b7cbab49195c40
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-09-05 18:38:05 -0400
Commit message:

 Update createAccuracyGraph() to show y lab values
Package: RAIDS
Commit: 37db9b678e9ef36c25bfe931e0754e8a7b4b422a
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2024-09-04 16:54:11 -0400
Commit message:

 Merge pull request #551 from belleau/main

Change csv2 to csv in generateMapSnvSel and others small update
Package: RAIDS
Commit: 930b62d29c292ade2c4910692b1fd2d494b0e943
Author: belleau <belleau@belleauMBP.cshl.edu>
Date: 2024-08-31 19:11:47 -0400
Commit message:

 In generateMapSnvSel change read.csv2 to read.csv
Package: RAIDS
Commit: 79712a42e8599ad1ca82b114250700f91c608982
Author: belleau <belleau@belleauMBP.cshl.edu>
Date: 2024-08-31 17:09:43 -0400
Commit message:

 Updata addStudyGDSSample in gdsWrapper_internal.R
Package: RAIDS
Commit: 63740226e889692ffcb5220faf9a1c5405100c88
Author: Pascal Belleau <pascal_belleau@hotmail.com>
Date: 2024-08-19 18:07:03 -0400
Commit message:

 Merge branch 'KrasnitzLab:main' into main
Package: RAIDS
Commit: fad869acbd822cc5efab387b625fec2c0e091b71
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2024-08-16 21:37:21 -0400
Commit message:

 Merge pull request #550 from adeschen/main

Add createAccuracyGraph() function, update doc and version
Package: RAIDS
Commit: 501ff815556210e3b943028934a0311dfb5afca6
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-08-16 19:09:45 -0400
Commit message:

 Update package version to 1.3.1
Package: RAIDS
Commit: aa1f9ab6f2d8f50aef1ce9c06fe73828900ebf4c
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-08-16 18:49:22 -0400
Commit message:

 Update action item to v4
Package: RAIDS
Commit: 4a66297dcce901b4dbd1a435e4ede548cfdcf115
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-08-16 18:28:14 -0400
Commit message:

 Update biocViews section
Package: RAIDS
Commit: 23f9fa526b893fcc8d3218dc8e75af43be9211ef
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-08-16 18:12:20 -0400
Commit message:

 Update to r 4.4 and bioc 3.19
Package: RAIDS
Commit: f539afbb6f99edf70e7f8a32aa3f1771c7534ab6
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-08-16 17:56:41 -0400
Commit message:

 Update test to correct error
Package: RAIDS
Commit: 38d46f1e740495cd28422565507b8a11b400df31
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-08-16 17:36:40 -0400
Commit message:

 Add createAccuracyGraph() function; change itemize to describe in doc
Package: RAIDS
Commit: 6d7c721fe46a7eaf22e2f842046ebe6036b9dd60
Author: Pascal Belleau <pascal_belleau@hotmail.com>
Date: 2024-08-05 17:46:23 -0400
Commit message:

 Merge pull request #1 from adeschen/patch-1

Update check-bioc.yaml
Package: RAIDS
Commit: 4a878216c06e2a18d44d3cb8df686861c85213a1
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2024-08-05 17:44:42 -0400
Commit message:

 Update check-bioc.yaml
Package: RAIDS
Commit: d135565ef7a1fa6cb8f5a5e725dd165574b420f3
Author: belleau <belleau@ROSE2.cshl.edu>
Date: 2024-08-05 09:41:43 -0400
Commit message:

 We stop to use pedProfile rownames. We changed function addStudyGDSSample.
Package: GSVA
Commit: 426708ca41c7eb4f867738de0e6ddb5177fd8cdd
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-10-16 17:16:30 +0200
Commit message:

 Merge branch 'devel' of github.com:rcastelo/GSVA into devel
Package: GSVA
Commit: 577c8e3a2f632b1c6561ec1bdf3ee093c9cb5de1
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-10-16 17:16:09 +0200
Commit message:

 Bump version
Package: GSVA
Commit: 1ee014ae0b3d27a5b09cba0633258f4d6c7bb218
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2024-10-16 17:09:06 +0200
Commit message:

 Merge pull request #208 from rcastelo/203-missing-data-shiny

203 missing data shiny
Package: GSVA
Commit: 65cfc9511f0fead4d913766225ba52a9d40ff587
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2024-10-16 16:10:27 +0200
Commit message:

 Merge branch 'devel' into 203-missing-data-shiny
Package: GSVA
Commit: ecf6866f52fd46e566835fd8c300fba24c08275d
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2024-10-16 15:47:56 +0200
Commit message:

 Merge pull request #207 from rcastelo/177-improve-annotation-mapping-through-readgmt

177 improve annotation mapping through readgmt
Package: GSVA
Commit: 836f86d9879d180674ca4d2cdf42e5757c477c72
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2024-10-16 15:37:18 +0200
Commit message:

 Merge branch 'devel' into 177-improve-annotation-mapping-through-readgmt
Package: GSVA
Commit: 4e259c2ee97300e3e43252c133c036d17f9116af
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2024-10-16 00:34:35 +0200
Commit message:

 add new arguments for ssGSEA missing values to Shiny app
Package: GSVA
Commit: 615667c633a690127cf860bbd16fb0f0876d87cf
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2024-10-15 21:15:11 +0200
Commit message:

 add check for readGMT() input and examples section
Package: scone
Commit: 4ef3d20e05afc7def7a623f628889e3ab5586d7b
Author: Davide Risso <risso.davide@gmail.com>
Date: 2024-10-16 17:09:13 +0200
Commit message:

 Fix version conflict
Package: scone
Commit: 19885a62e71f1b4e2a9090ca982831e7de894f09
Author: Davide Risso <risso.davide@gmail.com>
Date: 2024-10-16 17:06:16 +0200
Commit message:

 Fix problem with DelayedArray
Package: iSEEpathways
Commit: 90b7a0b755be6e4ce4267db90ed2e8650b714488
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2024-10-16 15:36:14 +0100
Commit message:

 update github action to use devel branch (#35)
Package: bedbaser
Commit: 58f6b285f975bf6fa0fb935fe1d0b7d0603e1045
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2024-10-15 17:31:26 -0400
Commit message:

 Fix @return
Package: bedbaser
Commit: c01ba939e0f9661397eaa00f93ff20179d511f9f
Author: jwokaty <jwokaty@users.noreply.github.com>
Date: 2024-10-15 17:28:49 -0400
Commit message:

 Set cache path when creating BEDbase instance (#13)

* Add bb_save
* Modify bb_save to save bedsets
Package: bedbaser
Commit: 7d0b10f3227d563ffec85ccea4674b8235c41005
Author: jwokaty <jwokaty@users.noreply.github.com>
Date: 2024-10-09 23:05:05 -0400
Commit message:

 Add restriction to AnVIL dependency (#7)
Package: xenLite
Commit: 497a06321590650222224799ee338ff9266c1894
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2024-10-16 09:54:30 -0400
Commit message:

 improve ingest handling of SCE colnames
Package: MetCirc
Commit: e4317236347cd168d03ad5a56969f07016595648
Author: Thomas Naake <thomasnaake@gmx.de>
Date: 2024-10-16 15:04:52 +0200
Commit message:

 bump to version 1.35.1 in devel
Package: MetCirc
Commit: 320bc4754839e284bc735b92babf6c2a9e0279f0
Author: Thomas Naake <thomasnaake@gmx.de>
Date: 2024-10-16 15:04:29 +0200
Commit message:

 bug fix: adjust error message for shinyCircos
Package: MetCirc
Commit: 7327b4781704c68f8b84b30230637dc54273e9c0
Author: Thomas Naake <thomasnaake@gmx.de>
Date: 2024-10-16 14:46:27 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: MetCirc
Commit: 097538c07d8ced275fb5d9eb74568bb2bc9a874d
Author: tnaake <thomasnaake@gmx.de>
Date: 2023-04-18 16:44:59 +0200
Commit message:

 Update main.yml
Package: MetCirc
Commit: cde376dcb00b1449f8ee0c3f2afa2f5b0eea7f09
Author: tnaake <thomasnaake@gmx.de>
Date: 2023-04-18 16:37:11 +0200
Commit message:

 Update main.yml
Package: MetCirc
Commit: 403fc0a2987da9f8acd13856225ad86aeef0e226
Author: tnaake <thomasnaake@gmx.de>
Date: 2023-04-18 16:34:26 +0200
Commit message:

 Update main.yml
Package: MetCirc
Commit: 2bed3a8d4d27a2d16c7b681a03db5193904847b1
Author: tnaake <thomasnaake@gmx.de>
Date: 2023-04-18 16:26:39 +0200
Commit message:

 Update main.yml
Package: geomeTriD
Commit: 0e92d442e5cf1049d9b8e65e6528fef39e8ae80e
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2024-10-16 08:12:22 -0400
Commit message:

 update basic_check workflows.
Package: geomeTriD
Commit: 1404825116f46d124661b04fdb47d7f875d76efb
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2024-10-15 09:10:17 -0400
Commit message:

 try to fix the warning of rgl.init with unloaded X11.
Package: beadarray
Commit: e16312bd4ade2a730f80ab4f980a9cf6074432f6
Author: Mark Dunning <markdunning@ra172016200198.shef.ac.uk>
Date: 2024-10-16 12:08:21 +0100
Commit message:

 Correct typo in chunk options

bump version number
Package: tidybulk
Commit: c521054cb2e79bdf255cd4a27238924f9cf167ea
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2024-10-16 21:03:15 +1030
Commit message:

 version UP
Package: tidybulk
Commit: f62606a891b9cac705cd0fd3c810740dd0c81c2b
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2024-10-16 20:59:19 +1030
Commit message:

 fix tests for new Bioconductor
Package: tidybulk
Commit: a0bdd3ff739b9f05576d6e9154f736b3f95ed127
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2024-10-16 20:18:57 +1030
Commit message:

 fix tests
Package: demuxSNP
Commit: 566ce5ac7316b8405e9ab198d2ae5b79bb7e5034
Author: michaelplynch <89206184+michaelplynch@users.noreply.github.com>
Date: 2024-10-16 10:37:06 +0100
Commit message:

  Changes to be committed:
	modified:   NEWS.md
Package: CTexploreR
Commit: 1ae75989d866a9024d4a7398f0513fb1539902d3
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-10-16 11:26:37 +0200
Commit message:

 fix news
Package: CTexploreR
Commit: ff46195d2c52fb9f486cc474ff74880c6bef2018
Author: Julie Devis <julie.devis@uclouvain.be>
Date: 2024-10-08 18:52:53 +0200
Commit message:

 updated vignette with all the new functions
Package: CTexploreR
Commit: b9f5150df64c4b5172f3450768352f7cc1508257
Author: Julie Devis <julie.devis@uclouvain.be>
Date: 2024-10-08 18:52:25 +0200
Commit message:

 Added na.omit option to hESC methylation to avoid bug
Package: CTexploreR
Commit: 3c538107b1a3325c816391236a6591bc928fdd2d
Author: Julie Devis <julie.devis@uclouvain.be>
Date: 2024-10-08 18:47:15 +0200
Commit message:

 Adapted CTdata dependancy
Package: CTexploreR
Commit: a64538b2895d0a328b61531401eb6b4d73497fb7
Author: Julie Devis <julie.devis@uclouvain.be>
Date: 2024-10-08 18:46:20 +0200
Commit message:

 Correcting typo in doc
Package: CTexploreR
Commit: baa042385162302dee7be0993a66586b83ab3ef6
Author: Julie Devis <julie.devis@uclouvain.be>
Date: 2024-10-04 19:00:15 +0200
Commit message:

 Correction following a check()
Package: CTexploreR
Commit: 4f8cd550aa042b892cf0181829bac9d739f852f6
Author: Julie Devis <julie.devis@uclouvain.be>
Date: 2024-10-04 18:17:58 +0200
Commit message:

 Update following experimentHub update
Package: CTexploreR
Commit: cc5ea2e4feb2bf0541228284272b26958fc10c47
Author: Julie Devis <julie.devis@uclouvain.be>
Date: 2024-10-04 18:01:20 +0200
Commit message:

 Added updates
Package: CTexploreR
Commit: 8c82b2033c69890cf1c22500d9d5c8bf4e52fc0a
Author: aloriot <axelle.loriot@uclouvain.be>
Date: 2024-10-04 17:57:52 +0200
Commit message:

 new function
Package: CTexploreR
Commit: 0f0d061979ec8a5c94f802e5e2000ec6b79afc73
Author: Julie Devis <julie.devis@uclouvain.be>
Date: 2024-10-04 17:38:40 +0200
Commit message:

 Dependant of CTdata latest version
Package: CTexploreR
Commit: ba61223c91d159b1c77ee6d59f2a6d71612e2824
Author: Julie Devis <julie.devis@uclouvain.be>
Date: 2024-10-04 17:38:19 +0200
Commit message:

 new dependencies with new functions
Package: CTexploreR
Commit: 4bf95ad4a562d1945b87cc911d32f16038f84a32
Author: Julie Devis <julie.devis@uclouvain.be>
Date: 2024-10-04 17:37:29 +0200
Commit message:

