Update Joseph Paulson email to joseph.paulson@yale.edu (v1.39.16)

Updated Authors@R person() entry for Joseph N. Paulson from
jpaulson@jimmy.harvard.edu to joseph.paulson@yale.edu.

R CMD check: 0 ERRORs, 0 NOTEs, 2 pre-existing vignette WARNINGs.
 

 Fix email address in DESCRIPTION (v1.39.15)

Updated Maintainer and Author email from mcmurdie@alumni.stanford.edu
to joey711@gmail.com as requested by the Bioconductor team. The alumni
Stanford address was flagged as potentially unreachable.

R CMD check: 0 ERRORs, 0 NOTEs, 2 pre-existing vignette WARNINGs.
 

 moving README content to a more-examples vignette
 

 Fix #8: document write_biom() 2^31-1 byte size limit (v1.39.13)

Added @details to write_biom() documentation explaining that jsonlite
serialises the entire BIOM object to a single R character string, which
is subject to R's 2^31-1 byte limit on character scalars. Users with
very large datasets are now explicitly directed to write_hdf5_biom()
which streams to HDF5 and has no such limitation.

Regenerated man/write_biom.Rd via roxygen2::roxygenise().

R CMD check: 0 ERRORs, 0 NOTEs, 2 pre-existing vignette WARNINGs.
 

 Fix #4 #6: make_biom() NULL id as {}, taxonomy as bare array (v1.39.11)

Issue #4: NULL id was serialised as {} (empty JSON object) by jsonlite
because toJSON(list(id=NULL,...), auto_unbox=TRUE) maps NULL to {}.
Fix: make_biom() substitutes 'No Table ID' when id is NULL, matching
the BIOM spec default and ensuring write_biom() -> read_biom() is a
lossless round-trip. validObject() now succeeds on the round-tripped
object.

Issue #6: when observation_metadata (or sample_metadata) is a
data.frame with list columns (e.g. a 'taxonomy' column holding
character vectors of rank assignments, as produced by dada2),
the metadata was serialised as a bare JSON array ([[...]]) instead
of a named JSON object ({taxonomy:[...]}). The BIOM spec and
downstream tools (phyloseq import_biom(), the Python biom library)
require the named-object form. Root cause: as.matrix() on a
list-column data.frame produces a list-matrix; as.list(row) then
strips field names. Fix: detect list-column data.frames and build
per-row metadata directly as named lists, bypassing as.matrix().
Closes #6. Also resolves user-support Issue #9 (dada2 -> biom ->
write_biom workflow now works correctly).

Adds 4 regression tests in test-IO.R.

R CMD check: 0 ERRORs, 0 NOTEs, 2 pre-existing vignette WARNINGs.
 

 Add HANDOFF.md: GitHub issues + test gaps + vignette gaps for next agent
 

 add tests for HiCExperiment input, safe_mode=TRUE, and output_dir auto-creation
 

 convert key parameters from section to paragraph
 

 remove post_scale_positions.txt, update vignette accordingly
 

 update vignette: add pre-code summary, fix mcmc progress and saved files descriptions
 

 remove 'contact matrix set successfully' from output
 

 simplify verbose output: remove redundant lines, condense phases to [Phase] Completed
 

 chore: migrate data.frame usage to tibble throughout (#28)

Replace data.frame(), as.data.frame(), and is.data.frame() with their
tibble equivalents (tibble(), as_tibble(), is_tibble()) across all R
source files. Add tibble to Imports in DESCRIPTION and NAMESPACE.

