vignette update with examples
 

 vignette update
 

 correct get_cached_file
 

 Fixing BiocFileCache
 

 Version bump.
 

 remove testXgene, docs, tests, and helpers
 

 Merge remote-tracking branch 'origin/main' into devel
I want to merge devel with main
 

 Merge pull request #4 from biodatalab/devel

performance updated 

 Version bump.
 

 Update README.md

Added the tutorial link. 

 Update README.md

Updated the p-value threshold. 

 Merge pull request #67 from boseb/minor-fixes

Minor fixes 

 update example and test for estimateHerit to use LDSC model
 

 add small precomputed ld-score dataset and docs
 

 apply bioc_style
 

 update man
 

 enable additional bioc tests
- provided plink and gcta are available, these will run
 

 move to suggests, as it only supports package vignette
 

 sp
 

 adjust test-AncestryCheck.R to use new toy reference panels
 

 Merge pull request #65 from boseb/vignette-update

Vignette: GXwasR in Action 

 apply bioc_style()
 

 adjust title and vignette index
 

 DataDir and file.copy fixes
- define writable location for DataDir. Begin Vignette by copying example data to this location
- ensure full.paths to results are returned so that copy succeeds
- overwrite = TRUE so that Results with the same name as a previous step may carry forward
 

 new vignette initial commit
 

 Merge pull request #64 from boseb/package-size

some fixes and removal of bzip example data 

 cleanup
 

 additional foutput var fixes
 

 add additional cleanup task to QCsample() test
 

 Merged origin/devel into package-size
 

 Update plink.R 

 update test conditions to match example data
 

 update test conditions
 

 don't error when multi-allelic not present
 

 initial removal of GXwasR_data
- restore uncompressed data, in preparation for pruned examples
- adjust example file paths
- adjust PlinkSummary test and add function return to evaluate
 

 misc fixes
- documentation
- missing params
- missing documentation
 

 Update GXwasR_helper_functions.R 

 Update GXwasR_helper_functions.R

Updated pgsFun from line 766 to add Macfadden and Liability scale and updated Validate argument function at 5645. 

 Update analysis.R

Added prevalence = NULL, liability_R2 = FALSE in ComputePGS 

 Update GXwasR_helper_functions.R

Removed "" around foutput in line 285. 

 Merge pull request #63 from boseb/function-messaging

Function messaging 

 additional path cleanup
 

 2026 helper function additions, based on May 22, 2026 email
 

 update build and git ignore
 

 fixes
 

 update
 

 tweak plink linux install instructions
 

 additional abort() added when error caught by tryCatch
 

 fix
 

 main functions message refactor
 

 initial messaging standardization
- begin using  rlang throughout
- swap for actual progress bar in fisher.method.perm
 

 adjust startup messaging to be less verbose
 

 update docs
 

 additional re-org
 

 Update maintainer email to wevanjohnson@gmail.com; bump to 1.29.2

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
 

 chore: bump version to 0.99.11
 

 fix: support the updated UniChem source schema
 

 fix: replace bundled GDSC metadata with download links
 

 Deprecated

 - unresponsive
 

 Deprecation

 - unresponsive
 

 Deprecation
 - unresponsive
 

 Deprecated

 - unresponsive
 

 version bump to 1.29.4
 

 [tests] skip_on_bioc() for parallel runs + bump 2.11.5
 

 Merge branch 'bugfix' into devel
 

 Bump version to 2.15.1

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
 

 Reduce running time and memory of ancom, ancombc, ancombc2, and secom

Shared-design multi-response least squares in ancom and in the iterative
estimators of ancombc and ancombc2; reuse of the lme4 model structure across
taxa and iterations in the random-effects path; blocked accumulation of the
sandwich variance; detached foreach environments and a vectorized
cross-validation loss in secom_linear and secom_dist. Results of all vignette
workloads are unchanged. Treat log(0) as missing in ancombc when pseudo = 0.
Add the timing harness and report under benchmarks/.

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
 

 Run devtools::document()
 

 Mention deprecation in NEWS
 

 Consolidate .setDataType()
 

 Define shared .wrapH5Id() helper
 

 Adjust missingArgError tests
 

 Make maxdims default value explicit
 

 Cite the methods, fix the stale CITATION version, make releases manual (#48)

* docs: cite the methods, and stop cutting releases by accident

Three things the Bioconductor submission guidance asks for, or that this
release made obvious.

**References.** The vignette had none. Every method the package calls is
published, and §3.3 of the submission guidance asks for formal citations
where they are. The new section lists the CTD release paper, the GSEA
method and the fgsea implementation separately because they are
different contributions, CAMERA and the limma package that provides it,
GSVA, EnrichmentBrowser for the interoperability section, the
independent-filtering paper the size-threshold reasoning rests on, and
the GEO accession behind the worked example. clusterProfiler is not
among them: it is no longer a dependency, and citing a package the
software does not use would be as wrong as omitting one it does.

Every DOI was verified rather than recalled: six from the manuscript
bibliography, limma from citation("limma"), EnrichmentBrowser from
Europe PMC, and the independent-filtering paper supplied by the
maintainer.

**CITATION.** It named the package version in a string, and that string
said 0.99.2 through eight releases because nothing made it move. It now
reads meta$Version from the DESCRIPTION, so it cannot go stale again. The
Zenodo concept DOI is unchanged and was checked: it resolves to the
current release rather than to a fixed version, which is what a reader
following a citation needs.

**Releases.** The workflow fired on every push to main, so a version bump
travelling with other work cut a release before the work around it was
ready. That is exactly what happened an hour ago: 0.99.9 was tagged and
deposited while its own citation file still named 0.99.2. It now runs on
workflow_dispatch only, and still refuses to act when the tag already
exists, so running it twice remains harmless.

* fix(ci): rebuild the pkgdown library instead of restoring a stale one

The pkgdown site build failed on main with:

    unable to load shared object '.../igraph/libs/igraph.so':
      libglpk.so.40: cannot open shared object file

igraph and clusterProfiler are no longer dependencies of this package,
so the system libraries they need are no longer installed on the runner.
The cached R library still held them, and the stale igraph.so could not
load against a libglpk that nothing installs any more. pkgdown reached
it while resolving a package reference in the documentation, and the
site build died on a dependency the package had already dropped.

Deleting the caches by hand fixed one run and not the next, because the
restore keys let an older library come back. Bumping cache-version
retires it properly.

The documentation reference that triggered the load is also reworded:
ora()'s history note said clusterProfiler::enricher() in code
formatting, which downlit autolinks by loading the package named. It now
names the package without writing a call, so nothing tries to load it.
The historical NEWS entries keep their original wording; they are a
record of what was true at the time, and rewriting them to work around
an environment problem would be the wrong repair. 

 chore(site): the author's name links to the author's site (#46)

Every product surface names the author or credits an ORCID, and none of
them leads to the person. ORCID is academic credit: it lands on a list of
publications, not on someone who can be hired. So the reader who asks the
natural question in front of a package, who maintains this and could they
do it for me, has nowhere to go.

pkgdown's authors.href turns the name into a link wherever it is already
printed, the footer of every page, the home sidebar and the authors page,
so this adds a path without adding a promotional block. The JSON-LD author
now carries the site as url with the ORCID kept as identifier and repeated
in sameAs, so search engines tie the person to both.

Measurable from the other side: the landing now records referrers, and the
last thirty days show one single visit arriving from any product surface. 

 docs(readme): accept SummarizedExperiment, and fix a stale dependency list

The README is the pkgdown home page and still described a matrix-only
API for CAMERA and GSVA: the method list, the quick-start snippets,
the input reference and the output reference all predate the change.

Separately, the Dependencies section was wrong on its own terms. It
listed rappdirs, dropped when the cache moved to BiocFileCache, and
plyr, which has never been an Import. It omitted BiocIO, BiocFileCache
and S4Vectors, which have been Imports since the same change. The list
now mirrors the Imports field of DESCRIPTION, and says so, since the
failure mode here is the two drifting apart unnoticed.
 

 feat(input): accept SummarizedExperiment for CAMERA and GSVA

enrichment_CTD() now takes a SummarizedExperiment wherever it took a
genes x samples matrix, and GSVA returns the container it was given:
a matrix in returns a matrix, an SE in returns an SE whose assay holds
the scores and whose colData is carried over. Per-sample scores arrive
with the annotation needed to read them, instead of in a bare matrix
the caller has to re-align by hand against a separate group vector.

The two methods treat the container differently, and deliberately so.
CAMERA reduces it to its assay, since a competitive gene-set test
returns one row per chemical and has no per-sample output to annotate.
GSVA keeps it, because GSVA is already SE-in/SE-out and degrading the
input to a matrix was throwing colData away for nothing.

.as_expr_matrix() is the single coercion point for both, so the assay
selector is interpreted in exactly one place. plot_CTD() learned the
SE path as well: without it the package would hand back objects its
own plotting function rejects.

The bundled GSE311566 example changes class from list(expr, coldata)
to SummarizedExperiment. This breaks code reading $expr, which is the
point: keeping the matrix and the sample table as two loose objects is
what lets a reorder desynchronise them silently. The .rds was converted
from the existing file rather than re-downloaded, asserting equality of
the numbers before overwriting.

SummarizedExperiment was already a hard transitive dependency through
GSVA, so adding it to Imports leaves the installation footprint
unchanged.

Requested by the Bioconductor core team on Contributions#4232.

Verified: 238 tests pass, R CMD check Status OK, BiocCheck 0 errors
0 warnings 9 notes (all pre-existing), vignette and RNA-seq tutorial
both render.
 

 version bump
 

 clean up news
 

 igblastr 1.3.23: use_germline_db() now emits warning if IMGT germline db
contains incorrect internal data.
 

 minor edits
 

 Update README.md: Warn BioC 3.22 users about invalid intdata generated
by igblastr 1.0.23
 

 Merge pull request #89 from seandavi/fix-doi-creation-recreated

Fix JSON structure, adjust to httr2 

 Merge pull request #88 from seandavi/copilot/fix-macos-latest-job

Stabilize `activitySince()` for empty GitHub results and remove brittle recent-activity assertions 

 Initial plan
 

 fix unit test (data changes remotely)
 

 Prepare version 2.17.2
 

 Skip unused IDOL probe statistics
 

 Remove unreachable mixed-model dependency
 

 Reduce attached package dependencies
 

 Avoid attaching reference data packages
 

 Add adult blood regression baseline
 

 annoating method removed
 

 Bump version
 

 Run devtools::document()
 

 Stop nudging towards using mirrors
 

 add as.data.frame from biocgenerics and version bump
 

 Bump version
 

 Add more H5D examples
 

 Add example to H5constants
 

 Some fixes and improvements of vignette; version number bumped to 1.47.1
 

 Rebuild BacDive sets from a complete harvest (v1.5.5)

TaxSEA_db: the 267 BacDive sets are replaced by 1,776 sets covering
9,045 taxa, built by bacdive_harvester v1.0.0 from every strain of 705
genera. Measured data only; names contain no spaces and follow
BacDive__; substrate use is split by assay context.
All other sources are unchanged.

NCBI_ids: add-only. Species and former names of BacDive members (with
spaces and underscores) and each member taxid as its own name; empty
entries filled; no existing taxid changed. Unresolved TaxSEA_db members
fall from 84 to 57.

Provenance ships in inst/extdata; inst/scripts/make_BacDive_sets.R
documents the build (gitignore narrowed to admit only that script).
Data docs, NEWS and tests updated; db-regression snapshots re-accepted
after review; new test-bacdive-sets.R covers invariants, lookup and
textbook physiology.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
 </pre>
    </div>
  
    

      Package: TaxSEA

      Commit: 90869ab34ea0c1ae3785f6f05e90e0aba83459c2

      Author:  Feargal Ryan <feargalr@gmail.com> 

      Date: 2026-09-17 11:35:40 +0930

      Commit message:


	  
		
 TaxSEA(): exclude BugSigDB by default and survive download failures

Breaking: bugsigdb now defaults to FALSE. Previously BugSigDB was
included whenever bugsigdbr was installed.

Each taxon set is tested against all the other taxa covered by the sets
being analysed. BugSigDB adds many extra taxa, so including it changes
the p-values of every set, not only the BugSigDB ones (by up to 0.26 on
the bundled test data), and results also drift between BugSigDB
releases. Off by default keeps results reproducible and TaxSEA() usable
offline. The vignette and README now pass bugsigdb = TRUE explicitly.

BugSigDB is served from Zenodo, which was returning 504s during this
work, and bugsigdbr fails in that case even with a cached copy. That
would have produced a build ERROR on the Bioconductor builders, since
the vignette downloads BugSigDB. Now:
- TaxSEA(bugsigdb = TRUE) warns and continues without BugSigDB.
- The vignette checks availability first and skips its BugSigDB chunk.
- Tests use skip_if_no_bugsigdb(), which probes the download itself;
  skip_if_offline() only checks DNS and did not catch the outage.

Also fixes two documentation bugs: the vignette and README read results
from $BugSigdB, which silently returns NULL, and the vignette documented
a nonexistent database argument. NEWS gains the missing 1.5.1 entry.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
 
    
  
    

      Package: TaxSEA

      Commit: 3118a907cee338f93e5018d427fc1d6b7b02f591

      Author:  Feargal Ryan <feargalr@gmail.com> 

      Date: 2026-09-16 20:34:20 +0930

      Commit message:


	  
		
 Polish: fix get_taxon_sets(), R dependency and BiocCheck notes (v1.5.4)

- get_taxon_sets() declared taxon_to_fetch = taxon, a default referring to
  an object that does not exist, so get_taxon_sets() with no argument
  failed with the confusing "object 'taxon' not found". It now reports the
  missing argument. Also removes unreachable rm() calls after return(),
  and wraps the membership test in any() so a lookup resolving to several
  NCBI IDs cannot produce a mis-sized logical vector for subsetting.
- Raise Depends to R (>= 4.6.0) to match Bioconductor 3.24.
- get_ncbi_taxon_ids(): vapply() instead of sapply(), and qualify the
  utils:: calls.
- taxon_rank_sets() examples use \donttest rather than \dontrun.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
 
    
  
    

      Package: TaxSEA

      Commit: 01861ef006f3f7248cc54df90968f49b70ea47b7

      Author:  Feargal Ryan <feargalr@gmail.com> 

      Date: 2026-09-16 20:31:35 +0930

      Commit message:


	  
		
 Add test suite for ssTaxSEA, ORA and database integrity (v1.5.3)

ssTaxSEA() and ORA mode previously had no tests at all.