 Merge branch 'main' of https://github.com/UCLouvain-CBIO/CTexploreR
Package: CTexploreR
Commit: 0559591815276ed614d2883e36f89d8cbd966d3c
Author: Julie Devis <julie.devis@uclouvain.be>
Date: 2024-10-04 17:36:55 +0200
Commit message:

 documentation update
Package: CTexploreR
Commit: 3e5e4ab6b2b62e70c23d94399564127ca39db2f6
Author: aloriot <axelle.loriot@uclouvain.be>
Date: 2024-10-03 19:49:51 +0200
Commit message:

 added new colors
Package: CTexploreR
Commit: d62ad4ddf9336597d1218bf8ced40dfd09d4381a
Author: aloriot <axelle.loriot@uclouvain.be>
Date: 2024-10-03 18:05:21 +0200
Commit message:

 new function to visualize met in hESC
Package: CTexploreR
Commit: 51b7bc2ba927357d4d722e52c147460720fd0464
Author: aloriot <axelle.loriot@uclouvain.be>
Date: 2024-10-03 18:05:10 +0200
Commit message:

 new function to visualize met in fetal germ cells
Package: CTexploreR
Commit: 7686da92cf132a0e58fac0e7717779e574be3691
Author: aloriot <axelle.loriot@uclouvain.be>
Date: 2024-10-03 18:04:30 +0200
Commit message:

 added new colors
Package: CTexploreR
Commit: f5a131876d38058b32e811409bb8bf04551e54c1
Author: aloriot <axelle.loriot@uclouvain.be>
Date: 2024-10-03 18:04:20 +0200
Commit message:

 minor modif
Package: CTexploreR
Commit: 844f671afaa0ab427d8fba946ff5261706f8de42
Author: aloriot <axelle.loriot@uclouvain.be>
Date: 2024-10-03 14:51:02 +0200
Commit message:

 created function to visualize expression in early embryos
Package: CTexploreR
Commit: 8bba71d980a5b6937ceeb6d013792594f4f86b0d
Author: aloriot <axelle.loriot@uclouvain.be>
Date: 2024-10-03 14:50:42 +0200
Commit message:

 created function to visualize expression in hESC cells
Package: CTexploreR
Commit: e70504cdae9d42783c446256b9b8cc63566d0d6e
Author: aloriot <axelle.loriot@uclouvain.be>
Date: 2024-10-03 14:50:24 +0200
Commit message:

 created function to visualize expression in oocytes cells
Package: CTexploreR
Commit: 5227d982b9a88ec5bba349081955a5924aebdbef
Author: aloriot <axelle.loriot@uclouvain.be>
Date: 2024-10-03 14:50:07 +0200
Commit message:

 created function to visualize expression in fetal germ cells
Package: CTexploreR
Commit: 8f89d20514e43156a6dec10b25835c8f5ce8c61f
Author: aloriot <axelle.loriot@uclouvain.be>
Date: 2024-10-03 14:49:24 +0200
Commit message:

 minor modif
Package: CTexploreR
Commit: bef24effdb44719fedac26151d4100786e3e2972
Author: aloriot <axelle.loriot@uclouvain.be>
Date: 2024-10-03 14:49:02 +0200
Commit message:

 added new color types
Package: CTexploreR
Commit: dbfa1cbaf72cc723735c6475ba6f4b8ccd0b44c6
Author: Julie Devis <julie.devis@uclouvain.be>
Date: 2024-09-30 18:14:08 +0200
Commit message:

 Minor changes
Package: CTexploreR
Commit: ddee3a27f47d20bd658ba90c1156fe3db75cf119
Author: Julie Devis <julie.devis@uclouvain.be>
Date: 2024-09-26 20:11:17 +0200
Commit message:

 Changes following CTdata update
Package: CTexploreR
Commit: 5b38f33dfb6c39c9a10e4a9b40781288ded43287
Author: Julie Devis <julie.devis@uclouvain.be>
Date: 2024-06-28 17:11:16 +0200
Commit message:

 Update vignette
Package: CTexploreR
Commit: c901c9520faf17eb835830d97b08fa8138892bc9
Author: Julie Devis <julie.devis@uclouvain.be>
Date: 2024-06-28 16:12:34 +0200
Commit message:

 Added import of all_genes in CTexploreR
Package: CTexploreR
Commit: 1e7acbf2b9fb4fb2a3dc159940ea427865fd81e1
Author: Julie Devis <julie.devis@uclouvain.be>
Date: 2024-06-26 16:43:05 +0200
Commit message:

 Updated function code following update in CTdata datasets
Package: CTexploreR
Commit: 203de242686d62063f69ce442b44c743bcd6a5ac
Author: Julie Devis <julie.devis@uclouvain.be>
Date: 2024-06-26 13:51:32 +0200
Commit message:

 updated data
Package: CTexploreR
Commit: 6df3aff56dc59e1e84def098a9bd09ad4344c4aa
Author: Julie Devis <julie.devis@uclouvain.be>
Date: 2024-05-08 17:43:34 +0200
Commit message:

 changed CT preliminary by all genes preliminary
Package: CTexploreR
Commit: 4fdea17d0b20ab023690704d8f2f527e20b75041
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-05-07 10:25:06 +0200
Commit message:

 bump version, depend on next CTdata
Package: CTexploreR
Commit: 2d31b168babfe113af2d73174f9d2e17de4375ce
Author: Julie Devis <julie.devis@uclouvain.be>
Date: 2023-11-29 15:37:10 +0100
Commit message:

 Added InteractiveComplexHeatmap to vignette
Package: CTexploreR
Commit: 5cfe6e38fe5b10e4e172fb8e33f35d26b430a6b8
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2023-11-10 16:20:18 +0100
Commit message:

 update versions
Package: demuxSNP
Commit: 132a61dc8867b4097d1a052ac9b7e5932c877db9
Author: michaelplynch <89206184+michaelplynch@users.noreply.github.com>
Date: 2024-10-16 10:22:49 +0100
Commit message:

  Changes to be committed:
	modified:   DESCRIPTION
Package: demuxSNP
Commit: 77c4245cd25e5490e44b0e17582fe74f9814f3d4
Author: michaelplynch <89206184+michaelplynch@users.noreply.github.com>
Date: 2024-10-16 10:20:12 +0100
Commit message:

  Changes to be committed:
	modified:   man/figures/README-unnamed-chunk-15-1.png
	modified:   man/figures/README-unnamed-chunk-17-1.png
	modified:   man/figures/README-unnamed-chunk-18-1.png
	modified:   man/figures/README-unnamed-chunk-7-1.png
	modified:   man/figures/README-unnamed-chunk-9-1.png
	modified:   man/figures/README-unnamed-chunk-9-2.png
Package: demuxSNP
Commit: f9925e78fd0add8070e8d2e8b807e11e0b4713ca
Author: michaelplynch <89206184+michaelplynch@users.noreply.github.com>
Date: 2024-10-16 10:18:33 +0100
Commit message:

 Merge remote-tracking branch 'origin/main' into devel
Package: demuxSNP
Commit: 576180cc8598a962e787fe0c30fcc18ce9fe8bb6
Author: michaelplynch <89206184+michaelplynch@users.noreply.github.com>
Date: 2024-10-04 12:09:28 +0100
Commit message:

 Remove development messaging
Package: demuxSNP
Commit: d4bfe02bcdbe79defc8996829e44f943e5feb3ea
Author: michaelplynch <89206184+michaelplynch@users.noreply.github.com>
Date: 2024-10-04 11:37:20 +0100
Commit message:

 Generalise new reassign function
Package: demuxSNP
Commit: 8a208e303819fde1691b8541316490b3407894a2
Author: michaelplynch <89206184+michaelplynch@users.noreply.github.com>
Date: 2024-10-03 16:08:12 +0100
Commit message:

 Merge branch 'devel' of https://github.com/michaelplynch/demuxSNP into devel
Package: demuxSNP
Commit: 0aa8ec22a77755a55edf3dbe6c73560f53fba7ba
Author: michaelplynch <89206184+michaelplynch@users.noreply.github.com>
Date: 2024-10-03 16:07:50 +0100
Commit message:

 add min_cells description for checks
Package: demuxSNP
Commit: ea398ac8a3f6dfd96d2335c59dc97c7a74b5c317
Author: Michael Lynch <89206184+michaelplynch@users.noreply.github.com>
Date: 2024-10-03 14:52:41 +0100
Commit message:

 Merge pull request #15 from michaelplynch/devel

Devel
Package: demuxSNP
Commit: 3bb67a36fd7c312c1c2013e7b0a3475a71ee2f4a
Author: Michael Lynch <89206184+michaelplynch@users.noreply.github.com>
Date: 2024-10-03 14:43:18 +0100
Commit message:

 Merge branch 'main' into devel
Package: demuxSNP
Commit: 1cc494c0e51a4cab3075b0b796c8b7d713f35757
Author: michaelplynch <89206184+michaelplynch@users.noreply.github.com>
Date: 2024-10-03 14:31:54 +0100
Commit message:

 update messaging and vignettes.
Package: demuxSNP
Commit: 782bbbde0ef311500623d7782e0835f0b3cb441b
Author: Michael Lynch <89206184+michaelplynch@users.noreply.github.com>
Date: 2024-03-13 17:26:09 +0000
Commit message:

 Merge pull request #14 from michaelplynch/devel

merge Devel
Package: demuxSNP
Commit: 2adcd1cf60b0e8fa9b882b946e9b944fc8c0b9f6
Author: Michael <michael.lynch@ul.ie>
Date: 2024-03-13 17:04:58 +0000
Commit message:

 version bump for bioc build
Package: demuxSNP
Commit: ae60c455e77effa8617f0d5c64556c74aa6e56e8
Author: Michael <michael.lynch@ul.ie>
Date: 2024-03-13 16:57:46 +0000
Commit message:

 update messaging in balanced function
Package: demuxSNP
Commit: 005a7ddf61d092c7d8005f62c20d4e872cdecdfe
Author: Michael <michael.lynch@ul.ie>
Date: 2024-03-06 16:58:20 +0000
Commit message:

 Merge branch 'devel' of https://github.com/michaelplynch/demuxSNP into devel
Package: demuxSNP
Commit: 2b1ab0464a394ffe045e0a0342905301b8dea5b3
Author: Michael <michael.lynch@ul.ie>
Date: 2024-03-06 16:58:05 +0000
Commit message:

 updates to reassign_balanced
Package: demuxSNP
Commit: b65b15da4b0e4e2d2f0f3682a28ac2481eeaf584
Author: Michael Lynch <89206184+michaelplynch@users.noreply.github.com>
Date: 2024-02-28 16:17:46 +0000
Commit message:

 Merge pull request #13 from michaelplynch/devel

Merge devel branch
Package: demuxSNP
Commit: e285385fea82d097b772f0ea45516b96c4a92bad
Author: Michael Lynch <89206184+michaelplynch@users.noreply.github.com>
Date: 2024-02-28 16:17:27 +0000
Commit message:

 Merge branch 'main' into devel
Package: demuxSNP
Commit: 9f57fae10eb456fd910416faedb6b09818ac3be9
Author: Michael <michael.lynch@ul.ie>
Date: 2024-02-28 15:47:27 +0000
Commit message:

 update documentation in knn_balanced
Package: demuxSNP
Commit: 5195268c43b58fef3f4fdc63153d983cca3c01b0
Author: Michael <michael.lynch@ul.ie>
Date: 2024-02-28 15:34:32 +0000
Commit message:

 update hex
Package: demuxSNP
Commit: 0b5ea28488c6c3d8f3b8807cef527d054ced0bda
Author: Michael <michael.lynch@ul.ie>
Date: 2024-02-28 15:19:47 +0000
Commit message:

 add knn balanced and hex sticker
Package: demuxSNP
Commit: 3132a0e8ffe2692fe50192833171c57c3b08abca
Author: Michael <michael.lynch@ul.ie>
Date: 2024-01-05 18:32:42 +0000
Commit message:

 add reassign with jaccard distance
Package: demuxSNP
Commit: 9693c3f81cca31c3873726f38c4f1e094b5e1532
Author: Michael <michael.lynch@ul.ie>
Date: 2024-01-04 17:02:05 +0000
Commit message:

 test commit
Package: demuxSNP
Commit: 56e66c010995b6cb0df039e938ac3f726baabe18
Author: Michael Lynch <89206184+michaelplynch@users.noreply.github.com>
Date: 2023-12-19 16:54:37 +0000
Commit message:

 Update check-bioc.yml

Update R and bioc version in GHA
Package: demuxSNP
Commit: 2b653274915169f30cae71b16d26cd10ba2b5925
Author: Michael Lynch <89206184+michaelplynch@users.noreply.github.com>
Date: 2023-12-19 16:35:07 +0000
Commit message:

 Update DESCRIPTION /nocache
Package: demuxSNP
Commit: 7e1ac2a46eeebd8f48c64282dd2a8797a58d4bbd
Author: Michael <michael.lynch@ul.ie>
Date: 2023-12-19 16:02:51 +0000
Commit message:

 update actions
Package: demuxSNP
Commit: 8dc01dba43623106153f7f89cd7b97464a5f0752
Author: Michael Lynch <89206184+michaelplynch@users.noreply.github.com>
Date: 2023-12-19 15:14:32 +0000
Commit message:

 Update DESCRIPTION

Checking GHA
Package: demuxSNP
Commit: 4dd2c90f159e1735d9c8d5f18c1c2a590035fcfd
Author: michaelplynch <89206184+michaelplynch@users.noreply.github.com>
Date: 2023-10-27 10:09:15 +0100
Commit message:

 Update DESCRIPTION bump develversion
Package: demuxSNP
Commit: c73c29114736b12bd989001958fcc00b66e56396
Author: michaelplynch <89206184+michaelplynch@users.noreply.github.com>
Date: 2023-10-26 19:00:21 +0100
Commit message:

 Update check-bioc.yml
Package: demuxSNP
Commit: baabfa14af946cbcbec81d0a1fa0691e0b751055
Author: michaelplynch <89206184+michaelplynch@users.noreply.github.com>
Date: 2023-10-26 18:08:36 +0100
Commit message:

 Update check-bioc.yml
Package: iSEEpathways
Commit: 6441c9f91175ec70d8ee09e4d67e2a7dd660291c
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2024-10-16 09:28:02 +0100
Commit message:

 opt in bootstrap 5 (#34)
Package: iSEEde
Commit: e6418a8b5baa9f5a805f26d2df0f85c3f5a5aed8
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2024-10-16 09:25:10 +0100
Commit message:

 Update _pkgdown.yml (#42)
Package: MetaboAnnotation
Commit: 8f4499b179937e43ff4ece330bcd838992e595b5
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2024-10-16 09:52:35 +0200
Commit message:

 Merge pull request #118 from rformassspectrometry/jomain

fix: missing dependency of ProtGenerics
Package: MetaboAnnotation
Commit: 6344dd59258985c0e96a230390568c49946791a2
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2024-10-16 09:42:25 +0200
Commit message:

 Merge branch 'main' into jomain
Package: MetaboAnnotation
Commit: 1400f6ff3e41dceaa39f1cc07298413217788ffe
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2024-10-16 09:42:07 +0200
Commit message:

 ci: add codecov token
Package: MetaboAnnotation
Commit: 88524bd0ab463c76ea7781319963e73f68c7d367
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2024-10-16 09:35:01 +0200
Commit message:

 fix: missing dependency of ProtGenerics
Package: iSEEde
Commit: f38fc01f2bcd9957a167f9519de110d85acbeed8
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2024-10-15 14:53:17 +0100
Commit message:

 opt in bootstrap 5 (#41)
Package: motifTestR
Commit: bd504e5a62e87e542258b67aa1d0b03d9fae33ad
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-10-16 15:32:04 +1030
Commit message:

 Fixed logo
Package: motifTestR
Commit: e4f5df319695f7a9704047187406f85adac934ff
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-10-16 15:18:33 +1030
Commit message:

 Documentation updates
Package: motifTestR
Commit: 343975ec22d91d7b32f7c1981d4ef87abac8bc3b
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-10-16 02:07:26 +1030
Commit message:

 Version bump to try correct gh-actions errors
Package: motifTestR
Commit: a70f0667746a32fd696c058f328ab50852a9cc77
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-10-16 01:57:37 +1030
Commit message:

 Updated pkgdown URL
Package: motifTestR
Commit: 1191940f871e667c63605f53477a9180f0c7a043
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-10-16 00:46:32 +1030
Commit message:

 Reformatted NEWS.md
Package: motifTestR
Commit: 2d8f43c9c795b9076aab018a93dbaa9139cb3add
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-10-16 00:07:46 +1030
Commit message:

 Updated _pkgdown.yml
Package: motifTestR
Commit: aa4ca99466a029b70bdfe86b092f5ddcfb4a2af9
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-10-15 23:56:17 +1030
Commit message:

 Bug fix in countPwmMatches & finished vignette revisions
Package: motifTestR
Commit: cdc53663a52b2f5a6a8e1d2fd81e83c31db331a0
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-10-15 18:54:11 +1030
Commit message:

 Renamed ex_pwm to ex_pfm. Reformed ar_er_peaks
Package: motifTestR
Commit: 083a55e6487ee1905b712a8e7bac1d539ad68852
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-10-15 01:13:13 +1030
Commit message:

 Typo
Package: motifTestR
Commit: e872aba1a6473dce7a01d96692a11b458d610c89
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-10-15 00:47:11 +1030
Commit message:

 Updated vignette
Package: motifTestR
Commit: 810267a03426d2a4eab1370b3feb7db66b027524
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-10-14 23:30:54 +1030
Commit message:

 Updated pkgdown
Package: motifTestR
Commit: c457f001ec8ab895beadb722cf47e0d7e1b58b7c
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-10-14 01:51:58 +1030
Commit message:

 First addition of clustering strategies
Package: motifTestR
Commit: b5f67eef8261114b6e2ae4dbfec8e384681f12fb
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-10-12 23:36:04 +1030
Commit message:

 Added cluster matching + counting
Package: motifTestR
Commit: 4325473eae04530f6c454ee804b2866f1f1e93ef
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-10-10 01:10:21 +1030
Commit message:

 First draft of getClusterMatches
Package: motifTestR
Commit: 55b99826447e1c5e4f343f733ec1da681c34ea04
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-10-09 00:02:45 +1030
Commit message:

 Started writing cluster testing functions
Package: motifTestR
Commit: 282f2602983ecb12467688b15b3289a135d69b88
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-10-07 00:04:33 +1030
Commit message:

 Added clusterMotifs
Package: motifTestR
Commit: 03df5cf9ce4860e14ddf8b84b6f6b65592457ae2
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-10-06 23:42:14 +1030
Commit message:

 Major bugfix: Enforced PWM not PPM
Package: motifTestR
Commit: aea96be4547c7e8bc6e91ccbb5c802b50a5c9c4a
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-10-05 22:52:33 +0930
Commit message:

 Sped up hypergeometric testing
Package: DFplyr
Commit: 4e8ba1b294c4e21fd4e04ac37c94b712738fcb2e
Author: Jonathan Carroll <github@jcarroll.com.au>
Date: 2024-10-16 10:29:53 +1030
Commit message:

 add Bioc install instructions, version bump
Package: CardinalIO
Commit: b6221570a3dc427273316708d552fe28ade83e1f
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-10-15 23:39:26 -0400
Commit message:

 update NEWS
Package: CardinalIO
Commit: b5f503ac2f1c48216bd6ffe97870c683c18e2e92
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-10-15 23:37:29 -0400
Commit message:

 add BiocParallel to Depends; add parallelized file writing
Package: spicyWorkflow
Commit: 8bb44060f88bdb260beb2e022595453cd4d131e4
Author: Nick <nickrrrr@gmail.com>
Date: 2024-10-16 14:09:35 +1100
Commit message:

 remove workflows
Package: spicyWorkflow
Commit: 29411365b9098ab7b8721b49b75fdaa09ce40708
Author: Ellis Patrick <ellis.patrick@sydney.edu.au>
Date: 2024-10-15 13:45:34 +1100
Commit message:

 bump
Package: spicyWorkflow
Commit: 4e70c0130d5887e789fa704c5f4a7d0a92d5f049
Author: Ellis Patrick <ellis.patrick@sydney.edu.au>
Date: 2024-10-15 13:42:14 +1100
Commit message:

 version bump
Package: spicyWorkflow
Commit: 83a6fffad5e7aac5b4821d16f70d0ae4284e8abf
Author: alexq <alexq@maths.usyd.edu.au>
Date: 2024-09-11 16:25:08 +1000
Commit message:

 new vignette with HNSCC data
Package: spicyWorkflow
Commit: a99dddbf490a90fd24606b45b84109e80cfefc07
Author: Nick <nickrrrr@gmail.com>
Date: 2024-08-02 16:23:42 +1000
Commit message:

 add github action
Package: spicyWorkflow
Commit: a2f450497307ede335c9170db33c14b372c49907
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2024-01-24 15:47:32 +1100
Commit message:

 ignore dev containers
Package: bsseq
Commit: 220215f8ab3a7d8540a8b8805b5aff12cbf35c11
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2024-10-15 18:12:55 -0400
Commit message:

 merge upstream
Package: bsseq
Commit: 7c309d33fa4c34b8fdd476eeadffcbd9454b5482
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2024-05-09 10:22:05 -0400
Commit message:

 Merge pull request #138 from yixuan-chen-elisa/read.modkit

Update strand information in read.modkit.R
Package: bsseq
Commit: b8886bc930c5858c200b68149790f3b38b4d8f42
Author: yixuanchen <116841407+yixuan-chen-elisa@users.noreply.github.com>
Date: 2024-04-29 17:10:07 -0400
Commit message:

 Update read.modkit.R - change read.table to fread
Package: bsseq
Commit: f4bb6e8a43a5ba44c56a778ce545c71dad914ea8
Author: yixuanchen <116841407+yixuan-chen-elisa@users.noreply.github.com>
Date: 2024-04-19 14:56:40 -0400
Commit message:

 Update strand information for read.modkit.R
Package: bsseq
Commit: 39ac79f179b07d80bdd4766165fc2e5a0bb6917f
Author: yixuanchen <116841407+yixuan-chen-elisa@users.noreply.github.com>
Date: 2024-04-18 14:36:20 -0400
Commit message:

 Update strand information in read.modkit.R
Package: bsseq
Commit: 94069c4270bbe3dec2dfe767e8f5b41cad60325b
Author: yixuanchen <116841407+yixuan-chen-elisa@users.noreply.github.com>
Date: 2024-04-18 13:21:03 -0400
Commit message:

 Update strand information in read.modkit.R
Package: bsseq
Commit: d32c2c6709fac68b59578fac79d0eda385104585
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2024-04-08 14:42:42 -0400
Commit message:

 Update DESCRIPTION

Previous merge had the wrong version number
Package: bsseq
Commit: c363f3bf8266880ead7fe75629574b87a614f883
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2024-04-08 14:42:15 -0400
Commit message:

 Merge pull request #137 from yixuan-chen-elisa/read.modkit

update functions on handling other modification bases
Package: bsseq
Commit: edf2866eb2f3b6cdb4e9619530aeddac397a8ae6
Author: yixuanchen <116841407+yixuan-chen-elisa@users.noreply.github.com>
Date: 2024-04-03 22:10:13 -0400
Commit message:

 Update test_read.modkit.R
Package: bsseq
Commit: c7d1993a8bcaeb625500c5a5fd51334b761b14c3
Author: yixuanchen <116841407+yixuan-chen-elisa@users.noreply.github.com>
Date: 2024-04-03 22:08:26 -0400
Commit message:

 Delete inst/extdata/modkit/chr22.HG002.top1000.bed.gz
Package: bsseq
Commit: 6d82b4e28a4cd7f4e558b0fc7b354e0a56af131a
Author: yixuanchen <116841407+yixuan-chen-elisa@users.noreply.github.com>
Date: 2024-04-03 22:07:46 -0400
Commit message:

 Add files via upload
Package: bsseq
Commit: 5de0ce3fd2b85eef50b3540d208043cfd4b2125f
Author: yixuan-chen-elisa <ychen590@jhu.edu>
Date: 2024-04-03 17:09:06 -0400
Commit message:

 fix read.modkit
Package: bsseq
Commit: 1b70d4dbf3fba87e71937ecbbd4a8924cd1602e9
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2024-03-29 14:39:49 -0400
Commit message:

 bumping version number, changing man page for BSmooth.tstat to reflect k=21
Package: bsseq
Commit: f243edb074bfe724b483cf4240caefb90748ac5d
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2024-03-29 12:07:44 -0400
Commit message:

 Updating the default value of k in BSmooth.tstat from k=101 to k=21
Package: bsseq
Commit: f2a24de44b7664dc40d0f52474dff09eb313239b
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2023-11-27 12:02:09 -0500
Commit message:

 Merge pull request #132 from yixuan-chen-elisa/update-test-data

update modbam2bed test data & NEWS.Rd
Package: bsseq
Commit: 46f5ffadc9b4848a47df3b53ad88e42e5cd5aa2d
Author: yixuan-chen-elisa <ychen590@jhu.edu>
Date: 2023-11-20 00:52:11 -0500
Commit message:

 update test data & news
Package: bsseq
Commit: 161f323e16ce261633ad135f60c9cb9e587a7731
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2023-11-15 21:06:37 -0500
Commit message:

 Update DESCRIPTION
Package: bsseq
Commit: 100025435207d81312846f01fbeac71be9b8448c
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2023-11-15 21:05:55 -0500
Commit message:

 Merge pull request #131 from yixuan-chen-elisa/read.modkit

Create a function read.modkit to read in methyl Bed files created by modkit to Bsseq object
Package: bsseq
Commit: 9add026b64f3a9569f5117ea89fd2321311cee9d
Author: yixuanchen <116841407+yixuan-chen-elisa@users.noreply.github.com>
Date: 2023-11-15 18:25:18 -0500
Commit message:

 Update NAMESPACE
Package: bsseq
Commit: 295ccb1b2575065deec9fde8cc2457028d23d83a
Author: yixuanchen <116841407+yixuan-chen-elisa@users.noreply.github.com>
Date: 2023-11-15 17:03:15 -0500
Commit message:

 Merge branch 'devel' into read.modkit
Package: bsseq
Commit: 7e547c97592ec623e3f85b38339315dcaf87e48c
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2023-11-15 16:21:51 -0500
Commit message:

 Update check-bioc.yml
Package: bsseq
Commit: c69811a774ea2d5b75acd213ab41fcf96fa07c76
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2023-11-15 16:16:00 -0500
Commit message:

 removing read.umtab/read.bsmooth. Various code and documentation fixes including adding examples and testing for class membership using is(). Address a number of issues report by Bioc Check
Package: bsseq
Commit: 086da6eba2f52ec3593fc64e9b0452de5de9fd89
Author: yixuan-chen-elisa <ychen590@jhu.edu>
Date: 2023-11-14 15:44:51 -0500
Commit message:

 updated test file
Package: bsseq
Commit: 9bcfd5b8548c113ce8eda6325481ec145ef0ef19
Author: yixuan-chen-elisa <ychen590@jhu.edu>
Date: 2023-11-13 16:09:13 -0500
Commit message:

 read.modkit
Package: bsseq
Commit: 612059e787692338537fe40432e7064c0bae2cdb
Author: yixuan-chen-elisa <ychen590@jhu.edu>
Date: 2023-11-13 16:01:06 -0500
Commit message:

 read.modkit
Package: bsseq
Commit: 85d763ec973871d7d78cc462ce67a72cb70dced9
Author: yixuanchen <116841407+yixuan-chen-elisa@users.noreply.github.com>
Date: 2023-11-13 15:50:26 -0500
Commit message:

 Delete inst/blood.cpg.other_mod.chr22.top1000.bed.gz
Package: bsseq
Commit: 6661d1f7d2d6dc7a91b6a46bf0f6c4ddd5d03d6b
Author: yixuanchen <116841407+yixuan-chen-elisa@users.noreply.github.com>
Date: 2023-11-13 15:50:17 -0500
Commit message:

 Delete inst/blood.cpg.chr22.top1000.bed.gz
Package: bsseq
Commit: cc8a75eeeb252d1bce28b4998b3ca827f8ce910d
Author: yixuanchen <116841407+yixuan-chen-elisa@users.noreply.github.com>
Date: 2023-11-13 15:49:33 -0500
Commit message:

 Add files via upload
Package: bsseq
Commit: 837e5678d9364f192e6bbeab35c36d45f3e63aef
Author: yixuanchen <116841407+yixuan-chen-elisa@users.noreply.github.com>
Date: 2023-11-13 15:33:26 -0500
Commit message:

 Delete inst/extdata/modkit/blood.cpg.other_mod.chr22.bed.gz
Package: bsseq
Commit: 31e51f6e4f085d3c6a620d0f988b224d9003bcbd
Author: yixuanchen <116841407+yixuan-chen-elisa@users.noreply.github.com>
Date: 2023-11-13 15:33:14 -0500
Commit message:

 Delete inst/extdata/modkit/blood.cpg.chr22.bed.gz
Package: bsseq
Commit: 12506e83a3109ec2430c1d380fbff96f720af762
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2023-11-10 13:39:59 -0500
Commit message:

 Update DESCRIPTION
Package: bsseq
Commit: 3c3e0f68848e4895db553cc378790711b68dd6d9
Author: yixuan-chen-elisa <ychen590@jhu.edu>
Date: 2023-11-03 11:11:22 -0400
Commit message:

 read.modkit
Package: bsseq
Commit: e10f4b9ad9c453f43cf52ae56eadb55cc65711da
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2023-11-01 16:52:39 -0400
Commit message:

 setting up for Github Actions
Package: bsseq
Commit: 4f05efbadd59cf8cef4f51deb3d675ee2fcddea3
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2023-11-01 16:50:12 -0400
Commit message:

 fixing merge conflicts
Package: bsseq
Commit: f8089e8b0136dbfd570207a4f3619e7e908a433c
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2023-11-01 16:48:04 -0400
Commit message:

 editing README
Package: bsseq
Commit: 7c3290bb1372a6d56292f04f00a9a727d7b44760
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2023-11-01 16:46:55 -0400
Commit message:

 editing README
Package: bsseq
Commit: 061e6b3433bef658e217f5b1c329a27245b57d1c
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2023-09-28 10:39:26 -0400
Commit message:

 removing ungizpped modbam2bed files
Package: bsseq
Commit: 712dbb7bbabc306ee58e3e1cb616b9f019c620b8
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2023-09-28 10:35:50 -0400
Commit message:

 Merge pull request #127 from yixuan-chen-elisa/fix-read.modbam2bed

Various fixes for support for modbam2bed, including fixes to read.modbam2bed, the BSseq constructor and adding a test.
Package: bsseq
Commit: a64b04dc444dcf5814bf82adf4c643877a86e7c3
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2023-09-28 10:32:41 -0400
Commit message:

 Merge branch 'devel' into fix-read.modbam2bed
Package: bsseq
Commit: 56fd75bc02d74cdbe80246c41d022442fc7af297
Author: yixuanchen <116841407+yixuan-chen-elisa@users.noreply.github.com>
Date: 2023-09-26 23:44:35 -0400
Commit message:

 Delete tests/.DS_Store
Package: bsseq
Commit: 302696751ea64ab7e31f793b874bfb7cb9749446
Author: yixuanchen <116841407+yixuan-chen-elisa@users.noreply.github.com>
Date: 2023-09-26 23:44:13 -0400
Commit message:

 Delete inst/.DS_Store
Package: bsseq
Commit: 4344fc3383c637d4a84ce87c6a4142d311c214dd
Author: yixuanchen <116841407+yixuan-chen-elisa@users.noreply.github.com>
Date: 2023-09-26 23:44:03 -0400
Commit message:

 Delete inst/extdata/.DS_Store
Package: bsseq
Commit: 0f24c4b63d772478cd89e063c3e3f9f434dc6d4f
Author: yixuanchen <116841407+yixuan-chen-elisa@users.noreply.github.com>
Date: 2023-09-26 23:41:52 -0400
Commit message:

 Update BSseq.Rd
Package: bsseq
Commit: 83b470b136e79cd280d1ca86e58594c7815b22bb
Author: yixuanchen <116841407+yixuan-chen-elisa@users.noreply.github.com>
Date: 2023-09-26 23:40:15 -0400
Commit message:

 Delete .DS_Store
Package: bsseq
Commit: 0c93fc6ec51cd64d99b21488099dc7743ad80aba
Author: yixuan-chen-elisa <ychen590@jhu.edu>
Date: 2023-09-26 23:38:39 -0400
Commit message:

 fix read.modbam2bed
Package: bsseq
Commit: 913297028500273c8eb79b52e046f02598f1ed91
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2023-09-21 10:44:53 -0400
Commit message:

 fixing NAMESPACE
Package: bsseq
Commit: ef1622372ee7d1800ef70e0fab522f902545f213
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2023-09-21 10:39:37 -0400
Commit message:

 bumping version following merge from Bioc trunk
Package: bsseq
Commit: aa458f960e095ffabf54126862c8e04b7862f2a5
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2023-09-21 10:36:46 -0400
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: bsseq
Commit: 8e310454e8962d44fe500ea6f28a546808ee8d53
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2023-09-21 10:36:40 -0400
Commit message:

 editing collate field
Package: bsseq
Commit: f449a95e78a68862a1aeda93409a781a63253d4c
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2023-09-21 10:24:10 -0400
Commit message:

 movign directory
Package: bsseq
Commit: d9568e7a6949d2ecb6b364c2962d83ae8033bd7f
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2023-09-21 10:22:29 -0400
Commit message:

 Delete .DS_Store
Package: bsseq
Commit: f7fea0a33c2ce186f811c6f74aa5e2532099e623
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2023-09-21 10:22:04 -0400
Commit message:

 Merge pull request #126 from yixuan-chen-elisa/read.modbam2bed

read nanopore data into bsseq
Package: bsseq
Commit: bebfaa47ba892330d2d89ad7e3d6e3cd88b32821
Author: yixuan-chen-elisa <ychen590@jhu.edu>
Date: 2023-09-21 01:12:39 -0400
Commit message:

 read modbam2bed
Package: matter
Commit: 8fbe66ba95253052fb52f1ac9bd3f5144bd67ff8
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-10-14 23:55:50 -0400
Commit message:

 update NEWS
Package: matter
Commit: 529cd3ef6a483e5027634b4b6fa7194ca7380da0
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-10-14 23:46:22 -0400
Commit message:

 bplocal() => bpislocal(); add bptrystart() and bptrystop()
Package: matter
Commit: 86245d504df69957cbdc7e681a466676a5bbc2e5
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-10-14 23:20:31 -0400
Commit message:

 fix broken fetch() and flash() tests
Package: matter
Commit: 3fa9f0a4044ff941bcedd4960c810b6930eac7da
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-10-14 22:23:55 -0400
Commit message:

 update fetch() and flash() docs
Package: matter
Commit: cada7f24db3ebe3d689a596fdca266dd8b137460
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-10-09 02:33:11 -0400
Commit message:

 add fetch() and flash() for base R types
Package: matter
Commit: a5446e630e3878d8aafa652fbb2a78fc19ec6f28
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-10-09 02:28:22 -0400
Commit message:

 update internal fetch() and flash() copying
Package: matter
Commit: 7fc2f7fe3a28faf5dd559d4114d52a04e0c53720
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-10-09 02:02:39 -0400
Commit message:

 refactor to use null coalescing operator where appropriate
Package: matter
Commit: 22aecb0b39619a24caae1d55c6f0804571894354
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-10-09 01:40:22 -0400
Commit message:

 update docs and show methods
Package: TENET.AnnotationHub
Commit: b71884d8aa171c087da301201f7e8be607556bed
Author: Ethan Nelson-Moore <nelsonmo@usc.edu>
Date: 2024-10-15 17:03:09 -0700
Commit message:

 Update installation instructions to use release version of Bioconductor and add version 1.0.0 to NEWS.md in preparation for Bioconductor 3.20 release
Package: SparseArray
Commit: 028d25475b7f320bb90b9b1a122c12c713db8184
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-10-15 15:13:11 -0700
Commit message:

 SparseArray 1.5.45

- Repair coercion of a RsparseMatrix derivative to SparseMatrix/Array.
  Some recent commit (99278dc or d4cbf82) broke it with a "node
  stack overflow" error (i.e. infinite recursion) that also broke
  extract_sparse_array() on RsparseMatrix derivatives.
  See https://github.com/Bioconductor/SparseArray/issues/18

- Add nzcount() method for TsparseMatrix derivatives.

- Replace nzvals() methods for ngCMatrix and ngRMatrix objects with single
  method for nMatrix derivatives.

- Implement coercions from dgTMatrix, lgTMatrix, or ngTMatrix, to
  COO_SparseMatrix/Array or SVT_SparseMatrix/Array, and vice versa.

- Add coercion from Array to TsparseMatrix. Based on the type() of the
  object to coerce, it just delegates to coercion to dgTMatrix or lgTMatrix.

- Make extract_sparse_array() and constructor function SparseArray() work
  on a TsparseMatrix derivative. Both return an SVT_SparseMatrix object.

- Implement coercion from a COO_SparseMatrix object to ng[C|R|T]Matrix
  and vice versa.

- Add the following coercions that are missing from the Matrix package:
    o from CsparseMatrix to ngCMatrix
    o from RsparseMatrix to ngRMatrix
    o from TsparseMatrix to ngTMatrix

- Fix small bug in constructor function SparseArray() when the input is a
  COO_SparseArray object.

- Minor tweaks to internal helper SparseArray:::.normalize_COO_SparseArray()
Package: TENET.AnnotationHub
Commit: be1f830ce0b444f04c9caf473b939685cad2ea4b
Author: Ethan Nelson-Moore <nelsonmo@usc.edu>
Date: 2024-10-15 15:49:21 -0700
Commit message:

 Update NEWS.md; bump version to 0.99.3
Package: Rsubread
Commit: 9db7a1601780dae80e1c1214b0e77d1032149ad0
Author: Yang Liao (Monash University) <yliao@m3-login3.massive.org.au>
Date: 2024-10-16 09:42:14 +1100
Commit message:

 Bug fixing of cellCounts
Package: TENET.AnnotationHub
Commit: 21c27c51da10ea984617ae857170f3017841019b
Author: Ethan Nelson-Moore <nelsonmo@usc.edu>
Date: 2024-10-15 15:34:37 -0700
Commit message:

 Use package short URL to avoid needing to update it when Bioconductor 3.20 is released
Package: Spectra
Commit: 424e9cedf36410ecdee446f492b823a011b644d9
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2024-10-15 22:15:22 +0200
Commit message:

 Merge pull request #335 from rformassspectrometry/jomain

feat: add new method backendRequiredSpectraVariables
Package: Spectra
Commit: 37d502933344ed5d9bc938f8cff2c5e189ac27d3
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2024-10-15 12:04:17 +0200
Commit message:

 feat: add new method backendRequiredSpectraVariables

- Add new method `backendRequiredSpectraVariables()` that allows a backend to
  specify which spectra variables are necessary to ensure proper
  functionality. Subsetting functions (like `selectSpectraVariables()`) should
  use these.
Package: glmGamPoi
Commit: 21e990894529ba874905fa09c6cdef8bddb10316
Author: Constantin <const-ae@users.noreply.github.com>
Date: 2024-07-22 10:53:54 +0200
Commit message:

 Merge pull request #64 from hpages/devel

Resync with recent developments in SparseArray/DelayedArray packages
Package: glmGamPoi
Commit: ace2c7e2c7c7940ef10afe88b2821dab8aaaa6e1
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-07-15 14:00:01 -0700
Commit message:

 Resync with recent developments in SparseArray/DelayedArray packages
Package: cqn
Commit: 511115ef3e6ad1bbe3e419108c1c3867925fa8a2
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2024-10-15 13:00:40 -0400
Commit message:

 various import fixes caused by upstream changes
Package: MOSClip
Commit: 6bf20f24533ba505a8b62cf6e30bc5133c8a9c2a
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-10-15 18:32:20 +0200
Commit message:

 correct test
Package: MOSClip
Commit: 2131d2b41b28459d1e691038454be40fff344689
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-10-15 18:14:14 +0200
Commit message:

 change link in vignette and bump version
Package: MOSClip
Commit: 45c317be8550ecbefad0b5fdac7a7e4ba16e4fe1
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-10-15 18:13:43 +0200
Commit message:

 fix heatmaps
Package: CATALYST
Commit: 4ff7b0284710e81dd598d0a9dedf3e463bb191c1
Author: HelenaLC <helena@crowells.eu>
Date: 2024-10-15 18:20:49 +0200
Commit message:

 bump v1.29.1>.2
Package: CATALYST
Commit: 85ddee8580d26559378cb69ef46c6238a21dfdfa
Author: HelenaLC <helena@crowells.eu>
Date: 2024-10-15 18:20:18 +0200
Commit message:

 track changes v1.29.2
Package: CATALYST
Commit: d7007b85efcb458f57f898b64595e8f1f49d2ee2
Author: HelenaLC <helena@crowells.eu>
Date: 2024-10-15 18:20:00 +0200
Commit message:

 drop aes_string()
Package: CATALYST
Commit: 8d84e8cecd508dfe4c3245ff9a95a8cd799fbe57
Author: HelenaLC <helena@crowells.eu>
Date: 2024-10-15 18:19:50 +0200
Commit message:

 bug fix 'calculateDR' failure when in put is a 'table'
Package: philr
Commit: 1d4f2f3d25e277228b1050bb33075cbc5a1b26bb
Author: Justin Silverman <jsilve24@gmail.com>
Date: 2024-10-15 11:48:49 -0400
Commit message:

 fix: bioconductor build error after mia function renaming
Package: gemma.R
Commit: 8882e11341ca5bed5a6f4e6f12826bc8ca9b78ef
Author: OganM <ogan.mancarci@gmail.com>
Date: 2024-10-15 08:36:04 -0700
Commit message:

 version bump
Package: gemma.R
Commit: 2647536614fd2cfea9e3df6bf2ce1af580d24022
Author: ogan Mancarci <ogan.mancarci@gmail.com>
Date: 2024-10-15 08:32:17 -0700
Commit message:

 get_platform_annotations fix
Package: MSnbase
Commit: 03e768f14bc5e6fe4fabf7f7077ee3b3bac2a29e
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-10-15 16:32:23 +0200
Commit message:

 add pkgdown conf
Package: Rdisop
Commit: 1a7306945da577b5a2f461fca3c1b3eddef83b91
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2024-10-15 17:28:06 +0200
Commit message:

 adapt github actions
Package: seqsetvis
Commit: e4f659b458989a65fa98a6555c2f5cd945a68512
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2024-10-15 10:58:01 -0400
Commit message:

 v bump 1.25.5

within_clust_sort now respects "none" sort strategy. was bugged
Package: OmnipathR
Commit: 646d05410776d7c8a8c89e2ce44fd2e9d8c39e40
Author: deeenes <turei.denes@gmail.com>
Date: 2024-10-15 17:12:02 +0200
Commit message:

 Bump version: 3.13.27 → 3.13.28
Package: OmnipathR
Commit: 7edc1d855318cfe3bc051393d1d387a88a15d56e
Author: deeenes <turei.denes@gmail.com>
Date: 2024-10-15 17:09:41 +0200
Commit message:

 `oma`: missing variable declaration for R CMD check
Package: OmnipathR
Commit: fc69d6df82c374d16b025e041644a9bd21be3ee9
Author: deeenes <turei.denes@gmail.com>
Date: 2024-10-15 15:57:45 +0200
Commit message:

 `stitch_remove_prefix`: use `data.frame` instead of `tibble` in doctest
Package: Rdisop
Commit: 1f0e3db22f63fb35bd9c16d3bb8b41489f027992
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2024-10-15 17:05:18 +0200
Commit message:

 Remove compiled library
Package: Rdisop
Commit: 208c3e0b61a26ae1c9e3dbffdfc53d63937c5432
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2024-10-15 17:03:56 +0200
Commit message:

 Tiny cosmetic changes fixing version, generated files and new contributor
Package: Rdisop
Commit: 82df879d2ff2c7fa14ff24bdb05b3f3ca5250de5
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2024-10-15 16:53:17 +0200
Commit message:

 Merge branch 'janlisec-master' into devel
Package: Rdisop
Commit: dfc0b430e8a165acc34b9584a81b4eb98739b192
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 14:15:58 +0200
Commit message:

 Ubuntu_dev excluded from GitHub action
Package: Rdisop
Commit: 78480d02c00d95093e22d400425961055ec7ddbb
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 14:05:07 +0200
Commit message:

 Put `rmarkdown` in Suggests.
Package: Rdisop
Commit: f0eff6b3ff4bcad081456722f1f9fee78d2b1da1
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 13:56:29 +0200
Commit message:

 GitHub Workflow fix
Package: Rdisop
Commit: 751c8309000acf55d2e4551236181989c8bd80eb
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 13:48:36 +0200
Commit message:

 GitHub Workflows fix
Package: Rdisop
Commit: e70c7a54bf6961ff7cc0dee92df901dca37aa5d6
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 13:39:51 +0200
Commit message:

 ReadMe fix
Package: Rdisop
Commit: f0169266c0460cfdcb9b005c12a6345092b006bc
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 13:21:21 +0200
Commit message:

 Vignette fix
Package: Rdisop
Commit: 3b49beab4304cf246edee65057b0c39a154bd5ab
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 13:08:06 +0200
Commit message:

 Rdisop-1.66.1 changes

Merge branch 'master' of https://github.com/janlisec/Rdisop

# Conflicts:
#	ChangeLog
#	DESCRIPTION
Package: Rdisop
Commit: 5d19de62b70375513e06b6499ea4ce3bc01445ae
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 12:39:16 +0200
Commit message:

 GitHub ReadMe set up.
Package: Rdisop
Commit: d80673fd5b03b286eddc6dc04c7cebbe59b97049
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 12:38:41 +0200
Commit message:

 Setting GitHub actions for PR and testing.
Package: Rdisop
Commit: c4c681276632586a35265fb014cac6fbd2a5d9fd
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 11:07:37 +0200
Commit message:

 - Namespace automized by roxygen2
- Description and Changelog revised
Package: Rdisop
Commit: 32afe37dde745ded3444cd2b25916c3f9366fe61
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 11:06:26 +0200
Commit message:

 several include statements out-commented (compose_f_gx_t) referencing deprecated functions
Package: Rdisop
Commit: 380e97b9138233db336c27764e0cf0aa41324fe1
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 11:05:50 +0200
Commit message:

 Rdisop.dll bound to R using R_useDynamicSymbols()
Package: Rdisop
Commit: ae58495dae92a9340c1bad90bceb89ac2ef63dd0
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 11:04:37 +0200
Commit message:

 `testthat` based testing environment set up
Package: Rdisop
Commit: 4897fe67055d0083372db7808baed78d1d032f6c
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 11:01:36 +0200
Commit message:

 - all R functions grouped to separate individual files
- all R functions documented using roxygen2
Package: Rdisop
Commit: e690014563d35d841c29773d3eef7d6dcd243a78
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 10:58:37 +0200
Commit message:

 Vignette format changed to Rmd. Minor corrections applied.
Package: Rdisop
Commit: 3e66e6d8141ceca7a58f1f4d0b0ebec582786120
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2024-09-30 11:14:22 +0200
Commit message:

 Bump version
Package: Rdisop
Commit: a75d7ba6a176318e0c118ba05059fbe1fcb14da6
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2024-09-30 11:09:45 +0200
Commit message:

 Merge branch 'yufree-master'
Package: Rdisop
Commit: 14300594ad8e37e14d372e9d6f0b35ab018c7766
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2024-09-30 11:07:06 +0200
Commit message:

 Merge branch 'master' of https://github.com/yufree/Rdisop into yufree-master
Package: Rdisop
Commit: 0907e7354efb5126367cd2cca7901c75802a4d5f
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2024-09-30 11:05:42 +0200
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/Rdisop
Package: Rdisop
Commit: 4939a2199daae72ce6e2105ab440e75647200f46
Author: yufree <yufree@live.cn>
Date: 2024-09-29 08:50:58 -0400
Commit message:

 remove unary_function
Package: Rdisop
Commit: d31cbbaeb7ec6926405f1d04fe0ccaa968e4e104
Author: yufree <yufree@live.cn>
Date: 2024-09-29 08:50:37 -0400
Commit message:

 remove binary_function
Package: Rdisop
Commit: 37d44575b7f2aa6530d79208c0fb05fcc7b84e19
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2024-05-29 16:21:07 +0200
Commit message:

 Merge branch 'master' of github.com:sneumann/Rdisop
Package: Rdisop
Commit: 700c83bb8715fe0c5c0210abcfcdd9c0ab108eae
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2024-05-29 16:14:25 +0200
Commit message:

 Fix merge conflict for two independent fixes for the same compile issue
Package: Rdisop
Commit: 880573120550e3c637a9a17271075cf01631f509
Author: yufree <yufree@live.cn>
Date: 2024-05-16 10:45:10 -0400
Commit message:

 Rf_error calls modified to include format string from @vjcitn
Package: Rdisop
Commit: 0bdf9fc4f82e794d9f5464655b75d815cc5dab43
Author: rickhelmus <37015911+rickhelmus@users.noreply.github.com>
Date: 2024-05-29 16:02:23 +0200
Commit message:

 Small if in case gcc's -Werror=format-security is enabled
Package: Rdisop
Commit: ed578481a01c10dce49b0a09c170a7a94a21de49
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2024-05-29 16:14:25 +0200
Commit message:

 Fix merge conflict for two independent fixes for the same compile issue
Package: Rdisop
Commit: 5fd08e7324becbeebe5a99d7bbfe2252d811b62e
Author: yufree <yufree@live.cn>
Date: 2024-05-16 10:53:12 -0400
Commit message:

 bump version with ChangeLog
Package: Rdisop
Commit: 64cde8fdad23d5e167730da5f71e71c71bbbbd29
Author: yufree <yufree@live.cn>
Date: 2024-05-16 10:45:10 -0400
Commit message:

 Rf_error calls modified to include format string from @vjcitn
Package: Rdisop
Commit: 74e8d34880c6e6d93cf8aad2c3fe9eac526adb60
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2024-04-30 10:17:29 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_19 branch
Package: Rdisop
Commit: 9eeb38673870b3bf5a2eb29eafc9a9df7b8b8345
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2024-04-30 10:17:29 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_19 branch
Package: Rdisop
Commit: a92d684e7bdb21a8f0912ccf65c735695dd52733
Author: J Wokaty <jennifer.wokaty@sph.cuny.edu>
Date: 2023-10-24 09:39:07 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_18 branch
Package: Rdisop
Commit: b06dc31e8bcfce146730cd0d7c995510d7bd064b
Author: J Wokaty <jennifer.wokaty@sph.cuny.edu>
Date: 2023-10-24 09:39:07 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_18 branch
Package: Rdisop
Commit: 711074b45991e3225b075a6cb25018ded294e83d
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2023-04-25 09:46:04 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_17 branch
Package: Rdisop
Commit: 5a70ea6abfa4f542c01bd9ff45fe79a4d6d31b30
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2023-04-25 09:46:04 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_17 branch
Package: Rdisop
Commit: edf079c84ebd7617865a26df83e53f657652ee1a
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2024-05-29 16:10:47 +0200
Commit message:

 Merge pull request #26 from rickhelmus/Rf_error-fix

Small compilation fix
Package: Rdisop
Commit: 6bbc1df63b3f27a8ed4ed44ef82aced08f4ae784
Author: rickhelmus <37015911+rickhelmus@users.noreply.github.com>
Date: 2024-05-29 16:02:23 +0200
Commit message:

 Small if in case gcc's -Werror=format-security is enabled
Package: ClustIRR
Commit: 7fc41684bc3a45c065518021f7d08fb6281c6cb9
Author: snaketron <snaketron@users.noreply.github.com>
Date: 2024-10-15 16:28:45 +0200
Commit message:

 Update README.md

Updated overview
Package: ClustIRR
Commit: e0191f8c62c6beb0756774ebd7b8b97d64bf68d7
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2024-10-15 16:18:48 +0200
Commit message:

 more bugfixes, tests and man files updates
Package: ClustIRR
Commit: 51c0f121d2ea01f2ef45e71c4f2e71c34061b85e
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2024-10-15 15:22:48 +0200
Commit message:

 major changes since 1.3.27, local clustering depreceated, will have to be implemented at different stage
Package: ATACCoGAPS
Commit: 8a0e634ee1b3c3f06e5f7462adc1c80f2c77ad42
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2024-10-15 09:45:29 -0400
Commit message:

 Deprecate

 - unresponsive
 - extended failure
Package: biodbKegg
Commit: 8f566c6ad90f9ac62dbc88100e24a6782471c579
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2024-10-15 09:44:28 -0400
Commit message:

 Deprecated

 - unresponsive
 - extended failure
Package: biodbExpasy
Commit: 07e10ca30eef157ab9374694700ffbc02416a582
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2024-10-15 09:43:11 -0400
Commit message:

 Deprecate

 - unresponsive
 - extended failure
Package: nanotatoR
Commit: e313e499974c9152a10ad6fc2d31fb74161fb844
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2024-10-15 09:41:45 -0400
Commit message:

 Deprecate

 - unresponsive
 - extended failure
Package: BRGenomics
Commit: acbd810498a9c9ac9ab15570ecdd414921756d7e
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2024-10-15 09:37:58 -0400
Commit message:

 Deprecated

 - extended failure
Package: immunogenViewer
Commit: 7048e6206bd1334b74beb230691c22f4dbd4b102
Author: Waury <kwy700@login3.cm.cluster>
Date: 2024-10-15 15:10:43 +0200
Commit message:

 Version bump
Package: MSnbase
Commit: 6df777f0a9d89eb9c07e3913f34b4fa9b9428e48
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-10-15 14:30:46 +0200
Commit message:

 remove can email
Package: MSnbase
Commit: a1c80f6e2925371918e04d4be9387f630c69ce9a
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-10-15 10:58:06 +0200
Commit message:

 fix pRolocdata dep version
Package: MSnbase
Commit: e113407cbb92072cb626b1499a2f29be8f2fc41a
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-10-15 10:51:15 +0200
Commit message:

 suggest magick
Package: MSnbase
Commit: d886670e2788218a68d0bddd7573d1fb530053d9
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-10-15 09:41:37 +0200
Commit message:

 install lgatto/pRolocdata
Package: MSnbase
Commit: 7df2372974b5e9a1a741bb247fa9c7441c93e8a9
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-10-15 09:07:02 +0200
Commit message:

 latest pRolocdata
Package: pRolocdata
Commit: 857f96dd91a8631b8b16787776dfdf02cdc45057
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-10-15 14:29:32 +0200
Commit message:

 Merge branch 'master' into devel
Package: pRolocdata
Commit: 9fcc9a13c8f0d4744bc4526695442b58cddb99d7
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-10-15 14:29:04 +0200
Commit message:

 add hyperLOPIT-SIData-ms3-rep12-intersect.csv.gz
Package: iSEEde
Commit: c41c29eb3de88e7d7710adaaaccd9cece6cfe58b
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2024-10-05 08:49:55 +0100
Commit message:

 update github action to use devel branch (#40)
Package: TrajectoryGeometry
Commit: 66c1cddc07369a2c0eb3fe3c595e634702fcae79
Author: Michael Shapiro <michael.shapiro@crick.ac.uk>
Date: 2024-10-15 12:03:51 +0100
Commit message:

 updating citation
Package: pRolocdata
Commit: 219f1411e6400bb0e088b1fb1e8845ebd3e88185
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-10-15 12:52:37 +0200
Commit message:

 Merge branch 'master' into devel
Package: pRolocdata
Commit: a9860e412c55fe61e0dcb785d48281e82e89b00b
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-10-15 12:52:27 +0200
Commit message:

 add Dunkley2006
Package: CytoMDS
Commit: d013ba87910f1726ad4d872ecc93c68754a0f330
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-10-15 12:01:35 +0200
Commit message:

 Merge branch 'main' into devel
Package: CytoMDS
Commit: cd528f893b87eb0a05c0efb317e79321abdc1d25
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-10-15 11:30:00 +0200
Commit message:

 implemented `pkgdown` customization
Package: MOSClip
Commit: 5e54b2ee2943789cbcee9c58384319ff612ea2df
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-10-15 11:40:35 +0200
Commit message:

 version bump
Package: MOSClip
Commit: d4c1a5c7fdce332358a0b5cbc8ed671e61cd2687
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-10-15 11:17:04 +0200
Commit message:

 new readme
Package: MOSClip
Commit: 80480f2cdac0a92d031c402ea0fd8d1bc4252407
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-10-15 10:59:24 +0200
Commit message:

 citation file
Package: MOSClip
Commit: e31d08c298dd745295462c7d02ae963f39ee07e7
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-10-14 10:44:44 +0200
Commit message:

 format R code
Package: MOSClip
Commit: 685448b3cad4dca5e78d5d7969ff9a08008b9a4e
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-10-10 11:03:27 +0200
Commit message:

 remove suppressMessages from plots
Package: MOSClip
Commit: 8c2073399383f074b4713c12a06b6494bcdc6e84
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-10-09 10:40:29 +0200
Commit message:

 update readme
Package: MOSClip
Commit: 947745efb7b1fc6365fdb7ec9995e170add9a4ea
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-10-09 10:34:51 +0200
Commit message:

 Merge branch 'readme' of github.com:CaluraLab/MOSClip into readme
Package: MOSClip
Commit: 76836b1fad73a13571edb30c7b7ace637ecae3e3
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-10-08 17:30:23 +0200
Commit message:

 add documentation for MOSClip package
Package: MOSClip
Commit: 4eb6897ab07a3d3e2a5858c8470cddba3410713d
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-09-26 16:22:45 +0200
Commit message:

 Update README.md

add image
Package: MOSClip
Commit: eacccee342eef6697681f0f4d39a3fc85456c2e6
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-09-26 16:24:31 +0200
Commit message:

 update .Rbuildignore
Package: MOSClip
Commit: 01199fa46a17ad8580b428dd5ab9a51aba71d97f
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-09-26 15:50:30 +0200
Commit message:

 new readme
Package: MOSClip
Commit: 8820dcc76cfe3def5a96d0f9e9c46a1cbd5295ef
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-09-26 16:32:26 +0200
Commit message:

 Merge branch 'readme' of github.com:CaluraLab/MOSClip into readme
Package: MOSClip
Commit: a91d9550a871f47c1cadd9d393f10966c92099c9
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-09-26 16:24:31 +0200
Commit message:

 update .Rbuildignore
Package: MOSClip
Commit: 5b1ecfb4526e61b70fbb224870ca8758c028974b
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-09-26 16:22:45 +0200
Commit message:

 Update README.md

add image
Package: MOSClip
Commit: d384fe141613b25a2b58f1154b4748219f2b6c7b
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-09-26 15:50:30 +0200
Commit message:

 new readme
Package: MOSClip
Commit: d87335e1fbfbbecc3b11d4ed0f56a278c705d10b
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-09-26 15:33:16 +0200
Commit message:

 gitignore
Package: EnrichDO
Commit: 994ea179c4c26cd9fcbe2fc2e847d4e40e583e37
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2024-10-15 17:23:08 +0800
Commit message:

 modification
Package: CytoPipelineGUI
Commit: 4c5002f0f5dda5aa8a56fc7dbb16d602122a1a4b
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-10-15 11:16:12 +0200
Commit message:

 corrected typo in `.pkgdown` file
Package: ggsc
Commit: 6e006c6c95ded5bc42965d0dd5c126c72d99276b
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-10-15 16:57:39 +0800
Commit message:

 update
Package: ggsc
Commit: f1b691cd8d9180ce54c3c3ff9bcce39833bd71c5
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-10-15 16:53:40 +0800
Commit message:

 Merge pull request #39 from xiangpin/master

using sp_mat in c++ and adjust the levels of features in plot_lisa_feature
Package: ggsc
Commit: 2e586b41f84ba7c1f00ce0f586e0461d974965fc
Author: xushuangbin <xshuangbin@163.com>
Date: 2024-10-15 12:07:08 +0800
Commit message:

 adjust features of plot_lisa_feature
Package: ggsc
Commit: 3580a1bd2f5c54987010c0f1abd898afa17fd26e
Author: xushuangbin <xshuangbin@163.com>
Date: 2024-10-15 12:06:21 +0800
Commit message:

 keeping sp_mat
Package: ggsc
Commit: 13d96428779f1aa352bcdbed727fee4e5600c391
Author: xushuangbin <xshuangbin@163.com>
Date: 2024-10-13 12:24:27 +0800
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: ggsc
Commit: e8b09e34f0b0b088b543dd216349aee17d27863c
Author: xushuangbin <xshuangbin@163.com>
Date: 2024-10-13 12:24:21 +0800
Commit message:

 add levels of features
Package: ggsc
Commit: 7aa68ff8860a88a326540d1d3ad0b9b93f2e0095
Author: xushuangbin <xshuangbin@163.com>
Date: 2024-09-12 21:59:13 +0800
Commit message:

 plot_lisa_feature add levels for lisa result
Package: CytoPipelineGUI
Commit: 47e1ec5793f1a0d4137f374a54ad3fba5fd92c8f
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-10-15 09:42:56 +0200
Commit message:

 implemented `pkgdown` site customization
Package: CytoPipelineGUI
Commit: ab3cc954c0d4c73106b84bda5d4dd462a55d992a
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-05-28 09:31:17 +0200
Commit message:

 removed /pkgdown/_pkgdown.yml
Package: CytoPipelineGUI
Commit: cf350c04d3dea200f149dad0f713c0c7f1d7269e
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-05-14 14:37:03 +0200
Commit message:

 test with empty `_pkgdown/_pkgdown.yml`file
Package: CytoPipelineGUI
Commit: c6e1d4f08bdedd5b57be10e19292ebf25969ab9d
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-05-14 14:27:03 +0200
Commit message:

 test adding pkgdown/_pkgdown.yml
Package: CytoPipelineGUI
Commit: 009e22812964d8f1be2c1ea32b809b97c2d55b74
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-05-14 10:42:09 +0200
Commit message:

 test deployment in GHA
Package: pRolocdata
Commit: 71aad64eb43d998538bf8d32642d4373effb7ab2
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-10-15 10:57:06 +0200
Commit message:

 Merge branch 'master' into devel
Package: pRolocdata
Commit: d962a6dc851fcf8bd03a459a58fe51f5f7e9aeae
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-10-15 10:56:37 +0200
Commit message:

 add files back
Package: StabMap
Commit: 65f94a9965f8622cd3992266f333b1b086dbb8a7
Author: shazanfar <shazanfar@gmail.com>
Date: 2024-10-15 18:37:23 +1100
Commit message:

 add sparseMatrixStats to suggests
Package: CytoPipeline
Commit: 36efdd1ea24ad8e192495714144a70ff169846b2
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-10-15 09:00:47 +0200
Commit message:

 extended pkgdown set-up to allow customization - forced move to bootstrap5 by pkgdown (use of a _pkgdown.yml)
Package: CytoPipeline
Commit: 276c88b9c0e243334b37751ddc6089ddd6a34cdf
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-10-14 20:06:16 +0200
Commit message:

 added alternative texts for generated plots in main vignette
Package: CytoPipeline
Commit: d924f2a9caa163322c7144ca0c2887bb6766d904
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-10-14 17:30:28 +0200
Commit message:

 - updated unit test to account for flowAI version change
- now suggesting `CytoPipelineGUI` package
- bumped to version 1.5.2
Package: gemma.R
Commit: 7a88a9c1cfe048f99d5731523d99651cf78a3461
Author: OganM <ogan.mancarci@gmail.com>
Date: 2024-10-14 21:12:38 -0700
Commit message:

 version bump
Package: gemma.R
Commit: 0d559a38a6d9d212507077845847f4d6b6b7137c
Author: ogan Mancarci <ogan.mancarci@gmail.com>
Date: 2024-10-14 21:07:37 -0700
Commit message:

 fix get_platform_annotations file io
Package: chevreuldata
Commit: 9c45adfe663d5a0e3071313f62b94fc79e030c40
Author: whtns <kevin.stachelek@gmail.com>
Date: 2024-10-14 16:04:14 -0700
Commit message:

 bump version; fix nginx config on server
Package: EBImage
Commit: eb528bda72038be848cdc681c69bd16dedad4d32
Author: aoles <andrzej.oles@gmail.com>
Date: 2024-10-15 00:35:40 +0200
Commit message:

 Apply patch from Kurt Hornik
Package: chevreuldata
Commit: 48bb6b4ff1dc80bb838c0da963422faed60fabe0
Author: whtns <kevin.stachelek@gmail.com>
Date: 2024-10-14 15:23:06 -0700
Commit message:

 bump version
Package: chevreuldata
Commit: 2c7ede56310bb1fefb162c2c53c5013b59d73ab1
Author: whtns <kevin.stachelek@gmail.com>
Date: 2024-10-14 15:22:34 -0700
Commit message:

 fix coordinate column
Package: chevreuldata
Commit: 7afca9079e33f587b8140566d01bbe8a8f881ccd
Author: whtns <kevin.stachelek@gmail.com>
Date: 2024-10-14 15:04:48 -0700
Commit message:

 bump version
Package: chevreuldata
Commit: 461085a417774b1a230f4fe90a74c3324212b845
Author: whtns <kevin.stachelek@gmail.com>
Date: 2024-10-14 15:00:25 -0700
Commit message:

 add human fetal retina dataset
Package: Organism.dplyr
Commit: 60e43ae3b1f686db9e738235e23a23c0164930ca
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2024-10-14 17:09:19 -0400
Commit message:

 update 'mini' databases for new annotations
Package: multtest
Commit: 1d45f73c968f617b7b68dd4ce93be8bee662e1b9
Author: kspollard <kpollard@gladstone.ucsf.edu>
Date: 2024-10-14 12:58:24 -0700
Commit message:

 Change Calloc and Free to R_Calloc and R_Free
Package: multtest
Commit: bdb8df7739623d0475691f91709a726f3089e60c
Author: kspollard <kpollard@gladstone.ucsf.edu>
Date: 2024-10-14 12:32:08 -0700
Commit message:

 Changed Calloc and Free to R_Calloc and R_Free
Package: NormalyzerDE
Commit: aafd0fecf71d329fbe325e3e0194d6f50d95fb9a
Author: Jakob Willforss <jakob.willforss@hotmail.com>
Date: 2024-10-14 20:47:26 +0200
Commit message:

 Version bump
Package: NormalyzerDE
Commit: dd2d6eac7b5570c730a8679bdbcacc6e801a2966
Author: Jakob Willforss <jakob.willforss@hotmail.com>
Date: 2024-10-14 20:45:34 +0200
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/NormalyzerDE into devel
Package: NormalyzerDE
Commit: 6185ffd1a293780b84892cff5870933d5ba8bfb9
Author: Jakob Willforss <jakob.willforss@hotmail.com>
Date: 2024-10-14 20:38:55 +0200
Commit message:

 Disable varying p-value testthat
Package: S4Arrays
Commit: abdba2838565283c182c5e3c07c214f969900295
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-10-14 10:34:52 -0700
Commit message:

 S4Arrays 1.5.11

Replace is_sparse() methods for dg[C|R]Matrix and lg[C|R]Matrix objects
with methods for [C|R|T]sparseMatrix derivatives.
Package: S4Arrays
Commit: b07b09b5e0e04906fac3a8db55782883043eeaad
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-09-28 10:36:03 -0700
Commit message:

 small tweak to internal helper Mindex_row_is_repeated()
Package: HuBMAPR
Commit: 6da954fc3aabcdc575163858a0b0e751f573b39f
Author: christinehou11 <chou11@jh.edu>
Date: 2024-10-14 13:37:51 -0400
Commit message:

 bump up after first review
Package: HuBMAPR
Commit: fd33bd6e0ec583cc3be98de0b140b90e8c866ca6
Author: christinehou11 <chou11@jh.edu>
Date: 2024-10-13 01:04:28 -0400
Commit message:

 edit codes for review comments
Package: bugsigdbr
Commit: b9738478d6f863af586e0da8e1a72cad0555cc12
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date: 2024-10-14 13:24:19 -0400
Commit message:

 getSignatures: fail when not specifiying tax.level with exact.tax.level=FALSE
Package: pgxRpi
Commit: bb7302a78d9001fe788cee4594f7eb510cb17b06
Author: hangjiaz <zhaohj314@gmail.com>
Date: 2024-10-15 00:32:48 +0800
Commit message:

 version bump
Package: pgxRpi
Commit: 7dc7b01ccb55a2d8d87b08dbe1c60a9e804c3b82
Author: hangjiaz <zhaohj314@gmail.com>
Date: 2024-10-15 00:31:57 +0800
Commit message:

 bug fix
Package: scrapper
Commit: ee1bcfd9a8d914ca4e634bdfa77be50d80b7d273
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-10-14 09:03:46 -0700
Commit message:

 Emit a warning if the number of neighbors is not as expected.

Also respect the user-supplied perplexity in t-SNE, don't try to infer
it from the number of neighbors - the R side already attempts to
synchronise the two, so if they're not consistent in the C++ side, we
assume that it was a deliberate choice of the user.
Package: scrapper
Commit: bcac405cb4e7f6fb0217917bd359d26b0ea0bfad
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-10-13 11:41:22 -0700
Commit message:

 Added Bioc badges to the README for prettiness.
Package: koinar
Commit: e5a8c69ae54b54c9080d5422d2599c4df40c1238
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-10-14 18:04:28 +0200
Commit message:

 Add mzR to suggests.
Package: GSEABase
Commit: e393a2722852b27d2f6aa32058fcaee440c16024
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2024-10-14 11:38:10 -0400
Commit message:

 version bump
Package: GSEABase
Commit: 16a0d20812183aa2ff70ce8e7ced64284a9b0ff0
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2024-10-14 11:37:47 -0400
Commit message:

 Merge branch 'axelklenk-devel' into devel

- closes #10
Package: GSEABase
Commit: 1d8b22faf769a19722992e1138a2602fcacec266
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2024-10-07 16:08:35 +0200
Commit message:

 fix misspelled argument in getGmt()
Package: SingleMoleculeFootprinting
Commit: 219a544dc897b26bf11967981d12715d45052cf8
Author: GuidoBarzaghi <guidobarzaghi@gmail.com>
Date: 2024-10-14 16:44:33 +0200
Commit message:

 BiocCheck round
Package: SingleMoleculeFootprinting
Commit: d1bd58295c4c8a58d1f686765f10ca2d1ade60ed
Author: GuidoBarzaghi <guidobarzaghi@gmail.com>
Date: 2024-10-14 16:05:43 +0200
Commit message:

 added Rproj to Rbuildignore
Package: SingleMoleculeFootprinting
Commit: 7fa55d76bdf86e8d85102eb1ab9358fcc0bb112e
Author: GuidoBarzaghi <guidobarzaghi@gmail.com>
Date: 2024-10-14 15:55:15 +0200
Commit message:

 stopped tracking Rproj file
Package: PRONE
Commit: b680c2d74e00163be997cb8b8fb48ae2f7cbfea9
Author: lisiarend <lisiarend@me.com>
Date: 2024-10-14 13:57:25 +0200
Commit message:

 version changed
Package: smoppix
Commit: 4bcf3769264712272fca17949df0c1f0d001d567
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-10-14 12:33:16 +0200
Commit message:

 Try to find bug on server
Package: smoppix
Commit: 96b49688b2a185bc2eed731522244dc92baa8189
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-10-14 11:57:39 +0200
Commit message:

 With Biocodnuctor reviewr comments
Package: smoppix
Commit: 7bd8592ff5c294151b5a875a01987052a0d08617
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-10-10 21:14:30 +0200
Commit message:

 SYncing news and description
Package: smoppix
Commit: 8c129b323cd646cf42e42ff79d3bcb9deb9c8229
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-10-10 18:56:31 +0200
Commit message:

 return ggplot object
Package: smoppix
Commit: f74eaa3105946113d8be792ab8b41da2026b9825
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-10-10 18:47:40 +0200
Commit message:

 Avoid multiple return statements
Package: smoppix
Commit: f71459bcd940bafb4df373262a7ceaead9746317
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-09-04 17:34:32 +0200
Commit message:

 mistake in writetoxlsx
Package: tripr
Commit: cc5f0504236f4828d78466be214b3f3f65d3e130
Author: KonstantinosKardamiliotis <k.kardamiliotis@gmail.com>
Date: 2024-10-14 12:29:01 +0300
Commit message:

 Oct 24 Bioc 10.14 new push
Package: COTAN
Commit: 8588ed6f6e4137efaa8e57e165307f5e4767302c
Author: trinetra75 <marco.fantozzi@gmail.com>
Date: 2024-10-13 23:53:53 +0200
Commit message:

 Updated NEWS.md and bumped-up version
Package: COTAN
Commit: fa78f5fbf4c445ee4451a621daaa9b9a680b2ae0
Author: Marco Fantozzi <57561972+trinetra75@users.noreply.github.com>
Date: 2024-10-13 19:01:24 +0200
Commit message:

 Exported existing utility functions about names arrays (#90)

The functions are: `conditionsFromNames()`,
`niceFactorLevels()`, `factorToVector()`
Package: RMassBank
Commit: 0df9d3bb10b18eb60fc216dac9585a5595edc2d9
Author: Michele <stravsmi@eawag.ch>
Date: 2024-10-14 07:09:11 +0000
Commit message:

 fixed flexAccessionBuilder
Package: BgeeDB
Commit: 9697b238cc0f896faac11e7e148885e4aca99be2
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2024-10-14 09:11:47 +0200
Commit message:

 use back the production release_v2.tsv file
Package: BgeeDB
Commit: 28921398d2bc9a3fd79c9621d5279ac72c3a2228
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2024-10-14 09:08:59 +0200
Commit message:

 add possibility to filter integrated calls based on anat. entity IDs
Package: PRONE
Commit: 5d3853136fc29b64c7d7d643ac3d7b291d4749b3
Author: lisiarend <lisiarend@me.com>
Date: 2024-10-14 08:30:41 +0200
Commit message:

 bioconductor installation + man pages changed
Package: Rsubread
Commit: d293f4b645963ffdb24ce41baae06b26652dfc39
Author: Yang Liao <liao_y@svr2672.licr.unimelb.edu.au>
Date: 2024-10-14 08:15:43 +1100
Commit message:

 Disabled all code in and after cellCounts in the vignettes to see why the build crashed on BioC website.
Package: ClustIRR
Commit: 9aaaeade263f1f6f204c05d82d0421cca9297dbb
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2024-10-13 22:53:50 +0200
Commit message:

 update dac dco, minor changes, testing
Package: DuplexDiscovereR
Commit: 6df4e0ba303d15a37fcd90492035b176d253df1b
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-13 19:59:50 +0200
Commit message:

 vignette links version bump
Package: ontoProc
Commit: d620293177f50b7104c2f97944d41ff26a2d651e
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2024-10-13 13:59:10 -0400
Commit message:

 new bioregistry exploration
Package: DuplexDiscovereR
Commit: 1e2e5e22138ab230cd4325c525f28e664e0618aa
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-13 19:39:27 +0200
Commit message:

 vignette links
Package: ClustIRR
Commit: 7f902839ddd933543ac1538c09f3431a48f88c58
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2024-10-13 19:26:51 +0200
Commit message:

 bugfixes and vignette
Package: DuplexDiscovereR
Commit: 1a029cb3def8c381161dd9bbfc6e96956b4aefd6
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-13 18:35:42 +0200
Commit message:

 merge review branch and version bump
Package: DuplexDiscovereR
Commit: d75f3896a3977f66f1404ecf615aa0d0ef0d9332
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-13 18:33:57 +0200
Commit message:

 styling
Package: DuplexDiscovereR
Commit: 720bfecda352967aecd35fae780656f25af637f3
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-13 17:49:35 +0200
Commit message:

 fixed spelling and minot changes fir rev. request
Package: DuplexDiscovereR
Commit: ef96897996a113a67e5f1d50673e8e704629a0f5
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-11 21:23:55 +0200
Commit message:

 applied styler
Package: DuplexDiscovereR
Commit: 8224898d855cf7047df5b836014237b05930040f
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-11 21:16:52 +0200
Commit message:

 updated Sj and news
Package: DuplexDiscovereR
Commit: 337dbaa57267b2019ca6999a248a76fe6d4c4da0
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-11 20:28:55 +0200
Commit message:

 fixed text in vignettes
Package: DuplexDiscovereR
Commit: 1d782f53f52282b92200d4a8591a07f4f5676b2b
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-11 17:28:14 +0200
Commit message:

 merged res_class into review branch
Package: DuplexDiscovereR
Commit: b5a19321aea21140915bb67d93eb27fc545309a7
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-11 17:26:11 +0200
Commit message:

 added examples to results class
Package: DuplexDiscovereR
Commit: 6437e1cccf1c55818a7121d6702a6c4bd6d18034
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-11 13:25:39 +0200
Commit message:

 applied styler
Package: DuplexDiscovereR
Commit: 01dc675b30a490abdbe568fc4587ae2ea4ae4b46
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-10 19:08:04 +0200
Commit message:

 changed link in pkg R
Package: DuplexDiscovereR
Commit: 0add3495f11ab94cd8a3f6143808f61d186fa2ac
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-10 18:56:41 +0200
Commit message:

 changed output to result calss in code, tests and vignette
Package: DuplexDiscovereR
Commit: 5767a15103cbd5ac1c8d380020ee1d4630bbd5d6
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-10 18:03:23 +0200
Commit message:

 added class
Package: DuplexDiscovereR
Commit: 1651655d1e3d20203731757bbbf785ebc69033ab
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-10 16:35:38 +0200
Commit message:

 added all non-binds to globals pl one
Package: DuplexDiscovereR
Commit: 6f1436b1888b020450133d138944f6f4be079f13
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-10 16:34:36 +0200
Commit message:

 added all non-binds to globals
Package: DuplexDiscovereR
Commit: eee2a56c92b3e6033bb8cb90a89a745951d9dacf
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-10 14:35:56 +0200
Commit message:

 fixing cmd check note
Package: DuplexDiscovereR
Commit: 1e78d373c9859900f51dc48006d3310542b42027
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-09 18:19:29 +0200
Commit message:

 fixing NOTES in bindings and 2->4 tabs
Package: DuplexDiscovereR
Commit: 340b056d8a7eb5dd568c64c518213d62474051c2
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-09 17:11:11 +0200
Commit message:

 changed vignette name and added another note on RNAduplex
Package: DuplexDiscovereR
Commit: ef793090d4797d9a3dcba1b47703a1b4eb5cc600
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-09 17:01:50 +0200
Commit message:

 added warning for RNAduplex license
Package: DuplexDiscovereR
Commit: b04d63fbe43b1e152f9df36b144c5ef7daa296dd
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-09 16:51:52 +0200
Commit message:

 changed system to system2
Package: DuplexDiscovereR
Commit: 7b64b7d9e9539d8b7670be94bec2cce39f41bd3a
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-09 16:37:32 +0200
Commit message:

 restored tracking for test plots, file removed
Package: DuplexDiscovereR
Commit: 2325c2a94488c322151e1d5dcef89df3d78dd7d6
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-09 16:36:24 +0200
Commit message:

 removed tracking for test plots
Package: DuplexDiscovereR
Commit: 488c47629e4a04b6d5b5f04f913c2d5413e15caa
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-09 16:34:41 +0200
Commit message:

 removed for-loop for comps clustering
Package: DuplexDiscovereR
Commit: 36439e6b9c10a3ce691aacca671937724a851240
Author: Semenchenko <esemenc@cl-meyer18.mdc-berlin.net>
Date: 2024-10-08 11:42:46 +0200
Commit message:

 removed duplicate gitignore
Package: AlphaMissenseR
Commit: d90e937812bd72b0382acdd1755e732941d1267b
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2024-10-13 11:53:31 -0400
Commit message:

 update README, NEWS, and pkgdown for benchmarking vignette
Package: AlphaMissenseR
Commit: 562b2c466d31491decfc8cd21c3664c9ee1ba0d1
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2024-10-13 11:48:46 -0400
Commit message:

 Merge branch 'ccb-hms-ProteinGym' into devel
Package: AlphaMissenseR
Commit: 417b1cc61b5d5e9e2158bf5743ee103e99b74c13
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2024-10-08 17:44:07 +0000
Commit message:

 removed dplyr from `suggests`
Package: AlphaMissenseR
Commit: e529ffeec5758f86cd0debe76d39027d523ba94a
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2024-10-08 17:35:24 +0000
Commit message:

 bumped version
Package: AlphaMissenseR
Commit: 13397c5953684f7a03e478fcf8c9237baabd1920
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2024-10-08 17:34:31 +0000
Commit message:

 Issues vignette after D. Benchmarking
Package: AlphaMissenseR
Commit: 5735e70494369039f1bad312a6e718cb64952539
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2024-10-08 17:32:43 +0000
Commit message:

 dependencies for benchmarking in `Suggests`
Package: AlphaMissenseR
Commit: f451845ae5819aa28f5238d595e40f9baaaa370d
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2024-10-08 17:28:54 +0000
Commit message:

 vignette for benchmarking with ProteinGym
Package: bugsigdbr
Commit: 5b35f874f1ebc58594b7d2a8926bfc5ba1d76c9c
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date: 2024-10-13 11:43:44 -0400
Commit message:

 importBugSigDB tests: check for different dimensions depending on source
Package: AlphaMissenseR
Commit: c6d478e446e4e6e27893f323e043257c2f5c7a6f
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2024-09-20 03:14:40 -0400
Commit message:

 refactor plot_granges() as gosling_plot()

- rename as gosling_plot(); renames files to Gosling.R / Gosling.Rd
- test for required packages as part of argument validation ('fail early')
- rename 'bars' option as 'bar', for consistency with gosling terminology
- separate compose_view_bar() and compose_view_lollipop() for code
  modularity
- separate gosling_app() for Shiny app creation. Only create app when
  create_app = TRUE (default when interactive()); facilitates running
  code in examples / vignettes during R CMD check
- revise example to maximize code run during R CMD check
- rename argument as `granges`, so users are less likely to puzzle over
  `gr_` meaning
- managing location of .gosling so that it is not created in the user
  working directory. Uses setwd() / on.exit() because shiny.gosling does
  not allow easy alternative specification
- link [`GenomicRanges::GRanges`] in man page to satisfy R CMD check
- version bump and NEWS update
Package: AlphaMissenseR
Commit: afe7401aaa0c3d0688a88a089f24339e00b2b1d8
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2024-09-20 02:08:32 -0400
Commit message:

 formatting changes so pull request follows package style

- run devtools::document() (renames man page to plot_granges.Rd, etc.)
- standardize roxygen documentation formatting
- update example argument 'mode = ' to 'plot_type = '
- use match.args() for plot_type argument validation
- avoid long lines and extra vertical spacing
- use standard code indentation in vignette
- do not use inline links []()
- wrap vignette text to 80 columns
- remove trailing whitespace
Package: AlphaMissenseR
Commit: 7191a7afd7727e5192d0755182ab905bd02d5f78
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2024-09-20 01:43:24 -0400
Commit message:

 minimize differences between pull request and devel

- retain original whitespacing in DESCRIPTION
- do not change vignette metadata order
- do not replace links [][] with inline links []()
- do not use shiny runtime in vignette
 </pre>
    </div>
  
    

      Package: AlphaMissenseR

      Commit: b22047e44330598b03e98f4771b590b155a6cb54

      Author:  Martin Morgan <mtmorgan.xyz@gmail.com> 

      Date: 2024-09-24 17:08:58 -0400

      Commit message:


	  
		
 Squash commit merges #6 'Add plot_granges` with the following commits:

Co-authored-by: lee-t <tyrone_lee@hms.harvard.edu>
Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com>
Co-authored-by: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Co-authored-by: lgeistlinger <ludwig.geistlinger@gmail.com>

commit aa46568508126ae8f31e3700040deb8e0e541818
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Thu Sep 19 14:25:40 2024 -0400

    change @details

commit b0b5a450a63edbeeecf85d6be07704fba63a445b
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Thu Sep 19 13:41:34 2024 -0400

    reformat DESCRIPTION

commit c65a35174a29a6cf53973307689ebfd696d0ccc5
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Thu Sep 19 13:30:56 2024 -0400

    format example

commit c9e90883a810e32127fdec3610f0cbcc6a3868d2
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Thu Sep 19 13:29:19 2024 -0400

    change to use `identical()`

commit 57cbc97d2903475f7edb802379ecf680cd7652c7
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Thu Sep 19 13:23:45 2024 -0400

    combine assertions into one `stopifnot()`, `plot_type` is already checked later in the plotting function at line192.

commit 73f173deacda4232a8a767b5802f1601008cdf59
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Thu Sep 19 13:17:17 2024 -0400

    change function indentation and input granges name

commit a24edaa16d43d7f1f80d4537c86119e4524d2b36
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Tue Sep 17 14:37:53 2024 -0400

    Rename plot_shinygosling to match function. Edit documentation wording. Change alphafold vignette to show images.

commit 916e254386cd918517477092ca9722115303279f
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date:   Wed Aug 21 17:00:43 2024 -0400

    some cosmetics to the gosling section

commit 48a05588655089c480718a209548d5ca15f27bfe
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Wed Aug 21 11:56:30 2024 -0400

    some message suppression and link fixes

commit e32322f4a10f43548f9b3c3dd7875ec6f4c12fdc
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Wed Aug 7 17:53:33 2024 -0400

    found the missing visual channel imports.

