fix: corrected the Session info layout at end of vignette
 

 refactor: removed duplicated knitr in imports
 

 refactor: added stats and utils import for auntile, head and tail
 

 refactor: no visible binding solved with .data$ for tidy coding to fix R cmd check. Still need to refactor validate package code style
 

 readPepo idatdir improvements
 

 Deprecate

 - maintainer requested
 

 Merge pull request #154 from drighelli/#151

#151 

 Adding confidence level as a parameter (#121)

Co-authored-by: seraidarian <ely.seraidarian@ecole.ensicaen.fr>
Co-authored-by: Leo Lahti <leo.lahti@iki.fi>
Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

 Version bump

Merge remote-tracking branch 'upstream/devel' into devel

# Conflicts:
#	DESCRIPTION
 

 Deprecate z transform in transformAssay (#584)

Signed-off-by: Daena Rys <rysdaena8@gmail.com>
Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

 Clarify detection (#580) (#581)

Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

 Minor fix to message (#576)

 

 Fixes to agglomeration (#556)

Signed-off-by: Daena Rys <rysdaena8@gmail.com>
Co-authored-by: Leo Lahti <leo.lahti@iki.fi>
Co-authored-by: Daena Rys <rysdaena8@gmail.com> 

 Use agglomerateByVariable when onRankOnly = FALSE (#570)

Signed-off-by: Daena Rys <rysdaena8@gmail.com>
Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

 add informative error message for strictly-negative values in rarefyAssay (#563)

 

 Fix critical issue with mergeFeatures (#478)

Signed-off-by: Daena Rys <rysdaena8@gmail.com> 

 Integrate agglomerateBy* functions (#554)

 

 Delete mia.Rproj (#553)

 

 Rename perSampleDominant* to getDominant and addPerSampleDominant* to addDominant (#527)

Co-authored-by: TuomasBorman <tvborm@utu.fi> 

 Rename getTop*, getPrevalent*, getUnique* and get Rare* functions (#526)

Co-authored-by: TuomasBorman <tvborm@utu.fi> 

 Fix agglomeration of trees (#551)

 

 Rename countDominant* functions to summarizeDominance (#528)

Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Co-authored-by: TuomasBorman <tvborm@utu.fi> 

 Tree agglomeration fix (#548)

 

 getHierarchyTree: empty cells (#547)

 

 Improve Tengeler2020 (#545)

 

 new generic function agglomerateByVariable (#507)

Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Co-authored-by: TuomasBorman <tvborm@utu.fi> 

 changed diversity input check (#520)

 

 use breaks_extended from scales package to calculate the breaks.
 

 add advIGD4C and getSignGenes functions
 

 DelayedArray 0.31.3

Implement a bunch of extract_sparse_array() methods, one for each
existing OLD_extract_sparse_array() method. No unit tests yet (they'll
follow soon).
 

 update GHA for Bioc 3.19
 

 SparseArray 1.5.9

Rename internal helper .abind_SVT_SparseArray_objects() ->
abind_SVT_SparseArray_objects().
 

 Small fix to internal helper .Ensembl_getMySQLCoreDir()

Fix
    ftp_dir <- "ftp.ensembl.org/pub/release-112/mysql"
    txdbmaker:::.Ensembl_getMySQLCoreDir("hsapiens_gene_ensembl", ftp_dir)
after breaking change in Ensembl 112 directory layout. 

 pwaling -> biostrings, in 3.19
 

 minor bugfixes
 

 Renamed the search functions to be more general than just metadata text. (#11)

- Added support for filtering on user, timestamp (if available).
- Consolidated all query type creation into a single function.
- Shortened the query maker function name for ease of use. 

 DelayedArray 0.31.2

Add coercion from SparseArraySeed to COO_SparseArray.
 

 update, remove unused namsesaces
 

 fixed outdated man
 

 Require harmony '1.2.0'

- Reenable temporarily broken unit test
- Give helpful error message for outdated harmony version
 

 temporarily removed tutorial
 

 Merge remote-tracking branch 'upstream/master'
 

 fix missing files, added parameter to plot_SS_simulation
 

 remove hmisc dependency
 

 bump version, push simpler vignette
 

 add note about citation() and DOI in DESC
 

 add references to README.md
 

 update .gitignore
 

 version bump 1.17.1
 

 updated vignette, bumped version
 

 scDotPlot v0.99.2
 

 add bioRxiv DOI
 

 make coloring the same as in manuscript
 

 fix typo
 

 Version 2.7.1
 

 Merge pull request #112 from FertigLab/105-refactor-patternmarkers

105 refactor patternmarkers 

 fix inter-pattern bug
 

 update vignette, closes #105
 

 add axis switching back
 

 add score output to patternMarkers-method
 

 bump version
 

 Merge pull request #103 from FertigLab/102-patternmarkers-all-returning-empty-lists