New coverage:
- ORA: Fisher p-value and odds ratio against a hand-built 2x2, result
  ordering, and FDR columns.
- Enrichment: KS statistic and p-value against a direct stats::ks.test()
  call, pinning the fact that the background is restricted to taxa
  covered by surviving sets rather than everything supplied.
- TaxSEA(): mode inference, mode/input mismatch, both-args and
  neither-arg errors, square-bracket rejection, custom_db output shape,
  and per-category FDR recomputation.
- Regression snapshots of the results produced from the bundled test
  data, so a database update shows up as a diff to review rather than a
  silent change in the answers.

Adds a bugsigdb argument to TaxSEA() (default TRUE, preserving current
behaviour) so tests can run offline and deterministically. This also
surfaced that including BugSigDB shifts p-values in every other output
category by up to 0.26 on the test data: its signatures enlarge the
union of set members, which enlarges the background the competitive KS
test runs against. A test now documents that coupling.

The database integrity checks record two pre-existing data issues rather
than failing the build on them:
- 84 members of TaxSEA_db have no NCBI_ids entry and are dropped
  silently by taxsea_prepare(). Siderophore_producers keeps 25 of its 73
  members; the Valles-Colomer2019 Gut-Brain Modules lose 392 member-slots
  across 46 sets, and two of those sets fall below min_set_size and never
  appear in output.
- GutMGene_producers_of_Phenylalanine appears twice (14 and 2 members),
  so list lookup reaches only the first and two taxa are unreachable.

Both are pinned at their current values so a database update cannot make
them worse unnoticed. Also corrects the documented default for
max_set_size, which said 100 while the signature has been 300.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
 
    
  
    

      Package: TaxSEA

      Commit: 641fd130cee463c3dbe37b901a74f9a1f9ba5acd

      Author:  Feargal Ryan <feargalr@gmail.com> 

      Date: 2026-09-16 20:31:09 +0930

      Commit message:


	  
		
 ssTaxSEA(): score sets by mean CLR of their members (v1.5.2)

Replaces the ranked, cohort z-scored, ssGSEA-style running-sum statistic
with the mean centered log-ratio of a set's members within a sample.

  score[S, j] = mean of clr[i, j] for i in S

Breaking changes:
- Returns a numeric matrix with taxon sets as rows and samples as
  columns, rather than a list of two matrices oriented samples x sets.
  res$scores[sample, set] becomes res[set, sample].
- No p-values are returned. The score is descriptive; test it across
  samples with a test appropriate to the design.

The CLR is now computed across all supplied taxa before subsetting to
set members. The previous code filtered the matrix to set members first,
which made the geometric mean the CLR divides by depend on which sets
were being tested. On a simulated cohort with a planted signal, that
ordering drove a null set to a near-perfect mirror of the signal set
(difference -0.435, p = 2.9e-11); with the corrected ordering the same
null set sits at -0.043 while the planted signal is recovered at +0.826.
test-ssTaxSEA.R guards this directly.

Because the score no longer references the rest of the cohort, ssTaxSEA
now works on a single sample. Also adds a pseudocount argument (default
0.5) applied to every value rather than only to zeros, and rejects
proportion-like input, negative values, non-finite values and empty
samples instead of silently returning meaningless scores.

The vignette is rewritten: its previous argument for why cohort
z-scoring was essential no longer applies, and its code blocks now
execute so they are checked at build time.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
 
    
  
    

      Package: TaxSEA

      Commit: 63476b2ad6a5581cba163c1228be5798937b2047

      Author:  Feargal Ryan <feargalr@gmail.com> 

      Date: 2026-09-16 20:18:09 +0930

      Commit message:


	  
		
 Add Bioconductor devel CI workflow

Runs R CMD build, R CMD check and BiocCheck in the
bioconductor/bioconductor_docker:devel container on push and pull
request, so problems surface in minutes instead of in the next day's
devel build report.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
 
    
  
    

      Package: TaxSEA

      Commit: 261da4e43854a002dd78ca11585728482d1ff5ed

      Author:  Feargal Ryan <feargalr@gmail.com> 

      Date: 2026-09-16 20:18:09 +0930

      Commit message:


	  
		
 Clean baseline for Bioc 3.24: clear devel check warnings (v1.5.1)

Removes the two WARNINGs and two NOTEs reported by the Bioconductor
devel build, with no change to package behaviour.

- Delete R/TaxSEA_export.R. It defined a second, older taxsea_prepare()
  that shadowed the live one in R/taxsea_prepare.R; the correct version
  won only by source collation order.
- Declare methods in Imports and add importFrom directives for
  methods::is, stats::median and utils::URLencode/data, clearing the
  "'::' import not declared from: 'methods'" WARNING.
- Add utils::globalVariables() for NCBI_ids and TaxSEA_db, which are
  loaded via utils::data() and so are invisible to the code analyser.
- Resave data/ with optimal compression (NCBI_ids 136Kb -> 42Kb xz,
  TaxSEA_db 48Kb -> 35Kb bzip2), clearing the compression WARNING.
- Add .Rbuildignore entries for .claude, .Rhistory and .DS_Store, and
  gitignore inst/scripts/ (2.6 MB of local meta-analysis output).
- Declare S4Vectors in Suggests; it is used by the taxon_rank_sets
  tests but was undeclared.

R CMD check now reports Status: OK. Verified no behaviour change by
comparing all 12 result tables from TaxSEA() in both enrichment and ORA
modes against the previous commit; every value matches exactly.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
 
    
  
    

      Package: TaxSEA

      Commit: 03845a9958c42f4e9e7956020cc01d31700c8c4f

      Author:  Feargal Ryan <feargalr@gmail.com> 

      Date: 2026-09-16 17:07:07 +0930

      Commit message:


	  
		
 Merge branch 'devel'
 
    
  
    

      Package: TaxSEA

      Commit: 32dd820abcd957facceb2707373a6c7d43ea62f0

      Author:  Feargal Ryan <feargalr@gmail.com> 

      Date: 2026-02-12 13:57:48 +1030

      Commit message:


	  
		
 Merge branch 'devel'
 
    
  
    

      Package: anndataR

      Commit: 243bfa78c2f6a5b48051f5dc76fdc3409264398b

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-09-17 10:06:03 +0200

      Commit message:


	  
		
 Release 1.3.2 to Bioc devel (#522) 
    
  
    

      Package: anndataR

      Commit: 2f869bf4c44f94925ae2ea13917882432d5128ed

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-09-15 08:08:20 +0200

      Commit message:


	  
		
 Skip tests while rhdf5 2.57.12 warns about NA_character_ (#520)

* skip file closure tests on rhdf5 na warning

* add news entry

* fix linting issue 
    
  
    

      Package: anndataR

      Commit: 2087b7dac5d5b7eea2848c9f8d67ef00c279ddfe

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-09-10 10:16:44 +0200

      Commit message:


	  
		
 Strip the as.na attribute before h5diff comparisons (#519)

* also strip as.na attribute before h5diff

* add news entry 
    
  
    

      Package: anndataR

      Commit: 3d73cab8bc00ca74de84f5343dd35d9babbd3b82

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-09-08 20:16:39 +0200

      Commit message:


	  
		
 Pin mudata<0.4 in the CI workflows (#518)

* pin mudata<0.4 in ci workflows

* add news entry 
    
  
    

      Package: anndataR

      Commit: 9c8fd33c1d138e497a68cf9eab81a09c806ed233

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-08-31 11:38:01 +0200

      Commit message:


	  
		
 Pin mudata<0.4 in python vignette (#512) 
    
  
    

      Package: anndataR

      Commit: c105c1e11e282d661d83077a298e41e3d4f65364

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-08-31 09:00:52 +0200

      Commit message:


	  
		
 Class rename with anndata >= 0.13 and add warning (#510)

* Support the anndata.AnnData class name from Python anndata >= 0.13

* check anndata version instead of class name 
    
  
    

      Package: anndataR

      Commit: 7242e711865052ec2964ce29710f067d439117dc

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-15 14:18:53 +0200

      Commit message:


	  
		
 Revert workaround for LZF compression on VLen strings (#497)

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> 
    
  
    

      Package: anndataR

      Commit: 656864b4ea03530332c6f600ea50715040e4e0e5

      Author:  Juan Andrés Tejedor Serrano <111349478+JuanTejedor@users.noreply.github.com> 

      Date: 2026-08-15 14:06:57 +0200

      Commit message:


	  
		
 Fix logical matrices losing their shape when written to H5AD (#496)

* Fix logical matrices losing their shape when written to H5AD

hdf5_write_boolean_dataset() called as.integer(value) before checking
dim(value) to compute the dataspace shape. as.integer() drops the dim
attribute, so the check always fell through to the flat-vector branch,
and any 2D+ logical matrix (X/layers/obsm/varm) was written as a 1D
dataset. Reading it back then failed since the shape no longer matched
(n_obs, n_var).

Capture dims before the conversion, and align H5Screate_simple()'s
native argument with hdf5_write_dataset() a few lines above (native =
FALSE), which is what write_h5ad_dense_array() already transposes
values for.

Fixes #495

* Add NEWS entry

* Update NEWS.md

Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com>

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com> 
    
  
    

      Package: anndataR

      Commit: e9a4c4d8a5947b9e5f39ae66340ea128e79ff206

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-08-15 11:29:57 +0200

      Commit message:


	  
		
 Run BiocCheck on release branches too (#504) 
    
  
    

      Package: anndataR

      Commit: 8320a69fb27628ba61c8803e949f21444196cbfa

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-08-14 08:26:36 +0200

      Commit message:


	  
		
 Check each branch against its own Bioconductor version (#502)

* check RELEASE_ branches against bioc release

* Drop the `ubuntu-latest` Bioconductor release leg from the matrix
* Derive `bioc-version` from the target branch instead of the matrix
* Run the workflow on pushes to `RELEASE_**` as well as `devel`

* add NEWS entry

* pin each RELEASE_ branch to its own bioc version

`RELEASE_3_22` needs Bioconductor 3.22 and R 4.5, not whichever release
happens to be current. Derive the version from the branch name in a small
`bioc-version` job and feed it to the matrix. 
    
  
    

      Package: anndataR

      Commit: c5cf4beffeaa15dd8a3b981b58f71d9b7d28ec38

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2026-08-13 11:55:35 +0200

      Commit message:


	  
		
 Add support for `nullable-string-array` (#480)

* Add read_h5ad_nullable_string() helper

* Add read_zarr_nullable_string()

* Add write_h5ad_nullable_string()

* Add write_zarr_nullable_string()

* Update example files

* Update example data files

* Add tests for nullable strings

* Use zarr_format

* Add nullable string roundtrip tests

* Style

* Update NEWS

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> 
    
  
    

      Package: anndataR

      Commit: 731115983f3ac28a5451b76c9a462ae03b762adb

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-09 09:24:05 +0200

      Commit message:


	  
		
 Remove zarr v3 rec array special handling (#498) 
    
  
    

      Package: anndataR

      Commit: 3d77218514dd7c9561d16a19a4bb0c2a12914661

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-07-27 23:27:17 +0200

      Commit message:


	  
		
 Bump bencherdev/bencher from 0.6.10 to 0.6.11 (#491)

Bumps [bencherdev/bencher](https://github.com/bencherdev/bencher) from 0.6.10 to 0.6.11.
- [Release notes](https://github.com/bencherdev/bencher/releases)
- [Commits](https://github.com/bencherdev/bencher/compare/v0.6.10...v0.6.11)

---
updated-dependencies:
- dependency-name: bencherdev/bencher
  dependency-version: 0.6.11
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 
    
  
    

      Package: anndataR

      Commit: cccaec740b87952cd1a1c040997de049555116b2

      Author:  Artür Manukyan <artur-man@hotmail.com> 

      Date: 2026-07-27 22:29:16 +0200

      Commit message:


	  
		
 Write support for anndata-zarr v3 (#455)

* Write strings as VLen-UTF8

- This follows the anndata file format spec
- This allows compatibility with zarr python for zarr version 3

* Ensure only one array-bytes codec is present

* Bump minimal required Rarr version

* Write support for anndata-zarr v3

* devel Rarr is already 2.1.7

* setup bioc devel

* redundant zarr version call

* check zarr version of every written array/group

* remove some skips upon updates to Rarr

* some change for upstream

* add zarr version to roxygen2

* update zarr version interface

* update examples, vignette and lint

* air

* update vignette

* zarr_version to zarr_format

* add withr chunks to zarr tests

* add formats to write_zarr_attr

* lint

* air

* set v3 format as default, update documentation

* fix withr

* remove get_zarr_format

* lint and air

* revert changes to rec array reading

* reformat

* PR review fixes

* more PR review fixes

* add additional tests

* remove another dot in roxygen2

* drop recarray zarr v3 warning suppression

* fix some tests

* add jsonlite to Suggests

`write_zarr_string_array()` and `write_zarr_string_scalar()` patch the array
metadata with `jsonlite::read_json()`/`write_json()`, but jsonlite was never
declared, so R CMD check reports it as an undeclared '::' import.