Also fix three related issues found during the migration:
- Correct all_of() call in creators-chromatograms.R to pass a single
  character vector instead of multiple arguments
- Qualify bare tibble() calls in @examples as tibble::tibble() so
  examples run without the package namespace attached
- Expand get_metadata() docs with @section entries covering all nine
  dispatch methods (MChromatograms, XChromatograms, XChromatogram,
  XcmsRawList, ExternalDataSource, DBIConnection) 

 Remove built package tarball
 

 KS
 

 address bioconductor reviewer feedback (almeidasilvaf)

- fix url/bugreports typo in description (hispar not hispa)
- expand unit tests to cover non-square input, invalid output_dir, filter_quantile with/without loci removed, safe_mode=false, verbose=false
- add su1_contact_mat and hicexperiment class descriptions to vignette
- move key parameters section before the example code chunk
- add output description section after example chunk (verbose output, return value, model interpretation)
- replace devtools/r cmd install instructions with biocmanager::install in readme
 

 KS
 

 KS
 

 KS
 

 KS
 

 Bump version
 

 Remove private headers
 

 Remove outdated README
 

 Milestone 6: updated vignette with HDF5, tidy, SE, purrr sections (v1.39.10)

Extended the package vignette with four new sections, all guarded with
requireNamespace() so the vignette builds cleanly when optional Suggests
packages are absent:

* HDF5 (BIOM v2) I/O: read_biom() magic-byte routing, write_hdf5_biom()
  round-trip, and JSON->HDF5 conversion example.
* Tidy long-format: as.data.frame(biom) producing one row per
  (feature x sample) pair with metadata joined; as_tibble.biom().
* purrr-style workflows: per-sample total counts and Shannon diversity
  using purrr::map_dbl + dplyr, with base-R tapply fallback.
* SummarizedExperiment interop: biom_to_SummarizedExperiment() and
  as(x, 'SummarizedExperiment'), showing assay/colData/rowData access.
* Session info section.

Vignette renders cleanly (50 chunks, 0 errors) with all Suggests
packages present. R CMD check: 0 ERRORs, 0 NOTEs, 2 pre-existing
vignette WARNINGs (inst/doc absent; built by Bioconductor BBS).
 

 Milestone 4: sparse-direct generate_matrix() for HDF5/BIOM-v2 (v1.39.8)

Rewrote generate_matrix() (internal, called by read_hdf5_biom()) to build
the count matrix directly as a sparse Matrix from the CCS triplets stored
in the HDF5 file, instead of first constructing a dense base::matrix via
sapply() and then wrapping rows in lapply().

Key changes:
- Coerce rhdf5::h5read() 'array' objects to plain atomic vectors with
  as.integer() / as.numeric() before passing to sparseMatrix(); the
  'array' class is not accepted by sparseMatrix()'s x= argument.
- Build j_vec from rep(seq_len(n_samp), diff(indptr)) and i_vec from
  indices + 1L, then call sparseMatrix(i, j, x, dims) directly.
- Handle the all-zero edge case (length(vals) == 0L) explicitly.
- Return value is unchanged: list of named numeric vectors, one per
  observation row, as expected by the biom() constructor.

R CMD check: 0 ERRORs, 0 NOTEs, 2 pre-existing vignette WARNINGs.
 

 Merge modernise/03-tidy-interop into devel (v1.39.7)
 

 Update to v0.99.2
 

 Milestone 2: SummarizedExperiment interoperability (v1.39.6)

R/SE-methods.R (new):
  - biom_to_SummarizedExperiment(): converts biom object to SE, placing
    count matrix in assay('counts'), sample metadata in colData(),
    feature metadata in rowData(); NULL metadata -> empty DataFrame
  - as(biom, 'SummarizedExperiment') S4 coercion registered when SE available

man/biom_to_SummarizedExperiment.Rd (new):
  - Hand-written Rd (will be regenerated by roxygenise() in Milestone 5)

DESCRIPTION:
  - Bump version 1.39.5 -> 1.39.6
  - Add SummarizedExperiment, S4Vectors to Suggests
  - Add SE-methods.R to Collate

tests/testthat/test-SE.R (new):
  - 6 tests: class, assay values, colData, rowData, as() coercion,
    NULL metadata; all skipped gracefully without SE installed
 

 Milestone 1: drop plyr dependency, tighten Matrix imports (v1.39.5)

DESCRIPTION:
  - Remove plyr (>= 1.8) from Imports entirely
  - Bump R dependency to >= 4.1