commit 008b5d6ba002d853c2a4702276627fd476aa00cd
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Wed Aug 7 17:36:31 2024 -0400

    reverting importFrom, cache order

commit 963a9ff7cc077a20ca6cc95244168e61190bdf9d
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Wed Aug 7 16:55:43 2024 -0400

    imports and cache creation reverted

commit 0c66dc92edf9719b9a0b2104a26b0595443f4f0c
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Wed Aug 7 15:18:16 2024 -0400

    fixing vignettes, trying to pass R CMD check

commit 00c57a76c297d5811113cb81ee72c5c3d78936f8
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Wed Aug 7 12:10:24 2024 -0400

    sync help page for plot_shinygosling.rd

commit c265cf240fa7ac38e4a915fd39c1f2289204808b
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Wed Aug 7 12:03:34 2024 -0400

    remove runtime from intro

commit b4a28bbcd90e3b22bd6ec33d21868234e88f1861
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Wed Aug 7 12:03:16 2024 -0400

    text and example changes to alphafold.Rmd; fix spelling of 'lollipop'

commit e6137b2e3715bfd352bd111a8af8f9d87c4da320
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Wed Aug 7 11:49:12 2024 -0400

    replace tabs with spaces (on Windows-1252)

commit 96fa7f52945231456c03ba0c344b17453d7cd0d1
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Tue Aug 6 17:52:38 2024 -0400

    'plot_type' selects between bars and lolipop plots

commit af48390b4ddbf8f011f49c4f070d0ddfbaaedc2a
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Tue Aug 6 16:48:30 2024 -0400

    add tooltips to lolipop plot

commit b9b73887130b96f5006975a57b45d021d648728f
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Tue Aug 6 16:46:47 2024 -0400

    use cache for gosling dir

commit bbc4def826905eabbba01d864c78b802449cd16a
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Tue Aug 6 16:30:31 2024 -0400

    add validation for input types

commit 6dfd4b288f8a9c1f960de17c2fbf1ae0e0faea1d
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Tue Aug 6 13:47:23 2024 -0400

    rename as_granges->gr, get_range - > g; fix GRanges accesssors in zoom view

commit 64e4de00de7e28f029ac2638c7b877c211d98c7a
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Fri Aug 2 16:58:33 2024 -0400

    fixes for example

commit 7f445879c8c881310188779deb403f0c949a62f1
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Fri Aug 2 16:51:21 2024 -0400

    no `gosling` R package

commit 94837cffc54d1f03745036bb560a66e1191a0100
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Mon Jul 29 16:55:39 2024 -0400

    whitespace DESCRIPTION

commit a4a6785a04774e189aea48972f359f7484f88731
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Mon Jul 29 16:52:56 2024 -0400

    add contributors to DESCRIPTION

commit 70ca8d65bffcf32ac41179fc4ff79f0665948251
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Mon Jul 29 16:46:07 2024 -0400

    edit vignettes; remove gosling.shiny vis from intro, add to alphafold

commit 4eefe8728cc91cdbb470a69e2f3d5291adba6d09
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Mon Jul 29 16:36:59 2024 -0400

    modify function; change colormap, change example, fix categories

commit 424fe6b0182e7ce735a3443e9856dcf243b9b798
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date:   Mon Jul 29 19:43:15 2024 +0000

    checks for directory .gosling

commit 9e9170aa5cc90f23e14a692701dc11331a1af127
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date:   Mon Jul 29 15:30:23 2024 -0400

    Fixes

commit 236aa27d454ac32acfcafeab20015c1c0c512cfa
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date:   Mon Jul 29 15:10:34 2024 -0400

    Remove .RData

commit 1790d52a70e6b8df503a466dfc309e29c48c4c16
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date:   Mon Jul 29 15:09:19 2024 -0400

    revert changes to ignores

commit ea6f464975ff2d97d8e13b7b5bb55b088995fe76
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date:   Mon Jul 29 15:06:10 2024 -0400

    Remove .gosling repo

commit 75428d28da58803e38070d846653d5e4cf048216
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date:   Mon Jul 29 15:00:35 2024 -0400

    Remove d_clinvar.R, fix DESCRIPTION

commit 4bac60a31896423625a2b1cd742b4a8be858d61c
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date:   Mon Jul 29 14:28:26 2024 -0400

    Remove .Rproj

commit 123c788b894a7c9a96545878ffc3ad8bc2e7f2ce
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date:   Mon Jul 29 14:26:31 2024 -0400

    Remove z_scratch.Rmd after consulting with Tram and Tyronne

commit 7fa695488c4b3a60df29ea23346e63f8db981a20
Merge: 2aba65e 1214ac9
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date:   Mon Jul 29 14:24:45 2024 -0400

    Merge branch 'devel' into vis_shinygosling

commit 2aba65ed4c56aefd713d1d86c2b832e6c6446cfc
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Mon Jul 29 10:56:41 2024 -0400

    wrap lolipop plotting in function "plot_shinygosling" examples and other plots in scratch Rmd

commit 224e5f2d27814b0aa1a8546ee3cd56860593ef1e
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Thu Jun 20 14:56:02 2024 -0400

    fix knitting error: seperating track objects

commit b6a735822def4ca28a331cbd56b2cb968ff0ae4a
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Thu Jun 20 14:47:09 2024 -0400

    update b_vis vignette. take screenshots for presentation

commit 1886cb436018b612bfe8338bd0504f4ef759895d
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Wed May 29 13:59:10 2024 -0400

    update suggests w/shiny.gosling, fix runtime and library calls, update gitignore

commit b4c413650f9f14040443712c1acd33f3d7484661
Merge: f3dcd5a 199e755
Author: Tyrone Lee <tyrone_lee@hms.harvard.edu>
Date:   Tue May 28 16:40:29 2024 -0400

    Merge branch 'mtmorgan:devel' into vis_shinygosling

commit f3dcd5acb1e0477ce5a823bc64218f8ff9134d50
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Tue May 28 15:12:52 2024 -0400

    minor labels

commit ffbeac36f9ad7621aa6198b4054c6edbe1defc04
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Fri May 24 17:31:58 2024 -0400

    add integrated shiny.gosling plot embedded into vignette, first pass
 

    

  
    

      Package: ontoProc

      Commit: 07575140bde0d0d6d16e0c992c9f8ee5005cd2a7

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2024-10-13 08:24:30 -0400

      Commit message:


	  
		
 adding object caching in setup_entities2
 

    

  
    

      Package: SpaNorm

      Commit: fc96b27613996d3e01ba1259354079c11d903b6c

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 22:12:21 +1030

      Commit message:


	  
		
 Addressed bioc reviewer comments (triggering build)
 

    

  
    

      Package: SpaNorm

      Commit: 519192b6b1eaf5064231095df3357a52ea0047df

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 11:21:37 +0000

      Commit message:


	  
		
 bug fix in plotSpatial and doc update
 

    

  
    

      Package: SpaNorm

      Commit: 6668baa269ab2661faa28c6f35df0ef3294eb076

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 11:08:14 +0000

      Commit message:


	  
		
 changed isbio to wtype to represent covariate types more broadly
 

    

  
    

      Package: SpaNorm

      Commit: f2bc1ec948f9ea411f80101b38ef0b473950b0bf

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 20:22:03 +1030

      Commit message:


	  
		
 spell check in vignette and documentation
 

    

  
    

      Package: SpaNorm

      Commit: 57fecb05be2c74857b7b7547dbef16aa321d683c

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 14:49:52 +1030

      Commit message:


	  
		
 fixed warnings caused by setting lazydata to false
 

    

  
    

      Package: SpaNorm

      Commit: babfd815b55bebc9c0925ca69204ac9871e41c6e

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 14:26:11 +1030

      Commit message:


	  
		
 malformed authors field in description
 

    

  
    

      Package: SpaNorm

      Commit: 35168e10a401046ac0c88235bdda8637d983278f

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 14:17:28 +1030

      Commit message:


	  
		
 typo in description file
 

    

  
    

      Package: SpaNorm

      Commit: f3f3f23b0d0e3fe21ce56a36aba62d3675b5f209

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 02:50:24 +0000

      Commit message:


	  
		
 added spatial plotting function and swapped the previous function in the vignette
 

    

  
    

      Package: SpaNorm

      Commit: 9c92dcef8b2aaded8df4e1f90f07b4052f25d7c4

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 00:58:01 +0000

      Commit message:


	  
		
 Added citation file
 

    

  
    

      Package: SpaNorm

      Commit: 7a841d499f3f7eb89359a762c65f3dafe9d8ccbe

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 00:47:04 +0000

      Commit message:


	  
		
 changed dontrun to donttest in examples
 

    

  
    

      Package: SpaNorm

      Commit: 2145a76099906c6481740302fdb5631926dc72e9

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 00:39:54 +0000

      Commit message:


	  
		
 Added CellBiology to biocViews and set LazyData to false
 

    

  
    

      Package: SpaNorm

      Commit: 75844786de19c4f54262b5e3cfc213df6d7d4b9d

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 00:39:14 +0000

      Commit message:


	  
		
 changed loop from 1:... to seq_len
 

    

  
    

      Package: SpaNorm

      Commit: e437d612107ea2380b28a6defc9b845efd0b5dc5

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 00:09:35 +0000

      Commit message:


	  
		
 explicit call to str in show method for SpaNormFit
 

    

  
    

      Package: SpaNorm

      Commit: 48ad449963e21aa900965d3c14b1b6c162f62a94

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 00:07:21 +0000

      Commit message:


	  
		
 bug fix due to typo (W -> Wsub)
 

    

  
    

      Package: SpaNorm

      Commit: 0c43c108c2d1794dcec6ab4773f7ef18c66ac149

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 00:03:01 +0000

      Commit message:


	  
		
 explicit namespace import
 

    

  
    

      Package: SpaNorm

      Commit: 3384ab60c93f06cccaa7e7a20383f2faf2322be7

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 00:02:29 +0000

      Commit message:


	  
		
 added news file
 

    

  
    

      Package: SpaNorm

      Commit: 315b705708255b07608bca21191ede1f6ea5e77a

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 00:02:21 +0000

      Commit message:


	  
		
 removed unnecessary files
 

    

  
    

      Package: edgeR

      Commit: 9b2e2ea00b6fb4035dee7f71b5f8d1b21dc44c6d

      Author:  Yunshun Chen <yuchen@wehi.edu.au> 

      Date: 2024-10-13 15:05:31 +1100

      Commit message:


	  
		
 Update the edgeR user's guide
 

    

  
    

      Package: ggsc

      Commit: 86ac61edf63336c76a7e8c048a4a9cd2e4ce9595

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2024-10-13 11:18:28 +0800

      Commit message:


	  
		
 Merge pull request #37 from MingLi-929/devel

fix the function of features parameter 

    

  
    

      Package: ggsc

      Commit: 61bae901cc4e805708ca9ebc0e6498b3f8dc634a

      Author:  li ming <limiang929@gmail.com> 

      Date: 2024-10-13 10:37:37 +0800

      Commit message:


	  
		
 fix the function of features parameter
 

    

  
    

      Package: EpiDISH

      Commit: e107fce62c1e85b9b888f0885aed095acc9a6a20

      Author:  Shijie C. Zheng <shijieczheng@gmail.com> 

      Date: 2024-10-12 22:05:00 -0400

      Commit message:


	  
		
 Version bump after fixing cp
 

    

  
    

      Package: EpiDISH

      Commit: 38ef4b34046d0dc8cd41598e2a9563ad14ed5e8f

      Author:  xiaolong guo <85536994+tednb@users.noreply.github.com> 

      Date: 2024-10-05 12:41:51 +0800

      Commit message:


	  
		
 Correct the DoCP function 

    

  
    

      Package: EpiDISH

      Commit: 9735edcc71b51b697101a56b9544c7758b9f0858

      Author:  xiaolong guo <85536994+tednb@users.noreply.github.com> 

      Date: 2024-09-02 22:24:35 +0800

      Commit message:


	  
		
 Delete man/centCAB100i.Rd 

    

  
    

      Package: EpiDISH

      Commit: 0bcaedfc4c8bc5201a4f9f73e28f8009cec61940

      Author:  xiaolong guo <85536994+tednb@users.noreply.github.com> 

      Date: 2024-09-02 22:08:42 +0800

      Commit message:


	  
		
 add 19 CT blood reference 

    

  
    

      Package: EpiDISH

      Commit: 6093187c0b8de9c1f2a00574e50b9c700142c2b3

      Author:  xiaolong guo <85536994+tednb@users.noreply.github.com> 

      Date: 2024-09-02 22:08:00 +0800

      Commit message:


	  
		
 Delete man/centCAB100i.rda 

    

  
    

      Package: EpiDISH

      Commit: 509efee6053a3c9553bcdf839a17f70bcf42b42b

      Author:  xiaolong guo <85536994+tednb@users.noreply.github.com> 

      Date: 2024-09-02 20:55:39 +0800

      Commit message:


	  
		
 add 19 blood CT reference 

    

  
    

      Package: EpiDISH

      Commit: a2039722bc7024d39a4782197a1b236a93ee873c

      Author:  xiaolong guo <85536994+tednb@users.noreply.github.com> 

      Date: 2024-09-02 20:52:53 +0800

      Commit message:


	  
		
 Add files via upload

add a 19 CT reference matrix 

    

  
    

      Package: SpliceWiz

      Commit: 2839410ea6b844e500fa86b4c65ee76fd2a66f6a

      Author:  alexchwong <80015046+alexchwong@users.noreply.github.com> 

      Date: 2024-10-13 10:41:26 +1100

      Commit message:


	  
		
 Version bump 1.7.6

Fix uninformative message when gene ontology species not available
 

    

  
    

      Package: ontoProc

      Commit: c383cbf13b629aa6789f3bb75b721772eec57af4

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2024-10-12 12:45:01 -0400

      Commit message:


	  
		
 passes check on mac
 

    

  
    

      Package: ontoProc

      Commit: 13961bd3113f4108c727dab85cb80615332011ba

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2024-10-10 08:48:50 -0400

      Commit message:


	  
		
 conditioning owl2cache example
 

    

  
    

      Package: ontoProc

      Commit: 782024e36b4ca46a3ac7f62d4d25c2e170e16869

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2024-10-10 05:32:35 -0400

      Commit message:


	  
		
 various changes to condition on availability of owlready2
 

    

  
    

      Package: ontoProc

      Commit: 402590c5ac3d09922825c8469480a4d4cce7e025

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2024-10-09 11:19:18 -0400

      Commit message:


	  
		
 Merge branch 'devel' into with_pkgdown
 

    

  
  


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