* use the format of an existing zarr store when writing to it

* Add `get_zarr_format()` and use it in `ZarrAnnData$new()` so that opening an
  existing store no longer takes the format from the `anndataR.zarr_format`
  option. Writing into a v2 store while the option was 3 produced a store with
  v3 nodes inside it, which Python `anndata` reads without an error but with
  the affected slot silently missing.
* Error when `zarr_format` asks for a different format than the store on disk,
  instead of quietly writing the other one.
* Truncate the store for `mode = "w"`, as documented and as `HDF5AnnData` does.
  Rewriting a v2 store as v3 used to leave both `.zgroup` and `zarr.json` at
  the root, after which the store could not be read back at all.
* Add `check_zarr_format()`; `zarr_format` was not validated anywhere, so a
  typo could delete an element and downgrade the failure to a warning.
* Make `zarr_node_format()` fail on nodes carrying both v2 and v3 metadata and
  add `expect_zarr_store_format()`, which walks the whole store rather than
  just the root, so a v3 array nested in a v2 group is caught.

* stop ignoring all python warnings in the roundtrip tests

* Replace the blanket `warnings.filterwarnings("ignore")` that was added to
  eight roundtrip test files with two message filters in `skip_if_no_zarr()`,
  next to the one that was already there. The only warnings these tests emit
  are "zarr v3 autosharding will be the default" and "Consolidated metadata is
  currently not part in the Zarr format 3 specification", both from Python
  zarr; ignoring everything also hides warnings we do want to see.
* Put blosc back in the compression test. It works fine here with Rarr 2.1.18
  for both v2 and v3, and it is still an accepted value of `compression`.
* Compare the store sizes before removing the compressed store. The `unlink()`
  ran first, so the size compared against was always zero and the expectation
  could never fail.

* document the zarr format without leaking the option

* Drop `options(anndataR.zarr_format = 2)` from the `write_zarr()` example and
  the vignette. Neither restored it, so the example leaked the option into
  every example that runs after it in the same R CMD check session, and the
  vignette silently wrote every later store as v2.
* Describe the Zarr format under `@details` in `write_zarr()`. It was only
  reachable through `...`, so there was nowhere on that page saying what
  `zarr_format` does or that v3 is the default.
* The two vignette examples both wrote v2, which did not show the difference
  they were meant to show. Keep the explicit argument and explain the option in
  prose instead. Also fixes "individual function all" and turns the two bare
  URLs into links.

* add NEWS entries for zarr v3 write support

* extract the vlen-utf8 metadata patch into a helper

`write_zarr_string_array()` and `write_zarr_string_scalar()` carried the same
46 lines of JSON patching, once each. Move it to `patch_zarr_vlen_utf8()` so
the v2 filter and the v3 codec only have to be kept in step in one place.

Spell out that this is a temporary workaround for Rarr not being able to write
VLen-UTF8 itself, at the helper and at both call sites, so it is obvious what
to delete once Rarr issue 111 lands.

The bytes written to disk are unchanged.

* check jsonlite

* small updates to docs

* small fix to NEWS

* remove posit artifacts

* more

* again

* final try

---------

Co-authored-by: Hugo Gruson <git@hugogruson.fr>
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> 
    
  
    

      Package: MicrobiomeProfiler

      Commit: 921b9123e22507a9e4d564e047054ddb9bf1117d

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-17 12:07:07 +0800

      Commit message:


	  
		
 refactor(external-data): move the Disbiome and eggNOG builders into R/

`data-raw/` is listed in `.Rbuildignore`, so the builder scripts are not part of
the tarball. The tests exercising them could therefore only ever run against the
source tree -- under `R CMD check` they were skipped, which left the builders with
no coverage in the only check that matters.

Move the implementations into `R/` as internal (non-exported) functions, with the
function bodies unchanged, and leave `data-raw/*.R` as thin loaders so the
scheduled external-data update workflow keeps working without modification.

The four builder tests now run under `R CMD check`: SKIP 4 -> 0, PASS 114 -> 135.
 
    
  
    

      Package: MicrobiomeProfiler

      Commit: 4d51fb03bd671e87d4d9f94ce9859e6cf528ef4a

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-15 09:29:22 +0800

      Commit message:


	  
		
 test: skip the data-raw builder tests under R CMD check

data-raw/ is listed in .Rbuildignore, so the builder scripts are absent from
the tarball, and R CMD check runs the tests against the installed package
where test_path("..", "..", "data-raw", ...) does not exist. That made
`make check` fail with an ERROR while devtools::test() stayed green.

Guard the sys.source() and skip when the builder is unavailable, so the
source-tree run still exercises the builders.
 
    
  
    

      Package: MicrobiomeProfiler

      Commit: 95d9c1b8fd66fb67c4a865d3ecffabe19abbafe0

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-15 09:29:21 +0800

      Commit message:


	  
		
 fix(eggnog): build the app example from the published artifact

Clicking Example could never produce a result: the identifiers came from
head(unique(gsid2gene$gene), 10), which lands inside map01100 (132k genes)
and is dropped by the ORA maxGSSize of 500, so every submission ended in
"There is no significant result".

Derive the example from the loaded artifact instead, using a complete KEGG
pathway that fits the analysis window, and give the GSEA example background
identifiers from a second pathway - without them the permutation p-values
cannot be computed at all. Placeholder `OG0001`-style identifiers are gone
from the UI and the docs, a failed artifact download is reported instead of
silently filling the input with unusable IDs, and the `NA` condition in the
universe observer is guarded. Adds an offline testServer smoke test plus a
round-trip test that the example really enriches in both ORA and GSEA.
 
    
  
    

      Package: MicrobiomeProfiler

      Commit: b7f7dfcd4e8402b3ebd0d29e97437df5da066041

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-15 09:29:05 +0800

      Commit message:


	  
		
 feat(gsea): expose a seed argument on all GSEA entry points

The permutation engine drew a fresh random seed on every run, so identical
input could give different p-values and a result was not reproducible.
Forward an explicit `seed` to enrichit::gsea_gson() from gseKO(),
gseModule(), gseCOG(), gseMDA(), gseMBKEGG(), gseSMPDB(), gseHMDB() and
gseEggNOG(); FALSE keeps the previous behaviour and a number (or TRUE) makes
a run repeatable.

Bump enrichit to (>= 0.2.2), which applies pvalueCutoff to both pvalue and
p.adjust inside gsea_gson(), matching the historical clusterProfiler/DOSE
double-filtering behaviour.
 
    
  
    

      Package: MicrobiomeProfiler

      Commit: 5cc8964b5702a73ec3aed3c2654f0e4756677a0a

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-15 09:29:05 +0800

      Commit message:


	  
		
 chore: ignore docs/ and .workbuddy-ai/

Local build and agent scratch directories; keep them out of the source
tarball and out of version control.
 
    
  
    

      Package: ChIPseeker

      Commit: f87bb15bd4f07ab68169d0d012883e8e912eae81

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-17 10:52:55 +0800

      Commit message:


	  
		
 update docs
 
    
  
    

      Package: gdscloud

      Commit: 7363dced4038b00072de2fa60cf78311e4e64e5f

      Author:  Xiuwen Zheng <zhengxwen@gmail.com> 

      Date: 2026-09-16 21:24:24 -0500

      Commit message:


	  
		
 more checking & options
 
    
  
    

      Package: TPP

      Commit: be00cebe5ac8f22adcbb72995de03997ecee22c4

      Author:  Dorothee Childs <childs@embl.de> 

      Date: 2026-09-17 04:01:29 +0200

      Commit message:


	  
		
 bump version
 
    
  
    

      Package: TPP

      Commit: b58c8cf74a38136ea6b99358574d202a7a06463b

      Author:  Dorothee Childs <childs@embl.de> 

      Date: 2026-09-17 03:28:11 +0200

      Commit message:


	  
		
 Fix documentation checks
- Restore package startup messaging to `.onAttach`
- Add the `TPP` package anchor to cross-package Rd links
- Align NEWS entry formatting
 
    
  
    

      Package: TPP

      Commit: 320d665b6cc7488385950cac863923b665e1a51e

      Author:  Dorothee Childs <childs@embl.de> 

      Date: 2026-09-17 03:28:11 +0200

      Commit message:


	  
		
 Fix .Rd cross-references and startup message
 
    
  
    

      Package: HiCcompare

      Commit: add08eb490f20210e3a467727143845a7c9bcc42

      Author:  Mikhail Dozmorov <mdozmorov@users.noreply.github.com> 

      Date: 2026-09-16 20:56:34 -0400

      Commit message:


	  
		
 Prepare Bioconductor devel release 1.35.1

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 
    
  
    

      Package: HiCcompare

      Commit: e0dccc36541b243fec6253791ef52fe124c3f70b

      Author:  Mikhail Dozmorov <mdozmorov@users.noreply.github.com> 

      Date: 2026-09-16 20:55:37 -0400

      Commit message:


	  
		
 Merge remote-tracking branch 'bioc/devel'
 
    
  
    

      Package: HiCcompare

      Commit: 8471ef2524faeee9ada45f313f1b458198104ce6

      Author:  Mikhail Dozmorov <mdozmorov@users.noreply.github.com> 

      Date: 2026-09-16 20:39:54 -0400

      Commit message:


	  
		
 Merge pull request #36 from dozmorovlab/copilot/fix-vignette-building-error

Fix vignette failure for InteractionSet inputs in `create.hic.table()` 
    
  
    

      Package: HiCcompare

      Commit: 70334146c3f51992ce18cd6ae28654a543d838e1

      Author:  copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> 

      Date: 2026-09-17 00:25:30 +0000

      Commit message:


	  
		
 Fix InteractionSet conversion in create.hic.table

Co-authored-by: mdozmorov <864945+mdozmorov@users.noreply.github.com>
 
    
  
    

      Package: FlowSorted.Blood.EPIC

      Commit: d4de21053f6d8cf09a35d9a9efadf0e66893226d

      Author:  Lucas Salas <lucas.a.salas.diaz@dartmouth.edu> 

      Date: 2026-09-16 15:51:23 -0400

      Commit message:


	  
		
 Handle deprecated cord blood dependency

Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
 
    
  
    

      Package: igblastr

      Commit: 0d653ff2325dd290196107bbccb88e9dfb294d82

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-09-16 12:09:46 -0700

      Commit message:


	  
		
 igblastr 1.3.22: Add get_fwrcdr_widths_for_imgt_organism()

Also enable automatic intdata generation in:

  install_IMGT_germline_db("", "Ctenopharyngodon_idella")
  install_IMGT_germline_db("", "Equus_caballus")
  install_IMGT_germline_db("", "Felis_catus")
  install_IMGT_germline_db("", "Gallus_gallus")

and in:

  install_IMGT_germline_db("", "Danio_rerio", tcr.db=TRUE)
  install_IMGT_germline_db("", "Ovis_aries", tcr.db=TRUE)
  install_IMGT_germline_db("", "Pan_troglodytes", tcr.db=TRUE)
  install_IMGT_germline_db("", "Pongo_abelii", tcr.db=TRUE)
  install_IMGT_germline_db("", "Pongo_pygmaeus", tcr.db=TRUE)
  install_IMGT_germline_db("", "Sus_scrofa", tcr.db=TRUE)
 </pre>
    </div>
  
    

      Package: Rarr

      Commit: 64d6a8c44f508142204788406889751e17044c2c

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-16 15:57:02 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: Rarr

      Commit: d39e0dc2a752ab66680431c5026bebdf84fc516f

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-16 15:56:47 +0200

      Commit message:


	  
		
 Mention S3 improvement in NEWS
 
    
  
    

      Package: Rarr

      Commit: cc327be4c89d915d4581b55802ad5184c51182a3

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-16 16:06:47 +0200

      Commit message:


	  
		
 Do not generate docs for internal get_credentials()
 
    
  
    

      Package: Rarr

      Commit: 42e845c093667632a0cb93d97028ea2bfc7b8583

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-16 16:06:17 +0200

      Commit message:


	  
		
 Update snapshot
 
    
  
    

      Package: Rarr

      Commit: c9574e8e577b302450a9249875bd015ed5d1ad74

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-16 15:50:06 +0200

      Commit message:


	  
		
 Remove methods dependency
 
    
  
    

      Package: Rarr

      Commit: e68652a8eea732bb5648dae7866cb71c56285e0d

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-16 15:54:57 +0200

      Commit message:


	  
		
 Copy new get_credentials from paws.storage
 
    
  
    

      Package: Rarr

      Commit: c94823a9620c91c478f00bf9499197fc7e052e86

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-16 15:54:50 +0200

      Commit message:


	  
		
 Force S3 path style
 
    
  
    

      Package: Rarr

      Commit: 79b93a21b14e25e317030423a3b1ed460875d552

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-16 15:22:51 +0200

      Commit message:


	  
		
 Update EMBL test bucket to NetApp
 
    
  
    

      Package: Rarr

      Commit: 6a72d7fb35ed203c2f0f81e60564dbfa30d83577

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-14 18:57:43 +0200

      Commit message:


	  
		
 Add test for #241
Fixes #241
 
    
  
    

      Package: HuMMANet

      Commit: 88bea3d1bba03794a8b613a1a038672c30dd59ce

      Author:  Nalin Arora <nalin21478@iiitd.ac.in> 

      Date: 2026-09-16 12:39:35 -0400

      Commit message:


	  
		
 Merge Bioconductor devel into main
 
    
  
    

      Package: HuMMANet

      Commit: 41aee223963e901a8a276a292d042b6a46cfde65

      Author:  Nalin Arora <nalin21478@iiitd.ac.in> 

      Date: 2026-09-16 12:36:16 -0400

      Commit message:


	  
		
 Sync with bioc acceptance and updated taxa files for Lloydprice
 
    
  
    

      Package: scanMiR

      Commit: cfdbdc0a0ae583dc25191d08ab6fae656bee0661

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-09-16 18:32:15 +0200

      Commit message:


	  
		
 fixed 7mer-m8 bug just introduced...
 