R/BIOM-class.R:
  - make_biom(): replace alply() with lapply(seq_len(nrow(...)), ...)
    using obs_mat[i,] (not drop=FALSE) to preserve column names
  - make_biom(): use as.matrix(data) before t() so dispatch works for
    both base matrix and Matrix (dgeMatrix/dgCMatrix) objects
  - biom_data() dense path: replace laply() with do.call(rbind, lapply(...))
  - biom_data() sparse numeric path: replace ldply(x) with
    as.data.frame(do.call(rbind, x))
  - biom_data() sparse unicode path: replace ldply(x, function(x){...})
    with do.call(rbind, lapply(x, function(e) ...))
  - extract_metadata(): replace llply()/ldply() with lapply()/do.call()
  - parallel= argument: now no-op with deprecation warning in biom_data(),
    sample_metadata(), observation_metadata()

NAMESPACE:
  - Remove all importFrom(plyr, ...) entries
  - Replace import(Matrix) with importFrom(Matrix, Matrix, sparseMatrix, drop0)
  - Replace import(methods) with selective importFrom(methods, ...)

man/*.Rd:
  - biom_data-methods.Rd: update @param parallel (remove plyr/foreach links)
  - observation_metadata-methods.Rd: same
  - sample_metadata-methods.Rd: same

tests/testthat/test-accessors.R:
  - Add test that parallel=TRUE emits deprecation warning in biom_data(),
    sample_metadata(), observation_metadata()

R CMD check --as-cran: 0 ERRORs, 0 WARNINGs, 4 pre-existing NOTEs
 

 feat: add support for xcmsRaw, XChromatogram(s), and MChromatograms (#26)

Introduce XcmsRawList, a new S4 class wrapping one or more xcmsRaw
objects, and XcmsRawReader, a MsRawReader subclass that reads scan
headers and peaks directly from in-memory xcmsRaw slots without
opening a file connection. xcmsraw_to_readers() converts an
XcmsRawList to the named-list-of-readers expected by the rest of the
pipeline.

Add get_metadata() adapters for MChromatograms and improve the
sample_id_column fallback for XCMSnExp and MsExperiment so that
sample IDs are derived from file basenames when no explicit column is
provided.

Refactor the chromatogram creator into a unified create_chromatograms()
generic that dispatches on data object type, replacing the four
previous specialised generics (create_chromatograms_from_feature_ids,
create_chromatograms_from_features, etc.). This simplifies the public
API and makes it straightforward to add further input types. 

 Add HANDOFF.md: modernisation roadmap and agent handoff prompt

Documents the 8-milestone modernisation plan (v1.39.5 through v1.39.12):
  M1  modernise/01-drop-plyr            - drop plyr, tighten imports
  M2  modernise/02-summarized-experiment - SE interoperability
  M3  modernise/03-tidy-interop          - as.data.frame/tibble
  M4  modernise/04-sparse-matrix-fix     - generate_matrix() sparseMatrix
  M5  modernise/05-roxygen2-refresh      - regenerate NAMESPACE/man
  M6  modernise/06-write-hdf5            - write_hdf5_biom()
  M7  modernise/07-rhdf5-suggests        - rhdf5 -> Suggests
  M8  modernise/08-vignette              - updated vignette examples

HANDOFF.md added to .Rbuildignore so it is excluded from the built tarball.
 

 Resolve NEWS merge conflict: take HEAD (ca0a956) content verbatim

The conflict was between:
  HEAD (ca0a956): full cross-referenced NEWS entries for v1.39.2-v1.39.4
    with GitHub issue/PR URLs (Issues #3, #5, #14, #17; PRs #11, #12, #16)
  c069dba: earlier, less detailed milestone entries without cross-references

Resolution: take HEAD in full for all three 1.39.x entries. The upstream
commit (c069dba) is an older intermediate state of the same content;
HEAD is strictly a superset with all the same facts plus issue/PR links.
 