- rewrite method for `threshold="all"`
- fix passing custom `lp`
- improve documentation
- remove `threshold="cut"` until it's clear what I does  

 bump version
 

 add test that checks that all genes are returned for threshold="all"
 

 fix implementation of custom-provided lp
 

 refactor patternMarkers
 

 merge upstream
 

 clean up tests
 

 Merge pull request #108 from FertigLab/jacob-visualizations

getPatternGeneSet: replace pathways column with gene.set 

 remove cut from vignette
 

 test significant gene sets

Tests for gene set plotting now include a check for a sig_p1 gene set that should be associated with pattern 1.
 

 Merge pull request #106 from FertigLab/104-refactor-add-comments

commenting GAPSRunner.cpp 

 add trivial functional test for threshold=cut
 

 update description
 

 add the original method back
 

 adjust style and close #102
 

 simplify loop
 

 fix P dimensionality for sweeping
 

 add a test to check A and P dim across modes
 

 fix threshold="all" from #102
 

 Merge pull request #97 from jmitchell81/score_fill_for_geneset_plot

Score fill for geneset plot 

 add element_blank to namespace
 

 update ggplot2 importFrom
 

 remove axis max and old plot comment
 

 overlay gene set names
 

 Continuous score color fill
 

 remove padj text overlay

axis no longer needs to be manually scaled as that was to leave room for the written p-value.
 

 pl variable name

plot could conflict with functions in other namespaces like ComplexHeatmap
 

 Extend search clauses to project, asset, version names or path. (#10)

This is useful if the project/asset/etc. name contains important information
and we want to do full or partial matching on it within our query. 

 fix timeout
 

 Bugfix to correctly collapse OR'd text queries.

Also minor refactoring for better code re-use in query builder.
 

 fix smoothscatter
 

 refactor: shorten function lengths

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 fix: ensure compatibility between DataFrame and tibble

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 export view3dStructure.R
 

 fix scatter plot
 

 updated roxygen
 

 missed data call in examples
 

 documentation changes to address Bioc checks
 

 Merge branch 'devel' of git.bioconductor.org:packages/seqsetvis into devel
 

 tests for ssvAnnotateSubjectGRanges
remove mcf7 bam and updated splice count tests
 

 added missed sort options to within_clust_sort
 

 v bump 1.23.14
reimplemented "left" and "right" sort strategy
 

 Update
 

 Update
 

 update NEWS
 

 update Rmd vignette and use BiocStyle
 

 bump into 0.99.1
 

 rename data description file
 

 updated vignette and test cases
 

 remove plot_joint_graph -> now only plot_graph for both
 

 integration with databases
 

 bump version number
 

 Bumped up version and upated NEWS.md

Cleaned code according to linter
 

 Added UMAP for cells' clusters (#75)

* Added function getProbabilityOfZero()

Returns the matrix whose components are the probability of
zero reads for given gene/cell pair...

* Added function calculateLikelihoodOfObserved()

For each gene/cell it returns the likelihood of the observed
zero/non-zero reads with repect to the modeled probability of zero

* Improved function `UMAPPLot()`

Now the function will display cluster centroids when no elements
to label are passed in

* Fixed bug in `UMAPPlot()` code

* Completed extension of function `UMAPPlot()`

Now is able to plot the clusters' names at the centroids

Now can take an array of colors for the displayed things

* Fixed bug in vignette

Now max pointSize is 3.0 instead of 5.0

* Fixed minor bugs

* Added function `cellsUMAPPlot()`

Added option to return log-normalized data

Added option to override `umap()` meta-parameters

Updated vignette

* Added more options to the `method` used by `cellsUMAPPlot()`

Added possibility to tweak a few umap hyper-parameters

* Added possibility to store/recall GDI in the COTAN object

Added support for HVG in cellsUMAPPlots() using Seurat

Updated tests/examples/documentation

* Resolved last few bugs

* Updated NEWS.md and bumped-up version 

 Normalize paths to remove ~'s before entering C++ code.
 