    
  
    

      Package: quantiseqr

      Commit: 0588bbc0360d70d785644f2d047eec403941242a

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2026-09-16 18:22:17 +0200

      Commit message:


	  
		
 version bump, 1.21.2
 
    
  
    

      Package: quantiseqr

      Commit: 0f1c121b36ae0b5fcb69e094f55f74efc26ad408

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2026-09-16 18:22:08 +0200

      Commit message:


	  
		
 updating the name of the covariate after the GEOquery update (not having the dots anymore, using the whitespace/colon..)
 
    
  
    

      Package: quantiseqr

      Commit: 68a508aa082684fe38f16e3d3286cd130e0f8dbd

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2026-09-16 18:21:22 +0200

      Commit message:


	  
		
 using aes vs aes_string
 
    
  
    

      Package: bedbaser

      Commit: f0851a482b3385599228ad14e463998043f041c7

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-09-15 23:58:33 -0400

      Commit message:


	  
		
 Bump version to 1.5.1
 
    
  
    

      Package: bedbaser

      Commit: ae936d790f212fce46c9254403ae3a3c39007e40

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-09-15 23:57:49 -0400

      Commit message:


	  
		
 Update to bedbase 0.13.0
 
    
  
    

      Package: trackViewer

      Commit: 3305c15ac399e249a4c75879ba565f3782783212

      Author:  Jianhong Ou <jianhong.ou@gmail.com> 

      Date: 2026-09-16 10:54:32 -0400

      Commit message:


	  
		
 update documentation for track class.
 
    
  
    

      Package: universalmotif

      Commit: bbf44761acbddd438e01effabecc5faeea6ce5d4

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-09-16 15:42:36 +0100

      Commit message:


	  
		
 bump version
 
    
  
    

      Package: universalmotif

      Commit: aee941983225e8d546efb695aee19a013fdc783d

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-09-16 15:42:15 +0100

      Commit message:


	  
		
 Fix gapped motif scoring and metadata preservation

Add background and metadata regression tests, clarify motif and P-value documentation, and retire completed and obsolete backlog items.
 
    
  
    

      Package: universalmotif

      Commit: 237b69513ecc82e6f4503d530b2c1cb96c94cdba

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-09-16 14:32:41 +0100

      Commit message:


	  
		
 bump version
 
    
  
    

      Package: universalmotif

      Commit: 097aba292bd317ea6036ad070f5b0750234eb62e

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-09-16 14:30:23 +0100

      Commit message:


	  
		
 Fix inclusive score thresholds and document boundary handling
 
    
  
    

      Package: universalmotif

      Commit: 19926fd4ceb66b7d2fff48d92697635810b3e016

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-09-16 13:42:12 +0100

      Commit message:


	  
		
 new title
 
    
  
    

      Package: universalmotif

      Commit: 68a3ee18dc240ac501c31de48b544847968ff85a

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-09-16 13:36:27 +0100

      Commit message:


	  
		
 bump version
 
    
  
    

      Package: universalmotif

      Commit: f30712ee2dcb2304b5ebfd3edcf01d158e4aa9a3

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-09-16 13:36:16 +0100

      Commit message:


	  
		
 clean up
 
    
  
    

      Package: topdownr

      Commit: a98767e0ab082adf7526f401bb4fcdae05be17cd

      Author:  Sebastian Gibb <mail@sebastiangibb.de> 

      Date: 2026-09-16 12:08:04 +0200

      Commit message:


	  
		
 test: remove empty test_method-xml.R

tests were removed in 1719975 when defaultMs{1,2}Settings were set defunct.
 
    
  
    

      Package: RmzTabM

      Commit: 7bc9677f9d511e957d8a163374fc566f90a51666

      Author:  Johannes Rainer <5506112+jorainer@users.noreply.github.com> 

      Date: 2026-09-16 09:28:33 +0200

      Commit message:


	  
		
 Merge pull request #51 from rformassspectrometry/gabri

feat: add support to mzTab-profile field 
    
  
    

      Package: RmzTabM

      Commit: 88aaa0cf1cfd5932247151f24e1d40ac7d0960c3

      Author:  Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com> 

      Date: 2026-09-10 14:23:28 +0200

      Commit message:


	  
		
 Address Johannes comments
 
    
  
    

      Package: RmzTabM

      Commit: d1295e97f30bbdfb0f456cf89db3207e5f32c720

      Author:  Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com> 

      Date: 2026-09-09 17:08:36 +0200

      Commit message:


	  
		
 feat: add support to mzTab-profile field
 
    
  
    

      Package: RmzTabM

      Commit: 96e79f180031485cbf581971f3f3d8cac6979379

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2026-08-25 09:11:36 +0200

      Commit message:


	  
		
 Update readme
 
    
  
    

      Package: GOpro

      Commit: 84c3e792b3a6ca1fe7fdcd9b6fdacfa5e241bd6d

      Author:  Lidia <lidia@Lidias-MacBook-Pro.local> 

      Date: 2026-09-16 08:14:31 +0200

      Commit message:


	  
		
 version bump in devel
 
    
  
    

      Package: GOpro

      Commit: ca5662bfa440af37e24f55f3b05f2c45c87e8543

      Author:  Lidia <lidia@Lidias-MacBook-Pro.local> 

      Date: 2026-09-16 07:34:15 +0200

      Commit message:


	  
		
 fix removed non-exsisting suggest#
 
    
  
    

      Package: SplicingGraphs

      Commit: de90511b68f1d1b7b71e13ea2b6bbd7464e9eec6

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-09-15 17:59:53 -0700

      Commit message:


	  
		
 spelling
 
    
  
    

      Package: GenomicAlignments

      Commit: a8e7728b541b7cdca73c4b3ddd4117fed546820c

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-09-15 17:57:32 -0700

      Commit message:


	  
		
 spelling
 
    
  
    

      Package: CNVRanger

      Commit: e550d9a9d4db27ac0caeaeab2793c9e72c74e0ac

      Author:  lgeistlinger <ludwig.geistlinger@gmail.com> 

      Date: 2026-09-15 19:59:13 -0400

      Commit message:


	  
		
 plotRecurrentRegions: several fixes & improvements
 
    
  
    

      Package: S4Vectors

      Commit: ef821b40304f606aae72ebdf82d039a1536a171b

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-09-15 10:30:21 -0700

      Commit message:


	  
		
 S4Vectors 0.51.10: Add unit tests for selfmatchIntegerQuads()
 
    
  
    

      Package: S4Vectors

      Commit: 62f3c541cb09d9e9085f491a709b02a2cabe232c

      Author:  Adityarup Laha <adi24360526@gmail.com> 

      Date: 2026-09-16 01:26:41 +0800

      Commit message:


	  
		
 Compare the 4th key in compar4_stable() (#145)

The comparator used by qsort4() computed the comparison on the 4th
target but never returned it, so the ordering ignored that key while
_get_matches_of_ordered_int_quads() compared on all four. With
method="quick", selfmatchIntegerQuads() and matchIntegerQuads() then
returned nomatch for elements sharing the first three keys with an
earlier element.

Fixes #144

Co-authored-by: Claude Opus 5 (1M context) <noreply@anthropic.com> 
    
  
    

      Package: maaslin3

      Commit: 8c95d114b621321a6d504cd7c23f694cb7362561

      Author:  Will Nickols <willanickols@gmail.com> 

      Date: 2026-09-15 10:48:32 -0700

      Commit message:


	  
		
 Update DESCRIPTION
 
    
  
    

      Package: maaslin3

      Commit: 3cede82e3d0d5996d6165ca211c478927bf3a0a6

      Author:  Will Nickols <willanickols@gmail.com> 

      Date: 2026-09-15 10:39:53 -0700

      Commit message:


	  
		
 Fix contrast test dropping row on NA bug
 
    
  
    

      Package: maaslin3

      Commit: bb83025cec1fddc29fe30ce6bd75c65f191b79ff

      Author:  Will Nickols <willanickols@gmail.com> 

      Date: 2026-09-15 10:14:09 -0700

      Commit message:


	  
		
 Pin collapse package
 
    
  
    

      Package: BEclear

      Commit: 6f8c4e939f9cde0fc215f33fc6b69f1bb58d87a8

      Author:  Livia Rasp <livia.rasp@gmail.com> 

      Date: 2026-09-15 19:46:08 +0200

      Commit message:


	  
		
 fix of the logging test
 
    
  
    

      Package: BEclear

      Commit: 8d13d199bf288004d901ad5a5500c5f2d36e1dcd

      Author:  Livia Rasp <livia.rasp@gmail.com> 

      Date: 2026-09-15 19:33:49 +0200

      Commit message:


	  
		
 updated documentation
 
    
  
    

      Package: scanMiR

      Commit: f90ddbd302eb7ffbfab991941c302a9a8cd09edd

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-09-15 18:05:59 +0200

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: scanMiR

      Commit: 3b05b4f38777cb37e512dcfa5fa6140b50d12a75

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-09-15 18:03:00 +0200

      Commit message:


	  
		
 fixed 1) gapped/m8 confusion bug, 2) seed names lost with n1
 
    
  
    

      Package: rhdf5

      Commit: 94635c57f00b21d1632b497b8c553a655344b0cf

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-15 14:42:01 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: rhdf5

      Commit: 8da7a86546c6088317bd4e71f92eddcb6e710252

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-15 14:41:46 +0200

      Commit message:


	  
		
 Mention try() removal in NEWS
 
    
  
    

      Package: rhdf5

      Commit: 1dd20c4423978a6ec998fc848e156d5ce6b83089

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 15:38:28 +0200

      Commit message:


	  
		
 Remove try()

We want to avoid error early or let them surface
 
    
  
    

      Package: rhdf5

      Commit: ebf8c90d5c2e91ff666676d0a2614527864cb412

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-15 13:21:14 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: rhdf5

      Commit: a2fbd4e8e0fae632b2da1ba2e3b4a845f4e225bd

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-15 13:21:06 +0200

      Commit message:


	  
		
 Mention segfault fix in NEWS
 
    
  
    

      Package: rhdf5

      Commit: edcce3e5b392dc4ba5acdf311e557c1f1650176b

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-15 13:13:15 +0200

      Commit message:


	  
		
 Pass mem_space_id to H5Treclaim to indicate memory to free
 
    
  
    

      Package: rhdf5

      Commit: 2b585264d610ab45fa16ca62065b76554470315f

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-15 13:11:46 +0200

      Commit message:


	  
		
 Add reprex from #240 as test case
 
    
  
    

      Package: rhdf5

      Commit: 97a9d7fd1fe40135ce7a1fc7f844986b79110a7a

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-15 11:03:56 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: rhdf5

      Commit: 215d8ea6fae28c4de9d8d1f1114d4aca6941c614

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-15 11:03:40 +0200

      Commit message:


	  
		
 Avoid double negation
 
    
  
    

      Package: rhdf5

      Commit: 86324cdf49415202148644cd4bd8eba67215d822

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-09-14 22:16:49 +0200

      Commit message:


	  
		
 apply suggestions
 
    
  
    

      Package: rhdf5

      Commit: 51044fce07712aff9cb154ca35a5b795ee25e342

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-09-08 20:29:40 +0200

      Commit message:


	  
		
 fix na warning for numeric datasets
 
    
  
    

      Package: rhdf5

      Commit: 9a0d2ead679c483ef7a6e21a096dc94019ad3172

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-09-08 20:13:16 +0200

      Commit message:


	  
		
 add test for na warning on numeric datasets
 
    
  
    

      Package: ChIPseeker

      Commit: acc3a053c66b036c87f8f7a0fa84d15a4c92c91e

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-15 09:37:31 +0800

      Commit message:


	  
		
 fix sameStrand, geneChr/geneStrand factor codes and silent peak dropping

- getNearestFeatureIndicesAndDistances(): honour sameStrand when detecting
  overlaps. findOverlaps() was called with unstrand(features), so a peak
  with an unambiguous strand could be assigned to a feature on the opposite
  strand (#257, #258)
- annotatePeak(): report geneChr/geneStrand as characters. as.data.frame()
  returns 'seqnames'/'strand' as factors and assigning a factor into mcols()
  dropped the class, leaving integer codes (#233, #247)
- annotatePeak(): warn when peaks are dropped for lack of any feature in
  TxDb, instead of removing them silently (#251, #258)
- plotAnnoBar(): replace deprecated ggplot2::aes_string() with the tidy
  evaluation idiom already used by plotDistToTSS() (#268)

bump version to 1.49.2 and add unit tests

Co-Authored-By: WorkBuddy AI <noreply@workbuddy.ai>
 
    
  
    

      Package: MicrobiomeProfiler

      Commit: ba5d50fca796b613b28f84de7583619782e8a7c6

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-15 06:34:24 +0800

      Commit message:


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

      Package: MicrobiomeProfiler

      Commit: fa19b1492a1383882b438ac271c17a7c59efd4d5

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-15 06:33:36 +0800

      Commit message:


	  
		
 update
 
    
  
    

      Package: MicrobiomeProfiler

      Commit: e35c84e0888a7ca4f978960b7bd2529bf8d4b20e

      Author:  github-actions[bot] <github-actions[bot]@users.noreply.github.com> 

      Date: 2026-09-01 04:40:09 +0000

      Commit message:


	  
		
 chore: auto-update internal data in sysdata.rda
 
    
  
    

      Package: MicrobiomeProfiler

      Commit: 46099d6bc12f470f550f7abc32f64b195e7f7e7c

      Author:  github-actions[bot] <github-actions[bot]@users.noreply.github.com> 

      Date: 2026-08-01 03:38:30 +0000

      Commit message:


	  
		
 chore: auto-update internal data in sysdata.rda
 
    
  
    

      Package: MicrobiomeProfiler

      Commit: 7e47d8501c2231eb475333f30edd9dc49faf1e2e

      Author:  github-actions[bot] <github-actions[bot]@users.noreply.github.com> 

      Date: 2026-07-01 04:32:20 +0000

      Commit message:


	  
		
 chore: auto-update internal data in sysdata.rda
 
    
  
    