 Milestone 3: Matrix drop=FALSE + HDF5 magic-byte routing (v1.39.4)

R/BIOM-class.R - biom_data() drop=FALSE fix (PR #11 / PR #12):
  - Dense path: wrap laply() result with matrix(m, nrow, ncol) to force
    2-D shape before Matrix() coercion, eliminating dimension collapse
    when rows or columns has length 1
  - Dense path: apply Matrix() coercion for all sizes (not just >1 x >1),
    making single-row/col behaviour consistent with the full-matrix case
  - Sparse path: add drop=FALSE to m[rows, columns] subsetting so a
    single-row or single-column selection retains its matrix dimensions
    instead of collapsing to a dimensionless vector
  - Naming block: remove the is.null(dim(m)) branch; both paths now
    always produce a 2-D object so rownames()/colnames() apply
    unconditionally on every code path

DESCRIPTION:
  - Bump version 1.39.3 -> 1.39.4

NEWS:
  - Prepend CHANGES IN VERSION 1.39.4 with full description of both
    the drop=FALSE fix and the HDF5 magic-byte routing confirmation

tests/testthat/test-IO.R:
  - Add regression tests: sparse single-row, single-col, single-cell,
    and full-matrix dim() retention after drop=FALSE fix
  - Add regression tests: HDF5 magic-byte routing (no jsonlite error),
    correct JSON vs HDF5 fixture classification
  - Use literal 5L/6L in dim comparisons (avoids named-integer mismatch
    from biom_shape())
  - Add hdf5_file fixture path

tests/testthat/test-accessors.R:
  - Single-value block: use as.numeric()/as.vector()[1] to compare scalar
    values without S4 vs atomic type conflict
  - Single-row block: use as.matrix() on both sides for class-agnostic
    comparison (dgeMatrix vs dgCMatrix differ only in storage, not values)
  - Single-col block: same as.matrix() treatment

All 158 tests pass: FAIL 0 | WARN 0 | SKIP 0 | PASS 158
R CMD check --as-cran: 0 ERRORs, 0 WARNINGs, 4 pre-existing NOTEs
 

 Merge master into devel; resolve DESCRIPTION conflict (v1.39.2)

- Take Version base from devel branch (1.39.x series, Bioconductor devel)
- Bump z-component to 1.39.2 to capture Milestone 1 work from master
- Take updated Date (2026-03-14) from master branch
- Carry forward all Milestone 1 changes already staged:
    * NAMESPACE: add importFrom(stats,setNames), importFrom(utils,packageVersion)
    * NEWS: prepend CHANGES IN VERSION 1.39.2 entry
    * tests/testthat/test-IO.R: replace deprecated expect_that() with
      modern testthat 3.x equivalents (expect_true, expect_identical, etc.)
 

 version bump
 

 fixing function links in man page
 

 adding distance for left overlap joins
 

 a workable version of mcols joins
 

 import DFplyr in NAMESPACE also
 

 missing files
 

 Merge branch 'devel' of github.com:tidyomics/plyranges into devel
 

 start trying out a distance addition
 

 fallback to BH for all tests
 

 Merge pull request #80 from vjcitn/devel

biocPkgList: add handling of fnd field when present in Authors@R 

 Merge branch 'copilot/retrieve-fnd-field-value' of https://github.com/vjcitn/BiocPkgTools into copilot/retrieve-fnd-field-value
 

 Fix .extract_fnd() to parse formatted Author field instead of eval(parse()) on Authors@R

Co-authored-by: vjcitn <4624066+vjcitn@users.noreply.github.com>
 

 Initial plan
 

 added doc changes
 

 Convert one vignette to Rmd
 

 Add options for infercnv object output  and improve testing
 

 Update documentation
 

 Fix issues for bioconductor: plot save to file + add to documentation,  edit DESCRIPTION
 

 version bump
 

 Fix bfcdownload() parameter name and version bump

Use 'rid' instead of 'rids' in bfcdownload() call to fix
vignette build error: "!missing(rid) is not TRUE"