 Typo fixes in the docs.
 

 feat: add DataFrame as a dependency

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 ci: remove ACT env var and ci run condition for workflows

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 fix: remove unnecessary file references

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 fix: remove unnecessary files

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 build: update for better bumpversion behavior

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 fix: update the stored dataset to have no compression

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 fix: update the stored dataset to have gzip compression

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 ci: ensure only the last tag is shown

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 fix: clear all the linting warnings about hanging indents

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 docs: update the source of the vignette to 80 chars wide

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 build: update the minimym R version

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 fix: update the vignette with regular formatting

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 fix: remove unnecessary 'discordant' parameter

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 fix: add runnable examples

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 test: update the consensusConcordants tests in sync with code changes

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 build: update renv dependencies

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 test: update fixtures

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 test: add documentation examples

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 Merge pull request #53 from CogDisResLab/bioc/description

 

 chore(deps): update actions/checkout digest to 692973e (#55)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> 

 Merge branch 'devel' into bioc/description 

 Merge branch 'devel' into bioc/description

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com> 

 Bump version: 0.99.635 → 0.99.636
 

 Bump version: 0.99.634 → 0.99.635
 

 Bump version: 0.99.633 → 0.99.634
 

 Bump version: 0.99.632 → 0.99.633
 

 Merge branch 'devel' into bioc/description 

 Merge branch 'devel' into bioc/description 

 docs: ensure that description tags are properly populated

Fixes #38
 

 build: remove unnecessary workspace file

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 Bump version: 0.99.633 → 0.99.634
 

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 chore(deps): update actions/upload-artifact action to v4 

 build: ignore the renovate.json file when building the package

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 ci: remove unnecessary secret pull from github actions

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 docs: removed a single function name typo

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 docs: update the NEWS.md file

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 build: update the R package compatibility

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 docs: update the README file

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 build: add renovate config

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 Bump version: 0.99.592 → 0.99.593
 

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 add beachmat.hdf5 in suggests
 

 Merge branch 'RELEASE_3_19' into devel
 

 import mclust::estep*()
 

 merge conflict
 

 udpate news
 

 import mclust::estep()
 

 commit1-15-June-2024
 

 Reposition positions if there are negative values
 

 Update new position calculation scheme. Also changed default chromosome gap
 

 Reorganize position calculating code
 

 test fix and bump
 

 Merging 15 Jun Merge remote-tracking branch 'upstream/devel'
 

 better visualization of tooltip
 

 Use block processing strategy in coercion from CSC_H5SparseMatrixSeed
to SVT_SparseMatrix

This circumvents the current restriction that we cannot call
SparseArray:::make_SVT_SparseMatrix_from_CSC() on long vectors at the
moment because R does not yet support passing long vectors to the .Call
interface.
 

 HDF5Array 1.33.1

Add 'as.vector' argument to h5mread().

Add coercions from CSC_H5SparseMatrixSeed, H5SparseMatrix, and TENxMatrix
to SparseArray. These coercions allow the SparseArray() constructor
function to work out-of-the-box on CSC_H5SparseMatrixSeed,
CSC_H5ADMatrixSeed, TENxMatrixSeed, H5SparseMatrix, and TENxMatrix objects.
 

 Release 1.1.1
 

 commit1-14-June-2024
 

 add pgxMetaplot function; num_cores arg
 

 Merge pull request #126 from PhanstielLab/cool_files

(m)cool file integration 

 additional docs for cool plotting
 

 integration with plotting functions
 

 glue and rhdf5 dependencies
 

 cool file reading tests
 

 initial mcool file reading and helper functions
 

 Merge remote-tracking branch 'origin/main' into devel
 

 News update
 

 limma 3.61.2

- New argument `adaptive.span` for voomWithQualityWeights().

- New argument `adaptive.span` for normalizeCyclicLoess().

- voom() now returns the chosen `span` if `adaptive.span=TRUE`.
 

 Trying to solve conflicts.

Merge branch 'devel' of git.bioconductor.org:packages/DepecheR into devel

# Conflicts:
#	DESCRIPTION
 

 Correction
 

 Bump version
 

 fixed bug in shift footprints
 

 Merge branch 'devel' of git.bioconductor.org:packages/ggkegg into devel

# Conflicts:
#	DESCRIPTION
 

 error handling
 

 name_repair
 

 update plot methods
 

 add more viz tests to resolve #25
 

 fix alpha in plot_image()
 

 update eval_exprs(); rename eval_expr() => eval_at()
 

 version bump in devel
 

 Update README.md 

 Update README.md 

 bump version
 

 add phi and padj to weighted nnSVG
 

 1.35.3
 

 1.33.1
 

 Merge branch 'master' of https://github.com/rodrigarc/scifer into devel

merging master branch to devel 

 Merge branch 'master' of https://github.com/rodrigarc/scifer
rebasing with master branch to package in bioconductor
 

 update NEWS.md and minor text

Update package `NEWS.md` with the small changes that have been made.
 

 update quality thresholds

Update thresholds according to new values set on the manuscript 

 fix error of report not being found

change how the location of the `HC_individualized_report.Rmd` file is identified. 

 Merge branch 'devel'
 

 Merge branch 'compensation-bug'