      Package: MicrobiomeProfiler

      Commit: b53732acd37bcc6c3280f8c161a95ea5b1042a20

      Author:  github-actions[bot] <github-actions[bot]@users.noreply.github.com> 

      Date: 2026-06-01 04:55:41 +0000

      Commit message:


	  
		
 chore: auto-update internal data in sysdata.rda
 
    
  
    

      Package: MicrobiomeProfiler

      Commit: 6cbcacc9483dcc431773dcd4c75f489bff2418e6

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-05-26 08:55:19 +0800

      Commit message:


	  
		
 fix(eggnog): refresh runtime examples
 
    
  
    

      Package: MicrobiomeProfiler

      Commit: 707b214cc2f4bd171246209950240a46b898d7f8

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-05-25 08:26:37 +0800

      Commit message:


	  
		
 feat(ui): polish eggNOG GSEA form
 
    
  
    

      Package: MicrobiomeProfiler

      Commit: e8421db3a68fcb0edae289fc17a4993cf9ff194f

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-05-25 08:17:19 +0800

      Commit message:


	  
		
 feat(ui): add eggNOG GSEA frontend entry
 
    
  
    

      Package: MicrobiomeProfiler

      Commit: 4ade10ac7040c2a4c19d9af19ae8ac9daf36398c

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-05-25 07:04:39 +0800

      Commit message:


	  
		
 feat(ui): add eggNOG gene enrichment entry
 
    
  
    

      Package: MicrobiomeProfiler

      Commit: ac17d0a4b2d0a51b7e9c542cc9d66b506f973dcf

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-05-24 19:34:25 +0800

      Commit message:


	  
		
 fix(ci): allow external data partial publish
 
    
  
    

      Package: MicrobiomeProfiler

      Commit: 766efaf735c101a11b614155bdc7354aedef49b4

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-05-24 17:33:35 +0800

      Commit message:


	  
		
 feat(data): add eggNOG external dataset support
 
    
  
    

      Package: MicrobiomeProfiler

      Commit: 1187c830546a2fc7c924252bd1ce3e23876570d8

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-05-24 08:33:55 +0800

      Commit message:


	  
		
 feat(data): fetch Disbiome artifacts from upstream JSON

Replace the placeholder build_disbiome path that re-exported bundled data with a real upstream fetch -> normalize -> GSON build pipeline.

Also add fixture-based builder tests and make external-data validation avoid live Disbiome fetches in pull request CI.
 
    
  
    

      Package: MicrobiomeProfiler

      Commit: 3d35ee017b16f3321bb8b19a044d0ea236204c7f

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-05-23 23:47:38 +0800

      Commit message:


	  
		
 fix(ui): correct conditionalPanel true expressions

Replace the long-standing  typo in Shiny conditionalPanel expressions so panel visibility logic works reliably across enrichment modules.

This also unblocks local smoke testing for the BugSigDB/Disbiome UI flow.
 
    
  
    

      Package: MicrobiomeProfiler

      Commit: 1933e28e18612d9411c512e37e2ac0bb4c34bdc1

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-05-23 23:10:06 +0800

      Commit message:


	  
		
 feat(ui): add BugSigDB option to microbe enrichment module

Expose a data source switch in the Shiny microbe enrichment module so Disbiome and BugSigDB share the same result table and plots.

Update example input handling and add helper-level coverage for source-specific example taxa.
 
    
  
    

      Package: MicrobiomeProfiler

      Commit: 6693c3407dbe1211fc9a4164826893a3d8d27119

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-05-23 15:05:59 +0800

      Commit message:


	  
		
 feat(data): add user-facing external data management API

Expose helpers to inspect configured datasets, download remote artifacts, summarize cache contents, and clear cached external data.

Update the vignette and tests so external data delivery is documented and verified from the user perspective.
 
    
  
    

      Package: MicrobiomeProfiler

      Commit: 9c2ef1bf5cfa43f8ed0cc39a84ca3081d9f02a58

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-05-23 12:52:21 +0800

      Commit message:


	  
		
 fix(ci): push gh-pages updates from worktree branch
 
    
  
    

      Package: MicrobiomeProfiler

      Commit: 16936002de17ec5c6fb59e36bd6bce26d7e2a98c

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-05-23 07:15:14 +0800

      Commit message:


	  
		
 feat(data): 支持 BugSigDB/Disbiome 外部数据运行时

引入基于 registry、manifest 和 cache 的 external data runtime，按需下载并校验 gh-pages 发布的 BugSigDB 与 Disbiome 数据工件。

新增 enrichBugSigDB()，并让 enrichMDA()/gseMDA() 支持 remote-first 数据加载与 refresh 参数；当远程 Disbiome 不可用时回退到内置数据。

补充 external data 的构建、发布与校验 workflow，新增数据构建脚本、registry 配置、实现规范和 testthat 用例，覆盖缓存、registry、BugSigDB 富集和 Disbiome 远程加载路径。
 
    
  
    

      Package: DOSE

      Commit: ead77728c5650cdf323df94601f3a089835391b5

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-15 06:32:51 +0800

      Commit message:


	  
		
 merge
 
    
  
    

      Package: DOSE

      Commit: 965e8b2465843603677d182a71c137d9607bb02a

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-15 06:25:05 +0800

      Commit message:


	  
		
 update docs
 
    
  
    

      Package: DOSE

      Commit: fc5cdaf829c326394a886e069eee878c5147f725

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-07-27 19:14:38 +0800

      Commit message:


	  
		
 add optional llm explanation adapter
 
    
  
    

      Package: DOSE

      Commit: e87bb9b80853c11c9de3684991efb8fe5fbc6896

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-07-27 17:27:04 +0800

      Commit message:


	  
		
 enable combined disease and mouse-model interpretation

Open the cross-species interpretDisease path when explicit MGI/HOM contract files are supplied, preserving separate disease and mouse-model target slices with auditable evidence across single and multi-query inputs.
 
    
  
    

      Package: DOSE

      Commit: 50057fd26484db29ede646ceff575bed03438494

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-07-27 10:56:00 +0800

      Commit message:


	  
		
 add mouse-model evidence slice

Introduce a real-data-backed mouse-model ranking contract so genotype-defined MGI models expose auditable ortholog and phenotype evidence before the combined target path is enabled.
 
    
  
    

      Package: DOSE

      Commit: 80bf5840f84db21a0b2333f9168fe628b6d0d782

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-07-26 22:35:55 +0800

      Commit message:


	  
		
 add offline template disease explanations

Introduce explainDisease(method = "template") and wire interpretDisease(..., explain = "template") to produce evidence-grounded summaries offline while keeping the LLM adapter explicitly gated.
 
    
  
    

      Package: DOSE

      Commit: 8ffc98265e5ecc8b22883c403008e1783c986d97

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-07-26 20:25:20 +0800

      Commit message:


	  
		
 add multi-query gene set interpretation path

Extend interpretDisease to merge a named list of human gene sets into one doseInterpretResult with preserved query identity, deduplicated sources, and globally unique evidence rows.
 
    
  
    

      Package: DOSE

      Commit: 74ea98bc51664733fdda39a3f6368ca4a8babd94

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-07-26 18:39:03 +0800

      Commit message:


	  
		
 add ranked gene disease interpretation path

Map the ranked human gene workflow onto doseInterpretResult by adapting gseDisease output into canonical disease rows plus leading-edge evidence, with deterministic tests around the seeded GSEA comparison.
 
    
  
    

      Package: DOSE

      Commit: c9ff413b34b07b246082e99f5749fc8318d64baf

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-07-26 18:04:04 +0800

      Commit message:


	  
		
 add human gene interpretation path

Map the first supported human gene workflow onto doseInterpretResult so interpretDisease returns ranked disease rows and traceable driving-gene evidence without inventing a second analysis contract.
 
    
  
    

      Package: DOSE

      Commit: f4d8043b1b5b612d56a5cd90b4866f34164f22ee

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-07-26 17:06:53 +0800

      Commit message:


	  
		
 add interpretation contract scaffolding

Introduce the canonical doseInterpretResult object, early interpretDisease validation, and contract tests so the new interpretation API has one traceable public seam before ranking logic lands.
 
    
  
    

      Package: DOSE

      Commit: 66996f49e6f9a0d2dde7045eced497d6e5097b01

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-07-26 16:14:26 +0800

      Commit message:


	  
		
 update docs
 
    
  
    

      Package: NanoStringNCTools

      Commit: f9c7a363c00c054524c5415b4af757ada6d59048

      Author:  Maddy Griswold <mgriswold@nanostring.com> 

      Date: 2026-09-14 16:17:22 -0600

      Commit message:


	  
		
 update version
 
    
  
    

      Package: NanoStringNCTools

      Commit: a856efff82e792030119bab76ad058e2920f3d57

      Author:  Maddy Griswold <mgriswold@nanostring.com> 

      Date: 2026-09-14 16:16:16 -0600

      Commit message:


	  
		
 Merge branch 'dev' of https://github.com/Nanostring-Biostats/NanoStringNCTools into dev
 
    
  
    

      Package: NanoStringNCTools

      Commit: 87641dc10b73732fe981546c639781a384286793

      Author:  Maddy Griswold <40255151+maddygriz@users.noreply.github.com> 

      Date: 2026-09-14 15:29:24 -0600

      Commit message:


	  
		
 Merge pull request #44 from Nanostring-Biostats/vignette_build

build works - vignettes knit 
    
  
    

      Package: NanoStringNCTools

      Commit: 09e46e0dbb33debb6860e23eb104b36f304f6e31

      Author:  Maddy Griswold <Madison.Griswold@bruker.com> 

      Date: 2026-09-14 20:58:53 +0000

      Commit message:


	  
		
 build works
 
    
  
    

      Package: ramr

      Commit: 38eacd491b03d09d194edf7b5dc43ceb48d5d6c6

      Author:  Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no> 

      Date: 2026-09-14 22:50:24 +0200

      Commit message:


	  
		
 RNG test fix
 
    
  
    

      Package: ramr

      Commit: a055cc1d0091e28ed209ba98500334007e2425a5

      Author:  Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no> 

      Date: 2026-09-14 22:37:14 +0200

      Commit message:


	  
		
 RNG test fix
 
    
  
    

      Package: ramr

      Commit: c261bae91aae259e0275a08dbf1d459c6d2e2daa

      Author:  Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no> 

      Date: 2026-09-14 20:17:25 +0200

      Commit message:


	  
		
 fix RNG test
 
    
  
    

      Package: BEclear

      Commit: b042202d714183581c409d50adf0f4db0111a34a

      Author:  Livia Rasp <livia.rasp@gmail.com> 

      Date: 2026-09-14 22:03:58 +0200

      Commit message:


	  
		
 fixed a bug that made correctBatchEffect fail if glue wasn't installed and batch effects are detected in both directions again
 
    
  
    

      Package: BatchQC

      Commit: dedcb1d1af691e694e76fbc43e20f3f6e2eb909c

      Author:  technophilic03 <leng@bu.edu> 

      Date: 2026-09-14 15:46:34 -0400

      Commit message:


	  
		
 Fix Unicode character in run_kBET documentation and update version number
 
    
  
    

      Package: BatchQC

      Commit: 5730628e717c470fd507b1d73b98bf1038167737

      Author:  technophilic03 <leng@bu.edu> 

      Date: 2026-09-14 15:38:11 -0400

      Commit message:


	  
		
 Add .posit to .Rbuildignore
 
    
  
    

      Package: BatchQC

      Commit: d91795c7887e260720b81565b4cda88261b01b60

      Author:  technophilic03 <leng@bu.edu> 

      Date: 2026-09-14 15:37:55 -0400

      Commit message:


	  
		
 Replace Unicode chi in run_kBET docs to fix PDF manual
 
    
  
    

      Package: PhyloProfileData

      Commit: bb5f9bc589e5d2334eea2bbbc2e93976064ce398

      Author:  trvinh <trvinh@gmail.com> 

      Date: 2026-09-14 19:37:40 +0200

      Commit message:


	  
		
 changed Vinh email
 
    
  
    

      Package: iModMixData

      Commit: aa769c2712b74ad530cdc01df8a39a4c2ac4ec9d

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 12:58:18 -0400

      Commit message:


	  
		
 unresponsive

secret found in software pacakge
 
    
  
    

      Package: PhyloProfile

      Commit: 424b6e8834ebf4515d23dd52dc111c4cf190cc8f

      Author:  trvinh <trvinh@gmail.com> 

      Date: 2026-09-14 18:03:18 +0200

      Commit message:


	  
		
 Change Vinh email
 
    
  
    

      Package: Spectra

      Commit: 6870c3bf15f8282e75a4b7797db0a0964c3b0de6

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2026-09-14 17:41:32 +0200

      Commit message:


	  
		
 tests: fix issue in one of the unit tests for MsBackends
 
    
  
    

      Package: BiocDuckDB

      Commit: 2c1b2678ca3c16fb2dba57480f769da592c89e23

      Author:  Patrick Aboyoun <aboyoun.patrick@gene.com> 

      Date: 2026-09-14 08:37:08 -0700

      Commit message:


	  
		
 fix: correct scoreMarkers's true.auc AUC computation and add correlatePairs significance testing (0.99.24)

.compute_true_auc_sql_DuckDBMatrix() had three independent bugs, all affecting
scoreMarkers(..., true.auc = TRUE): it matched SQL results back to R against
seq_len(ngenes) instead of the actual row-key-to-position mapping, so
subset.row either left genes NA or silently mapped results to the wrong row;
its lfc threshold shifted every cell's value identically regardless of group,
a no-op on rank order that made lfc have zero effect; and it derived its gene
universe from stored rows only, so a gene with zero stored values anywhere in
the matrix (a fully implicit-zero row) was dropped instead of getting the
correct all-ties AUC of 0.5. All three fixed at the root, with regression
tests against a from-scratch brute-force AUC oracle.