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 

 Deprecated
unresponsive
 

 Deprecated
unresponsive
 

 Deprecated
unresponsive
 

 bug fix: noiseq
 

 Deprecate
unresponsive
 

 Deprecated
unresponsive
 

 Deprecated
unresponsive
 

 Deprecated
unresponsive
 

 Deprecate
unresponsive
 

 Deprecate
unresponsive
 

 Deprecated
unresponsive
 

 Deprecate
unresponsive
 

 Deprecate
unresponsive
 

 Deprecated
unresponsive
 

 Deprecated
 unresponsive
 

 deactivating biomart in vignettes
 

 fix: update basilisk env version
 

 Deprecated

unresponsive
 

 Deprecated
 unresponsive
 

 Add missing word
 

 Mention archive arg removal in NEWS
 

 Bump version
 

 Use getCurrentEnsemblRelease() instead of .currentEnsemblVersion()
 

 deal with warning("", t) where there is no %d in the string.
 

 fixed IS_S4_OBJECT
 

 bump version
 

 refactor: improve performance of rbindFill

- Performance improvement of `rbindFill()`: avoid costly conversion from
  `matrix` to `data.frame` and back if only matrices are joined.
 

 Merge pull request #141 from Adafede/main

`GNPS` similarities in C (with few additional things) 

 Update gnps.R 

 up
 

 fix test
 

 up
 

 Merge branch 'main' into main 

 up
 

 lint
 

 up
 

 up
 

 up
 

 up
 

 Version bump.
 

 Complete compute_V_gene_delineations()'s man page
 

 bump to 1.11.1
 

 bump to 0.99.1
 

 add keyType
 

 Merge branch 'devel'

merge branch devel into master to incorporate latest updates
 

 Merge branch 'master' of https://github.com/pablof1988/goSorensen
 

 Update test_gosorensen_funcs.R

Added comment on potential speed-up due to parallelization 

 updating allSorenThreshold v 1.8.1
 

 updating README v1.8.1
 

 Update vignette DissMatrix - 1.8.1.
 

 updating outputs and vignette 1.8.1
 

 v-1.8.1.
 

 v_1.8.1
 

 v 1.8.1
 

 KS
 

 Remove non-API ENVFLAGS/SET_ENVFLAGS usage from plugin framework (#273)

Replace namespace-unlocking approach (using internal R C-level macros
ENVFLAGS and SET_ENVFLAGS) with a dedicated environment for storing
dynamically registered plugin functions.

- Add .openCyto_plugin_functions environment in pluginFramework.R
- Add .resolve_plugin_function() helper that checks plugin env first,
  then falls back to package namespace for built-in functions
- Update .register()/.unregister() to use the new environment
- Update .gating_adaptor() and .preprocessing() to use the resolver
- Remove unlockNamespace.cpp and its cpp11 bindings

This eliminates the Bioconductor check warning about non-API entry
points while maintaining full backward compatibility for both built-in
gating methods and dynamically registered plugins.

Passes R CMD check with 0 errors, same pre-existing warnings/notes. 

 remove data/simuResult.rda man/simuResult.Rd
 

 Add backport to unbreak build on R-4.5 (#3)

See https://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Some-backports 

 remove SET_S4_OBJECT calls
 

 fix unit tests
 

 Fix DESCRIPTION conflict
 

 update DESCRIPTION NAMESPACE
 

 Address Bioconductor review: use readVcf() for VCF import, return S4Vectors::DataFrame, replace magrittr with native pipe, replace incremental rbind with lapply/do.call, and fix vignette (startup messages, print, table vs count, dataset description)
 

 Bump version to 2.27.2 and add genefilter
 

 Test adding secur32 library when LinkingTo from windows
 

 Trigger R-universe workflow manually only
 

 Bump version
 

 Add user agent to all requests send by biomaRt
 

 Bump version
 

 Mention Depends and NAMESPACE changes in DESCRIPTION
 

 Clean up NAMESPACE and move packages to Suggests
 

 Move packages from Depends to Imports
 

 Remove references to a in docs
 

 Make vignette section using "a" static
 

 v2.13.3 backport DATAPTR support for older R versions
 

 Add backport to unbreak build on R-4.5
See https://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Some-backports
 

 Document HDF5 version update
 

 Remove H5Pget_version() entirely
 

 Remove obsolete reference to version
 

 Remove H5I_REFERENCE

Release notes say:

>     - Remove H5I_REFERENCE from the library
>
>      This ID class was never used by the library and has been removed.

https://github.com/HDFGroup/hdf5/blob/9b290ab389b9b560c32e751d0c92f2687a731b8e/release_docs/HISTORY-1_10_0-1_12_0.txt#L252C1-L254C72
 

 Update to HDF5 1.14
 

 fix: remove piano from Suggests (not used in any code)

piano is only mentioned in vignette prose but never imported or called.
Its unavailability on the macOS arm64 builder causes CHECK to fail.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 

 KS
 

 Bump version
 

 Test marking libaec build as static
 

 Vendor HDF5 1.14.6
 

 Add CRAN machines GHA
 

 bump version to 1.1.2
 

 clean up python scripts
 

 Use memcpy() instead of loop to copy string buffer
 

 KS
 

 version bump
 

 version bump
 

 Merge pull request #11 from daisybio/RELEASE_3_22

Release 3 22 

 igblastr 1.1.23

Rename the following functions:
  compute_imgt_intdata -> compute_V_gene_delineations
  read_V_ndm_data -> read_ndm_data
  write_V_ndm_data -> write_ndm_data
  check_V_ndm_data -> validate_ndm_rows
 

 Bump version to 0.99.3 for Bioconductor rebuild
 

 KS
 

 adding v3 files
 

 version and date
 

 Bump version
 

 KS
 

 Update DESCRIPTION
 

 Fix

Co-Authored-By: prodakt <bioinformatyka@gmail.com>
 

 Fix error

Co-Authored-By: prodakt <bioinformatyka@gmail.com>
 

 Update README.md 

 Bioconductor 0.99.3 review changes

* Implemented comprehensive unit tests reaching >80% package coverage.

* Optimized confusion matrix calculations and performance evaluation pipeline.

* Added accessibility-friendly color palettes (Okabe-Ito) for all visualization functions.

* Merged recent feature updates and refactors into the main branch via Pull Request.

Co-Authored-By: prodakt <bioinformatyka@gmail.com>
 

 Simplify col_to_filter construction
 

 Use dedicated lengths() function instead of vapply()
 

 Add package man page
 

 Fix image links in README for venn diagrams

Updated image links in README to point to the correct directory. 

 v2.13.2 remove DATAPTR() usage
 

 add xlist to chunked_list and XS to chunk_mapply
 

 KS
 

 Bump version from 1.3.4 to 1.3.5 

 Remember that biscale is suggested not imported
 

 feat(advanced-options): Set up advanced options panel for subnetwork search (#178) 

 feat(response-curves): download dose response curve plots (#174) 

 resolve merge conflict, bump version
 

 Updated DOSE::setReadable to clusterProfiler::setReadable as Bioc 3.23 DOSE does not export setReadable anymore
 

 Updated badge colors
 

 Updated workflows
 

 Update Bioconductor download stats
 

 Added data.table to DESCRIPTION, updated badge gh action workflow
 

 Updated and fixed vignettes for pkgdown docs, fixed GitHub Actions workflows
 

 Added Docker files, accessible example data, pkgdown docs with new vignette and GitHub Action workflows
 

 KS
 

 new version 1.1.1
 

 add python
 

 changing version
 

 1.37.3 (patch) - Update tests for createDatabase for CI/CD 

 v1.37.2 - fix subsetting of grouped data frame (#109)

* Fix subsetting of grouped data frame

The `grpid` column in `pa@grped_df` is an integer factor.
The comparison `pa@grped_df$grpid==as.numeric(grp_idx)` fails when `grp_idx`
is 100000 because `as.numeric` returns type `double`.

`pa@grped_df$grpid == 100000` returns `FALSE` for all items even if 100000 is present.
`pa@grped_df$grpid == 100000L` returns `TRUE` for items that are 100000.