Also fixed a temp-table naming collision risk shared by 7+ call sites in this
file: unique names were drawn from sample.int() off R's global RNG stream at
second-level resolution, so a collision under overwrite=TRUE could silently
corrupt results instead of erroring -- the same anti-pattern already found and
fixed once in the sibling DuckDBArray package. Replaced with a monotonic,
PID-qualified counter.

correlatePairs,DuckDBMatrix-method computed its Pearson correlation but never
the significance test its own documented return value promised -- added the
standard Pearson t-test plus BH-adjusted FDR, verified against cor.test().
 
    
  
    

      Package: GOfuncR

      Commit: 7dcd31740f1e2763df11687c0860f1d660fcf91e

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 11:39:38 -0400

      Commit message:


	  
		
 Deprecate
https://github.com/sgrote/GOfuncR/issues/12#issuecomment-4163503142
 
    
  
    

      Package: DRIMSeq

      Commit: 89597e3e8d5e3af881729de2f170f8aae7f3e892

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 11:37:02 -0400

      Commit message:


	  
		
 unresponsive

 - data package large file
 
    
  
    

      Package: ELMER

      Commit: c9ed56c2e36c02e79f46f1252c2702470c54d78a

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 11:35:40 -0400

      Commit message:


	  
		
 unresponsive

 - data package had large file
 
    
  
    

      Package: GSCA

      Commit: 94bd64f1103c60d0a900c3b30113aa77b1cec99e

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 11:34:11 -0400

      Commit message:


	  
		
 unresponsive

 data large file
 
    
  
    

      Package: MMDiff2

      Commit: 765d9b16cd37135bf8f0e10e6432a101ee495fbc

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 11:32:57 -0400

      Commit message:


	  
		
 unresponsive

 data package with large file
 
    
  
    

      Package: ChAMP

      Commit: 124b5c1a473ef87893c5b16debd9d0e307b99f33

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 11:29:34 -0400

      Commit message:


	  
		
 unresponsive

 data package large file
 
    
  
    

      Package: ELMER.data

      Commit: f027ed17c7fa61a0ad30cc97d5ce7eb7f0054605

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 11:25:54 -0400

      Commit message:


	  
		
 unresponsive

 - large file
 
    
  
    

      Package: Single.mTEC.Transcriptomes

      Commit: ca9a870091cc24f01a5b19438f64714cc926d5a5

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 11:24:58 -0400

      Commit message:


	  
		
 unresponsive

 - large file
 
    
  
    

      Package: mammaPrintData

      Commit: b6be046e715c5370b91ffd9e5a0a46dd3f793983

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 11:23:08 -0400

      Commit message:


	  
		
 unresponsive

- large file
 
    
  
    

      Package: GeuvadisTranscriptExpr

      Commit: 04f2bb12a4ec9e4e92170a1bca5b64916d99b3ca

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 11:21:59 -0400

      Commit message:


	  
		
 unresponsive

 - large file
 
    
  
    

      Package: furrowSeg

      Commit: 5054de9d987157b36a1daf8016203c45d4012450

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 11:20:15 -0400

      Commit message:


	  
		
 unresponsive

 - large file
 
    
  
    

      Package: ChAMPdata

      Commit: 5eb766f3651df6e06e498c80790a793393e6c25c

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 11:18:56 -0400

      Commit message:


	  
		
 unresponsive

- large files
 
    
  
    

      Package: FlowSorted.CordBlood.450k

      Commit: ba53cb91e4e182c9844a966818eb8ee52dc704f8

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 11:17:31 -0400

      Commit message:


	  
		
 unresponsive

 - large file
 
    
  
    

      Package: ccdata

      Commit: 074b176ad62d756e79f535d3f30f118246ffc5cd

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 11:14:18 -0400

      Commit message:


	  
		
 unresponsive

 - large file
 
    
  
    

      Package: Affymoe4302Expr

      Commit: 81d317c06c65f2c52cec008be3455051a956d436

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 11:12:35 -0400

      Commit message:


	  
		
 unresponsive

 - large file
 
    
  
    

      Package: Affyhgu133Plus2Expr

      Commit: 44985db4ef6d3ff310ec9b3514696611ebcd9c7c

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 11:11:36 -0400

      Commit message:


	  
		
 unresponsive

 - large file
 
    
  
    

      Package: Affyhgu133aExpr

      Commit: e26ccfeb5734480d772344e0ce6e9d5e36e09136

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 11:09:48 -0400

      Commit message:


	  
		
 unresponsive

 - large file
 
    
  
    

      Package: Fletcher2013b

      Commit: 2f9e4a38afb67bfb013a5ed7102fa7fc6502aa22

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 11:07:29 -0400

      Commit message:


	  
		
 version bump for deprecation
 
    
  
    

      Package: ChIPXpressData

      Commit: c6c1d61ffa71c5a693e931bcf61ee1879f68d251

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 11:05:38 -0400

      Commit message:


	  
		
 unresponsive

 - large file and email bounced
 
    
  
    

      Package: SVM2CRMdata

      Commit: 7c525e5d0f66a48f9bfc666d90d91a4cff2e5930

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 11:01:14 -0400

      Commit message:


	  
		
 unresponsive

 - large file and bounced email
 
    
  
    

      Package: pd.atdschip.tiling

      Commit: 06328ecb107f0341a06c8a742e4853b4da3fef2a

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 11:00:03 -0400

      Commit message:


	  
		
 unresponsive

 - large file and bounced email
 
    
  
    

      Package: MMDiffBamSubset

      Commit: 87648aeb033bfa97317599c4571128f75524e2f9

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 10:58:27 -0400

      Commit message:


	  
		
 unresponsive

 - large file and bounced email
 
    
  
    

      Package: ListerEtAlBSseq

      Commit: 30bf58201e6a0a3b313977c71b154931b254bf91

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 10:56:30 -0400

      Commit message:


	  
		
 unresponsive

   - large file and bounced email
 
    
  
    

      Package: ConnectivityMap

      Commit: b4fefee7c9141f81783aa3e3974db926c902f9ed

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 10:54:56 -0400

      Commit message:


	  
		
 unresponsive

 - large data found and bounced email
 
    
  
    

      Package: TSAR

      Commit: de7879600e8b7df8a39794d1ba5986400caabd7e

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 10:51:43 -0400

      Commit message:


	  
		
 Unresponsive

 - secret found
 
    
  
    

      Package: RMassBankData

      Commit: 11e8215302f012325fb986461ef01dfb6d491eba

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 10:49:09 -0400

      Commit message:


	  
		
 unresponsive

 - secret found in software and non responsive
 
    
  
    

      Package: RMassBank

      Commit: fa37118e05405550ab40f7cc3e70267813a3880a

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 10:46:46 -0400

      Commit message:


	  
		
 unresponsive

 - secret found
 
    
  
    

      Package: iModMix

      Commit: f126c63a750cbcde1ae27f4a8abc89f5972e1e6f

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 10:43:55 -0400

      Commit message:


	  
		
 unresponsive

 - secret found
 
    
  
    

      Package: sevenbridges

      Commit: b76c33e7279f6f062c8d6638e2dc16f7f306cf24

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 10:41:37 -0400

      Commit message:


	  
		
 unresponsive

 - secret found and bounced email
 
    
  
    

      Package: ChIPXpress

      Commit: 674af9f9a4ce90302d4af0087ddae33ddbb6ad2d

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 10:40:04 -0400

      Commit message:


	  
		
 unresponsive
  - large file and bounced email
 
    
  
    

      Package: SwathXtend

      Commit: 36e4c19fc88597cb27ffb89d76e6737732c21873

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 10:38:00 -0400

      Commit message:


	  
		
 unresponsive
 - large file and email bounce
 
    
  
    

      Package: systemPipeTools

      Commit: 6cfdf7fde898d95c7d487d2f95cdb3f5bbaf8710

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-09-14 10:22:55 -0400

      Commit message:


	  
		
 User requested deprecation
 
    
  
    

      Package: methylclock

      Commit: 30be0284066fda7d2f81ec4bf427da56f0f89d1b

      Author:  dpelegri <43083225+dpelegri@users.noreply.github.com> 

      Date: 2026-09-14 13:29:34 +0200

      Commit message:


	  
		
 Remove author listed in error nad version bump

An author was listed by mistake and is not an author of the package.
Remove the incorrect entry from Authors@R and from the package
documentation.
 
    
  
    

      Package: consICA

      Commit: 6259579106af00df9006cba51c32d7dadc4257d0

      Author:  Maryna Chepeleva <maryna.chepeleva@gmail.com> 

      Date: 2026-09-14 11:26:39 +0200

      Commit message:


	  
		
 bump version 2.11.4
 
    
  
    

      Package: consICA

      Commit: 4f42431afccc9cd1646ed46b07baa34670d98ccb

      Author:  Maryna Chepeleva <maryna.chepeleva@gmail.com> 

      Date: 2026-09-14 01:33:01 +0200

      Commit message:


	  
		
 [doc] fix type
 
    
  
    

      Package: consICA

      Commit: bbadb887ca790745320e1e462196766d21db9368

      Author:  Maryna Chepeleva <maryna.chepeleva@gmail.com> 

      Date: 2026-09-14 01:06:41 +0200

      Commit message:


	  
		
 Merge branch 'main' of https://github.com/biomod-lih/consICA
 
    
  
    

      Package: consICA

      Commit: c4d32630930f79accaa21350f97b0b0f1f49a919

      Author:  Maryna Chepeleva <maryna.chepeleva@gmail.com> 

      Date: 2026-09-14 01:06:34 +0200

      Commit message:


	  
		
 [README.md] upd Quick start + add banners 
    
  
    

      Package: consICA

      Commit: 377b32b48bcc1e98de52e508643ce4e48f8f8b5c

      Author:  Maryna Chepeleva <maryna.chepeleva@gmail.com> 

      Date: 2026-09-14 00:00:34 +0200

      Commit message:


	  
		
 [tests] add structural cica invariants and tests for is.consICA(), sortDataFrame()
 
    
  
    

      Package: consICA

      Commit: 3995d545d9b01706ff7a2901b0ef2d9b180bf206

      Author:  Maryna Chepeleva <maryna.chepeleva@gmail.com> 

      Date: 2026-09-13 23:02:46 +0200

      Commit message:


	  
		
 [tests] reduce run time
 
    
  
    

      Package: gDR

      Commit: 0033587b1f7a12998ce25a478c3bef2204bbd8b0

      Author:  Arek Gladki <41166437+gladkia@users.noreply.github.com> 

      Date: 2026-09-14 09:55:05 +0200

      Commit message:


	  
		
 Merge pull request #63 from gdrplatform/GDR-3588

fix: drop the unresolvable gDRplots soft dependency 
    
  
    

      Package: gDR

      Commit: 4c936f536367ba5945e05313c207a84c0f4af466

      Author:  Arkadiusz Gladki <gladki.arkadiusz@gmail.com> 

      Date: 2026-09-14 07:56:20 +0200

      Commit message:


	  
		
 fix: drop the unresolvable gDRplots soft dependency
 
    
  
    

      Package: gDRutils

      Commit: ae267478479c94cda4076804939a4073a300b67d

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2026-09-14 09:37:37 +0200

      Commit message:


	  
		
 Merge pull request #198 from gdrplatform/GDR-3587

fix: default missing fit_source to gDR when merging assays 
    
  
    

      Package: gDRutils

      Commit: 4f5f3159969d5632b7484b191050eb43a5e5bc0e

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-09-14 08:10:00 +0200

      Commit message:


	  
		
 docs: use imperative verb in NEWS entry
 
    
  
    

      Package: gDRutils

      Commit: f20ad781253224c40bf60eb44a57c10714bd250b

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-09-11 14:49:04 +0200

      Commit message:


	  
		
 fix: default missing fit_source to gDR when merging assays
 
    
  
    

      Package: HiCaptuRe

      Commit: 5e7a09c13dbab252d0e2a17105781a90b120fb4e

      Author:  Laureano Tomás-Daza <lauretomas@gmail.com> 

      Date: 2026-09-14 09:06:34 +0200

      Commit message:


	  
		
 import as and version bump
 
    
  
    

      Package: gDR

      Commit: 852193f8765c50cc2029e31b0878f5511a03bc7b

      Author:  Arek Gladki <41166437+gladkia@users.noreply.github.com> 

      Date: 2026-09-14 07:31:43 +0200

      Commit message:


	  
		
 Merge pull request #62 from gdrplatform/GDR-3391

feat: add the infrastructure-agnostic report driver and its templates 
    
  
    

      Package: gDR

      Commit: 190b8ea18b08942d97753a832fd82e0233b10963

      Author:  Dariusz Scigocki <daro.scig@gmail.com> 

      Date: 2026-09-11 09:27:45 +0200

      Commit message:


	  
		
 feat: add the Incucyte helpers the Incucyte report templates call
 
    
  
    

      Package: gDR

      Commit: 1d88484ac6ffd10b8ad2e24c1d2d462987eca725

      Author:  Arkadiusz Gladki <gladki.arkadiusz@gmail.com> 

      Date: 2026-09-10 13:53:27 +0200

      Commit message:


	  
		
 fix: make gDR data.table-aware so report chunks evaluate correctly

run_report() calls rmarkdown::render() without envir, so each template is
evaluated in the driver's own function frame, whose enclosure is the package
namespace. With the driver in gDRinternal that namespace imported data.table
symbols; gDR lists data.table in Imports but had no importFrom in NAMESPACE and
does not set .datatable.aware, so [.data.table silently fell back to data.frame
semantics for every chunk in every report.

Two faces of the same fault, both reproduced end to end:

  3-analysis.Rmd [data_combinations]  Error in .(treatment) :
                                        could not find function "."
  3-analysis.Rmd [fit_data_heat_RV]   object 'normalization_type' not found

Importing := is enough to make the namespace data.table-aware, and matches what
gDRutils, gDRcore, gDRplots and gDRinternal already do.
 
    
  
    

      Package: gDR

      Commit: 6eb046dbc9d2676bb0439d9539bd2ef32743e5f3

      Author:  darsoo <daro.scig@gmail.com> 

      Date: 2026-09-08 12:50:23 +0200

      Commit message:


	  
		
 feat: add the infrastructure-agnostic report driver and its templates

Adds run_report(), which renders the report pipeline as a sequence of
RMarkdown steps and stages its inputs, together with the templates for
steps 1-3, the PRISM and chemical-genomics variants of step 3, and the
Incucyte set.

The driver carries no deployment-specific logic. Everything a particular
installation needs to do around a run is delegated to five optional,
NULL-safe hooks -- on_resolve_inputs, on_start, on_before_render,
on_success and on_failure -- and deployment-specific values reach the
templates through extra_render_params, where names colliding with
parameters the driver computes are dropped with a warning.

rmd_template_path accepts a vector of directories searched in order, so a
deployment can override individual templates and contribute steps the
shared set does not ship. Missing step templates are reported before
rendering starts rather than failing halfway through on a bare
"cannot open file".
 
    
  
    

      Package: scTensor

      Commit: 9729b3509e528995c9096c60b860bc92ccf723fb

      Author:  koki <k.t.the-answer@hotmail.co.jp> 

      Date: 2026-09-13 22:29:23 +0900

      Commit message:


	  
		
 v2.23.3: Fix R CMD check WARNINGs and NOTEs
 
    
  
    

      Package: igvShiny

      Commit: e34b9325a34972168fab449feea75d70cbab7060

      Author:  Arkadiusz Gładki <41166437+gladkia@users.noreply.github.com> 

      Date: 2026-09-13 13:59:38 +0200

      Commit message:


	  
		
 chore(demo): pin Connect Cloud manifest to 1.9.47 (a4159e4)
 
    
  
    

      Package: igvShiny

      Commit: a4159e4d915ac95c33ce7d0ddb21f2be6daaf2bd

      Author:  Arkadiusz Gładki <41166437+gladkia@users.noreply.github.com> 

      Date: 2026-09-13 13:58:45 +0200

      Commit message:


	  
		
 chore(release): bump version to 1.9.47 and update NEWS.md
 
    
  
    

      Package: igvShiny

      Commit: cc3ade6393d4ed6271b6d4c036963f6576de644a

      Author:  Arkadiusz Gładki <41166437+gladkia@users.noreply.github.com> 

      Date: 2026-09-13 13:32:05 +0200

      Commit message:


	  
		
 chore(demo): pin Connect Cloud manifest to cf920df
 
    
  
    

      Package: igvShiny

      Commit: cf920df2af8528b275c671bda9146529997c2a70

      Author:  Arkadiusz Gładki <41166437+gladkia@users.noreply.github.com> 

      Date: 2026-09-13 13:30:37 +0200

      Commit message:


	  
		
 fix(widget): prevent stacked duplicate viewers on mode switch
 
    
  
    

      Package: igvShiny

      Commit: 19002bf84a784f4c8985931b58bd6fad24034271

      Author:  Arkadiusz Gładki <41166437+gladkia@users.noreply.github.com> 

      Date: 2026-09-13 13:00:15 +0200

      Commit message:


	  
		
 chore(demo): pin Connect Cloud manifest to 86f7f8f

Related: #182
 
    
  
    

      Package: igvShiny

      Commit: 86f7f8f46e40ca022d1ccc2309327629564a912e

      Author:  Arkadiusz Gładki <41166437+gladkia@users.noreply.github.com> 

      Date: 2026-09-13 12:59:11 +0200

      Commit message:


	  
		
 feat(widget): handle genome host outages gracefully and add offline demo mode

- Attach .catch handler to igv.createBrowser() to render an in-widget
  error banner and emit igvError event to Shiny when remote genome servers
  are unreachable or return HTTP 5xx
- Add offline mode toggle to showcase demo (inst/showcase/igvShinyDemo.R)
  using bundled SARS-CoV-2 genome for zero-network execution
- Add reachability guards to tests that rely on external hg38 reference
- Add test-error-handling.R covering widget catch and demo offline mode

Related: #182
 
    
  
    

      Package: igvShiny

      Commit: 55d9f6fbc1f2356cb5943058d53a0567937c3f38

      Author:  Arkadiusz Gładki <41166437+gladkia@users.noreply.github.com> 

      Date: 2026-09-13 12:25:38 +0200

      Commit message:


	  
		
 chore(demo): add GenomeInfoDb and UCSC.utils dependencies to manifest
 
    
  
    

      Package: igvShiny

      Commit: a18c9fac6e0dbff7727f4859bf8dc3604f6c015d

      Author:  Arkadiusz Gładki <41166437+gladkia@users.noreply.github.com> 

      Date: 2026-09-13 12:05:59 +0200

      Commit message:


	  
		
 chore(demo): pin Connect Cloud manifest to a1ad70c
 
    
  
    

      Package: barmixR

      Commit: 1d3b628a2dfcb6999d105892202dfd18c318381d

      Author:  Mohammad Darbalaei <mohammad.darbalaei@uni-due.de> 

      Date: 2026-09-13 01:19:43 +0200

      Commit message:


	  
		
 Fix Stan models for Stan >= 2.33; bump version to 0.99.3

- Use new array syntax (array[] int etc.); old syntax was removed in
  Stan 2.33 and broke R CMD build/INSTALL on BioC 3.24.
- Rename internal dirichlet_multinomial_lpmf/_rng to barmix_dm_lpmf/_rng
  to avoid clashing with the built-in added in Stan 2.34.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: edgeR

      Commit: f47ecb9ab434419a6474a70ab3cbc9c675706766

      Author:  Gordon Smyth <smyth@wehi.edu.au> 

      Date: 2026-09-13 09:14:26 +1000

      Commit message:


	  
		
 edgeR 4.99.6 (continued)
- catchKallistoGene() and catchSalmonGene() now store TPM matrix.
- Revise value section of catchSalmonGene.Rd.
 
    
  
    

      Package: cellmig

      Commit: 986868ac4ff3d52f8c668028d1538ab939f2ff76

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-09-12 22:13:00 +0200

      Commit message:


	  
		
 citation
 
    
  
    

      Package: cellmig

      Commit: 72ca0aa680ae6b50df67dd758eac7b13c64bdbef

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-09-12 22:12:49 +0200

      Commit message:


	  
		
 bump
 
    
  
    

      Package: DuckDBDataFrame

      Commit: 2fec690b923848868bd64d2809817731fa4ad98d

      Author:  Patrick Aboyoun <aboyoun.patrick@gene.com> 

      Date: 2026-09-12 08:11:26 -0700

      Commit message:


	  
		
 fix: quote sql_fun() IN-list values via dbQuoteString (0.99.27)

sql_fun,DuckDBTable-method built its return_type/function_type IN (...)
predicates by pasting user-supplied strings between hardcoded quotes with
no escaping, so a return_type containing a ' (e.g. "x') OR 1=1 --") broke
out of the SQL literal before hitting dbGetQuery(). function_type wasn't
actually exploitable (match.arg() constrains it to a fixed enum first),
but both now go through DBI::dbQuoteString(conn, ...), the same
connection object already used elsewhere in the method.
 
    
  
    

      Package: HiCaptuRe

      Commit: ed8d70f0969a7f1a9460f4722bec8c469c1ddbb4

      Author:  Laureano Tomás-Daza <lauretomas@gmail.com> 

      Date: 2026-09-12 16:59:30 +0200

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: HiCaptuRe

      Commit: 6840857df95f206d486824645fd49edde7ae30cf

      Author:  Laureano Tomás-Daza <lauretomas@gmail.com> 

      Date: 2026-09-12 16:50:31 +0200

      Commit message:


	  
		
 Adding as.data.frame method
 
    
  
    

      Package: DuckDBSpatial

      Commit: 75a88a4c29a58b5778d4161ea2799f66b2b52b5d

      Author:  Patrick Aboyoun <aboyoun.patrick@gene.com> 

      Date: 2026-09-12 07:56:56 -0700

      Commit message:


	  
		
 fix: drop which() around lazy is.na() filters (0.99.7)

is.na()/! on a DuckDBColumn return another lazy DuckDBColumn (SQL-pushed),
not a base logical vector, so which(!is.na(df$type)) errored with
"argument to 'which' is not logical" and broke both R CMD build (vignettes)
and R CMD check (roxygen examples). The row-subset method already accepts
a logical DuckDBColumn directly as `i`, pushing it down as a SQL WHERE
filter, so which() was unnecessary. Fixed in both vignettes and the
DuckDBColumn-spatial.R/DuckDBTable-spatial.R/DuckDBDataFrame-spatial.R
@examples, and regenerated the affected .Rd files.
 
    
  
    

      Package: edgeR

      Commit: ac43b4f9ec93698be23a99e1eb1cad3ec1c14bed

      Author:  Gordon Smyth <smyth@wehi.edu.au> 

      Date: 2026-09-12 20:33:50 +1000

      Commit message:


	  
		
 edgeR 4.99.6
- New function catchKallistoGene().
 
    
  
    

      Package: maaslin3

      Commit: b6ab08e0fce281d150434c902a8d3c161730d5f2

      Author:  Will Nickols <willanickols@gmail.com> 

      Date: 2026-09-11 20:19:16 -0700

      Commit message:


	  
		
 Fix contrast test to use lmerTest::contest
 
    
  
    

      Package: gdsfmt

      Commit: 6ed9a78367905faed92d79ba066b91dddfef60cc

      Author:  Xiuwen Zheng <zhengxwen@gmail.com> 

      Date: 2026-09-11 21:45:03 -0500

      Commit message:


	  
		
 multiple enhance
 
    
  
    

      Package: igblastr

      Commit: 62b53bb8ffc4f9ff0ee8d7b3c268d616c99d63e3

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-09-11 17:40:28 -0700

      Commit message:


	  
		
 Enable automatic intdata generation in:

  install_IMGT_germline_db("", "Canis_lupus_familiaris")
  install_IMGT_germline_db("", "Macaca_fascicularis")
  install_IMGT_germline_db("", "Mustela_putorius_furo")
  install_IMGT_germline_db("", "Neogale_vison")
  install_IMGT_germline_db("", "Ornithorhynchus_anatinus")
  install_IMGT_germline_db("", "Pongo_pygmaeus")
  install_IMGT_germline_db("", "Rattus_norvegicus")
  install_IMGT_germline_db("", "Salmo_salar")

and in:

  install_IMGT_germline_db("", "Bos_taurus", tcr.db=TRUE)
  install_IMGT_germline_db("", "Canis_lupus_familiaris", tcr.db=TRUE)
  install_IMGT_germline_db("", "Felis_catus", tcr.db=TRUE)
  install_IMGT_germline_db("", "Gorilla_Gorilla_Gorilla", tcr.db=TRUE)
  install_IMGT_germline_db("", "Macaca_mulatta", tcr.db=TRUE)
  install_IMGT_germline_db("", "Mustela_putorius_furo", tcr.db=TRUE)

Also make a minor correction to the intdata generated in:

  install_IMGT_germline_db("", "Macaca_mulatta")
 </pre>
    </div>
  
    

      Package: AnnotatedBCGEData

      Commit: 72c4a55e4a7bbe674fcbc93ca900c1806fd4469a

      Author:  Heidi <heidi.climber@gmail.com> 

      Date: 2026-09-11 19:41:44 -0400

      Commit message:


	  
		
 updated R version dependency, improved helper code quality
 
    
  
    

      Package: AnnotatedBCGEData

      Commit: 958e155171aaa80576d6b7dee0acafbdd4a46f9f

      Author:  Heidi <heidi.climber@gmail.com> 

      Date: 2026-09-11 12:49:55 -0600

      Commit message:


	  
		
 added unit tests
 
    
  
    

      Package: Rgraphviz

      Commit: 67bdbcc24dafae4f27d5dfc0bc7e240d4e320f26

      Author:  Kasper Daniel Hansen <kasperdanielhansen@gmail.com> 

      Date: 2026-09-11 14:36:41 -0400

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: Rgraphviz

      Commit: 7229c65c53348da58c4f201434e5016f32615f87

      Author:  Kasper Daniel Hansen <kasperdanielhansen@gmail.com> 

      Date: 2026-09-09 12:38:15 -0400

      Commit message:


	  
		
 Merge pull request #29 from jeroen/fix-git-checkout-build

Fix compilation from a git checkout on modern Linux (fixes #28) 
    
  
    

      Package: Rgraphviz

      Commit: 386b42394ea34402c522688ac0444cbf6ed8f555

      Author:  Jeroen Ooms <jeroenooms@gmail.com> 

      Date: 2026-09-02 10:01:07 +0100

      Commit message:


	  
		
 Prevent autotools rebuild rules from firing in bundled Graphviz

When installing from a git checkout (rather than a source tarball), files
have quasi-random sub-second mtimes, so the autotools inputs of the bundled
Graphviz (configure.ac, Makefile.am, m4/*.m4) can appear newer than the
generated files shipped with it. This triggers the automake/autoconf rebuild
rules during make, which regenerate the build system with the (much newer)
host autotools and then fail in libltdl with "No rule to make target
'install'", leaving no gvc.h behind for the Rgraphviz compilation.

Extend the existing 'touch configure' workaround to touch all generated
autotools files (aclocal.m4 first, then configure, config.h.in, config-h.in
and every Makefile.in) so they are always newer than their inputs and the
rebuild rules can never fire.

Fixes #28

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
 
    
  
    

      Package: AnnotatedBCGEData

      Commit: 9fb2fccd0479ed6f1cc40529b154950a30b8e230

      Author:  Heidi <heidi.climber@gmail.com> 

      Date: 2026-09-11 11:18:48 -0600

      Commit message:


	  
		
 resolved error, added tests directory
 
    
  
    

      Package: rBLAST

      Commit: 6e6073d0e92c933cab053dc42998f37fcc912bd9

      Author:  mhahsler <michael@hahsler.net> 

      Date: 2026-09-11 11:39:36 -0500

      Commit message:


	  
		
 Added data.table support.
 