* v1.31.1 - updates following removal of library spectra from msPurityData package (too large for Bioconductor) (#108)

* Use zenodo reference to library spectra

* Update CI/CD

* troubleshoot vignette build issue

* Troubleshooting cache on github workflows

* Troubleshooting cache for github workflows

* more troubleshooting GH workflow cache

* Bump version and add entry to NEWS

* Fix email of contributor

---------

Co-authored-by: Thomas N Lawson <thomas.nigel.lawson@gmail.com> 

 docs: Weekly AI doc upgrade for `previewNetworkInBrowser` (#82) 

 KS
 

 changing version to v3 in upload_files_to_S3
 

 Merge pull request #380 from rformassspectrometry/jomain

refactor: improve matched peak reporting by compareSpectra 

 append taxa from newTaxa.txt to currentNCBIinfo
 

 fix build warnings
 

 Use scalar instead of vector of length 1
 

 Rebuild after server issue
 

 Removed extra file
 

 Bumped version
 

 igblastr 1.1.22: Add download_OGRDB_germline_json()
 

 Fix time out
 

 Fix CBS error causing vignette build failure
 

 Fix CBS error causing vignette build failure
 

 Fix CBS error causing vignette build failure
 

 Fix BiocCheck errors and vignette
 

 Remove Rproj file from repository
 

 Addressing warning message
 

 version and date
 

 add BPPARAM flags; fix normalization
 

 removed docs from this branch, then updated
 

 test for gh pages
 

 added depenency
 

 additional statistics added to leapR

These still require debug/testing here.
 

 add catalog-info.yaml file for forge catalog 

 Incremented the version. Added plotting throughout the vignette. Clarified a couple things in the vignette. Added a data inspection chunk
 

 small vignette modification 

 Added barplot function. Addtions to code, test, vignette, and autogenerated roxygen2 files
 

 added package level documentation
 

 fix to SampMin imputation

Imputation value writing was handled row by row in the proteomics data, which was incompatible with how Sample Minimum imputation data is calculated. Fixed imputed value assignment method for SampMin to fix that problem.
 

 updated documentation
 

 Added new readme and github actions to build
 

 added additional check to log transformation of data to ensure that log transformation only happens for non count based data
 

 add catalog-info.yaml file for forge catalog 

 add sampMin (sampleMinimum) to imputation methods
 

 added changes required for bioC submission
 

 added more to vignette
 

 fix to SampMin imputation

Imputation value writing was handled row by row in the proteomics data, which was incompatible with how Sample Minimum imputation data is calculated. Fixed imputed value assignment method for SampMin to fix that problem.
 

 updated gradient test with z test
 

 Merge pull request #81 from PNNL-CompBio/spatMicrobiome_fixes

spatMicrobiome fixes 

 Merge pull request #80 from PNNL-CompBio/79-count-based-differential-expression-get-log-transformed

fix to disable log transformation if dealing with count based data in differential expression. 

Nice catch! 

 Merge branch 'main' of https://github.com/PNNL-CompBio/spammR
 

 Merge pull request #78 from PNNL-CompBio/75-differential-expression-results-and-associated-proteins-not-aligned-correctly-in-calc_spatial_diff_ex-results

fix to calc_spatial_diff_ex 

 Merge pull request #74 from PNNL-CompBio/imputation

MinSamp imputation method 

 add catalog-info.yaml file for forge catalog 

 add sampMin (sampleMinimum) to imputation methods
 

 import utils head
 

 build ignore *_files folder
 

 update .Rbuildignore
 

 doc fix: default is geojson for listHoverNet
 

 use paws to list files from s3 type bucket
 

 Add export for plot_PVCA.df and update function parameters in documentation
 

 Refactor PVCA plotting functions and update documentation for consistency
 

 Remove unnecessary blank lines in test files
 

 Update .gitignore and .Rbuildignore to include additional files; refine documentation links in R scripts and vignettes
 

 Run devtools::document()
 

 Add 'add' and 'delete' method for lasso.
 

 Restore ros3 support
 

 Mention switch to CMake in NEWS
 

 Disable ROS3 for now
 

 Install openssl on macOS 15
 

 Add _build_ folders to cleanup
 

 Update HDF5 copyright location
 

 Remove outdated vignette
 

 Get lib version from settings file

Co-authored-by: LTLA <infinite.monkeys.with.keyboards@gmail.com>