    
  
    

      Package: ZygosityPredictor

      Commit: 14a9976cf642923e8eb6c1131e93e5fde3a1e66d

      Author:  mrheinnecker <marco.rheinnecker@gmail.com> 

      Date: 2026-09-11 16:39:16 +0200

      Commit message:


	  
		
 fixed issue, now ready for bioconductor remote
 
    
  
    

      Package: ZygosityPredictor

      Commit: d3e94f5012463934905c83e3ad4e93665526bb33

      Author:  mrheinnecker <marco.rheinnecker@gmail.com> 

      Date: 2026-09-08 21:58:49 +0200

      Commit message:


	  
		
 fixed error with function being moved from genomic alignments package to cigarillo package
 
    
  
    

      Package: ZygosityPredictor

      Commit: 1b6fc6e85819e05dfc7ab8d5146f88966e68d45e

      Author:  mrheinnecker <marco.rheinnecker@gmail.com> 

      Date: 2026-09-08 21:47:22 +0200

      Commit message:


	  
		
 added unit tests for major reimplementation
 
    
  
    

      Package: MetaboAnnotatoR

      Commit: 5d02c2345669efa4e6874d2bb288211c7bb1f0ed

      Author:  Goncalo Graca <ggomesda@ic.ac.uk> 

      Date: 2026-09-11 15:29:06 +0100

      Commit message:


	  
		
 file for the annotateSpectra function example
 
    
  
    

      Package: MetaboAnnotatoR

      Commit: e24ee1d4fa83e9fc1fc79dcf2d1158cf75ef0378

      Author:  Goncalo Graca <ggomesda@ic.ac.uk> 

      Date: 2026-09-11 15:27:54 +0100

      Commit message:


	  
		
 example updated
 
    
  
    

      Package: MetaboAnnotatoR

      Commit: def786dc8d3ea418414c05b4f9047dc32503c292

      Author:  Goncalo Graca <ggomesda@ic.ac.uk> 

      Date: 2026-09-11 15:06:43 +0100

      Commit message:


	  
		
 column mismatch bug fixed
 
    
  
    

      Package: cellmig

      Commit: a13dbcc80ff7df806828df0ddb0efe8ac82b1f99

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-09-11 13:14:50 +0200

      Commit message:


	  
		
 fix vector -> array
 
    
  
    

      Package: cellmig

      Commit: 31eff918d49c15f6f17f99dd6f28fe78f4517cfa

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-09-11 13:14:39 +0200

      Commit message:


	  
		
 bump
 
    
  
    

      Package: consICA

      Commit: 24896483b7a9853ef7c6c46f08e029d640274a35

      Author:  Maryna Chepeleva <maryna.chepeleva@gmail.com> 

      Date: 2026-09-11 12:10:16 +0200

      Commit message:


	  
		
 bump version 2.11.3
 
    
  
    

      Package: consICA

      Commit: 3a1d9fb76cfbaf0b19f3923b2b883d8ce4467246

      Author:  Maryna Chepeleva <maryna.chepeleva@gmail.com> 

      Date: 2026-09-11 12:08:48 +0200

      Commit message:


	  
		
 [README] bigger logo (line goes on top) 
    
  
    

      Package: consICA

      Commit: 519a7ffd3bd1a81ee045719bf03a0816e9530d6a

      Author:  Maryna Chepeleva <maryna.chepeleva@gmail.com> 

      Date: 2026-09-11 11:51:03 +0200

      Commit message:


	  
		
 [README] ump logo position
 
    
  
    

      Package: consICA

      Commit: d1e050d12c51fc728a871a5acdc64a5eea352d0a

      Author:  Maryna Chepeleva <maryna.chepeleva@gmail.com> 

      Date: 2026-09-11 11:45:36 +0200

      Commit message:


	  
		
 [README] add package logo
 
    
  
    

      Package: consICA

      Commit: 740dc14c9505285ac32e7185149fd7d6b03bd04d

      Author:  Maryna Chepeleva <maryna.chepeleva@gmail.com> 

      Date: 2026-09-11 11:41:17 +0200

      Commit message:


	  
		
 [tests] lighter seed test to fit R CMD check time limit
 
    
  
    

      Package: MetaboAnnotatoR

      Commit: 15f4284bce13d2d2fe4e7a6a71ddf887c5901d51

      Author:  Goncalo Graca <ggomesda@ic.ac.uk> 

      Date: 2026-09-11 10:53:19 +0100

      Commit message:


	  
		
 new version bump after additions/corrections
 
    
  
    

      Package: MetaboAnnotatoR

      Commit: 05d9206f9602622d8fb80d7749571ffb20eb19b9

      Author:  Goncalo Graca <ggomesda@ic.ac.uk> 

      Date: 2026-09-11 10:51:58 +0100

      Commit message:


	  
		
 polarity = NA option included
 
    
  
    

      Package: MetaboAnnotatoR

      Commit: bf6764d30ea7017c2ca9e7ced44f1d750bf5f2a4

      Author:  Goncalo Graca <ggomesda@ic.ac.uk> 

      Date: 2026-09-11 10:50:54 +0100

      Commit message:


	  
		
 MetaboliteNeg library detection bug fixed
 
    
  
    

      Package: MetaboAnnotatoR

      Commit: 714fcfa0661a55c62d995a4a61761523601c10f1

      Author:  Goncalo Graca <ggomesda@ic.ac.uk> 

      Date: 2026-09-11 10:49:29 +0100

      Commit message:


	  
		
 new function added
 
    
  
    

      Package: dinoR

      Commit: 3ddf4a8c7ff1eb285985d163ee577ba91cf57480

      Author:  xxxmichixxx <michaela.c.schwaiger@gmail.com> 

      Date: 2026-09-11 11:04:28 +0200

      Commit message:


	  
		
 Removed the prior.count option from diNOMeTest since edgeR does not support this anymore.
 
    
  
    

      Package: igvShiny

      Commit: a1ad70ccb5cfc48585b323b11ee2795f4e1fcd39

      Author:  Arek Gladki <41166437+gladkia@users.noreply.github.com> 

      Date: 2026-09-11 08:04:41 +0200

      Commit message:


	  
		
 feat(tracks): add trackHeight parameter and alignment sizing options (#181)

Related: #174

Add trackHeight parameter to alignment track loaders (loadBamTrackFromURL,
loadBamTrackFromLocalData, loadBamTrackFromLocalFile, loadCramTrackFromURL,
and loadCramTrackFromLocalData), validate finite pixel height, preserve
positional compatibility with 1.9.45, and expand the option allowlist for
alignment sizing and visibility. 
    
  
    

      Package: cellNexus

      Commit: 240ebe83db8f8a4ff9a3a74db77abba3326b46ce

      Author:  Mengyuan Shen <129487421+myushen@users.noreply.github.com> 

      Date: 2026-09-10 15:28:27 +1000

      Commit message:


	  
		
 Merge pull request #158 from myushen/new_metadata_counts

Update metadata 
    
  
    

      Package: cellNexus

      Commit: 851ff0b082ba294091d8e4b330476c5f26623fdb

      Author:  Mengyuan Shen <mengyuan.shen@outlook.com> 

      Date: 2026-09-10 12:14:24 +1000

      Commit message:


	  
		
 news and version bump
 
    
  
    

      Package: cellNexus

      Commit: f3544947b458ed8a40207e11ce2d7c7d667b513f

      Author:  myushen <mengyuan.shen@outlook.com> 

      Date: 2026-09-09 21:26:25 +1000

      Commit message:


	  
		
 update metadata and vignette
 
    
  
    

      Package: scTensor

      Commit: 10a5e8036f8af8e6891f7a120fb5326018ea7bd4

      Author:  koki <k.t.the-answer@hotmail.co.jp> 

      Date: 2026-09-11 09:28:02 +0900

      Commit message:


	  
		
 v2.23.2: Fix DOSE enrichDGN removal and add BuildSignedCCI
 
    
  
    

      Package: BiocDuckDB

      Commit: 403732a8e16fb89a7ce602daad67dd369834e1e5

      Author:  Patrick Aboyoun <aboyoun.patrick@gene.com> 

      Date: 2026-09-10 17:05:07 -0700

      Commit message:


	  
		
 feat: beachmat/tatami fast path + DuckDBIrlbaParam for correct, fast PCA on DuckDBMatrix (#1)

* feat: add beachmat integration
* feat: add DuckDBIrlbaParam class
* fix: update benchmark_results.rds
* docs: update NEWS.md file
* docs: update the date 
    
  
    

      Package: NetSAM

      Commit: f554b316d62cb21bd66f9d44a173776e1b5ff442

      Author:  Zhiao Shi <zhiao.shi@gmail.com> 

      Date: 2026-09-10 16:06:02 -0500

      Commit message:


	  
		
 add README, biocViews and NEWS, and update vignette install instructions to BiocManager
 
    
  
    

      Package: NetSAM

      Commit: d7e89383fe9a9dae7993ce2b84c8ce099c39cbd2

      Author:  Zhiao Shi <zhiao.shi@gmail.com> 

      Date: 2026-09-10 15:56:27 -0500

      Commit message:


	  
		
 wrap Ensembl-dependent mapToSymbol examples in try() and bump version to 1.53.1

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FkgD1by46Brw8uxGC6nyrc
 
    
  
    

      Package: DAssemble

      Commit: ca195c8a7bfea072c20198ccace2a62887268d0c

      Author:  Nalin Arora <nalin21478@iiitd.ac.in> 

      Date: 2026-09-10 14:52:41 -0400

      Commit message:


	  
		
 Merge Bioconductor devel into master
 
    
  
    

      Package: DAssemble

      Commit: 5ad2ebe53e7ac7beb5fb3260c093903c81c1d49b

      Author:  Nalin Arora <nalin21478@iiitd.ac.in> 

      Date: 2026-09-10 14:47:11 -0400

      Commit message:


	  
		
 Updated vignette with an example for longitudinal
 
    
  
    

      Package: DAssemble

      Commit: 9cbebe5d4bf2782ff86278e6239dc3acd0fa778f

      Author:  Nalin Arora <nalin21478@iiitd.ac.in> 

      Date: 2026-09-01 13:43:53 -0400

      Commit message:


	  
		
 updated handling of method args
 
    
  
    

      Package: DAssemble

      Commit: 311b862053ac10a83d347c466ca17ecf046c91f2

      Author:  Nalin Arora <nalin21478@iiitd.ac.in> 

      Date: 2026-08-28 11:47:37 -0400

      Commit message:


	  
		
 updated enhancer for LR, maaslin2 additional functionality and updated README
 
    
  
    

      Package: DAssemble

      Commit: 970c744216a8436511c3ad59daf9fedb84a3665e

      Author:  Nalin Arora <nalin21478@iiitd.ac.in> 

      Date: 2026-08-21 14:53:23 -0400

      Commit message:


	  
		
 updated news and description
 
    
  
    

      Package: DAssemble

      Commit: 9fa6bda0b1d43a4403fad48ae016e335673f0660

      Author:  Nalin Arora <nalin21478@iiitd.ac.in> 

      Date: 2026-08-21 14:38:14 -0400

      Commit message:


	  
		
 updated handling of linear separability
 
    
  
    

      Package: DAssemble

      Commit: 07e1605447641211f25f28e6ba670da93259206d

      Author:  Nalin Arora <nalin21478@iiitd.ac.in> 

      Date: 2026-08-21 13:22:19 -0400

      Commit message:


	  
		
 updated support for longitudinal and  multiple covariates
 
    
  
    

      Package: DAssemble

      Commit: fe388a2f6aea6f40ab434b119c88a8d79a45b8f5

      Author:  Nalin Arora <nalin21478@iiitd.ac.in> 

      Date: 2026-07-18 17:41:38 -0400

      Commit message:


	  
		
 Updated bioconductor accepted code
 
    
  
    

      Package: DAssemble

      Commit: b7d557fb312ba5ce9a28947a0a2682f8ca31663d

      Author:  Nalin Arora <nalin21478@iiitd.ac.in> 

      Date: 2026-07-09 19:51:13 -0400

      Commit message:


	  
		
 updated files
 
    
  
    

      Package: DAssemble

      Commit: 6b4585d1f696c704293656e5ea8d34b65393ed37

      Author:  Nalin Arora <nalin21478@iiitd.ac.in> 

      Date: 2026-07-03 09:51:13 -0400

      Commit message:


	  
		
 updated bioc
 
    
  
    

      Package: DAssemble

      Commit: e0d71b7741dcd5891b3c6e1103fad09e3dfeb0c8

      Author:  Nalin Arora <nalin21478@iiitd.ac.in> 

      Date: 2026-06-25 19:42:23 -0400

      Commit message:


	  
		
 updated unit tests
 
    
  
    

      Package: DAssemble

      Commit: 91b2edca67c496c5e138be1de81e0dfe846e334b

      Author:  Nalin Arora <nalin21478@iiitd.ac.in> 

      Date: 2026-06-25 17:16:58 -0400

      Commit message:


	  
		
 updated vignette and citation
 
    
  
    

      Package: DAssemble

      Commit: d5038b5e771dd883c7f118ff77e90364391595b3

      Author:  Nalin Arora <nalin21478@iiitd.ac.in> 

      Date: 2026-06-25 15:36:17 -0400

      Commit message:


	  
		
 updated bioconductor submission files
 
    
  
    

      Package: MSstatsResponse

      Commit: 164c1d1575d5ea83ae05f4c03f820c5e895dd520

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2026-09-04 10:32:22 -0400

      Commit message:


	  
		
 Bump version from 1.3.2 to 1.3.3 
    
  
    

      Package: MSstatsResponse

      Commit: 1a4ee69928178c1d923371f93e14ffde64463025

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2026-08-31 21:07:11 -0400

      Commit message:


	  
		
 refactor(createTurnoverRatios): Speed up code to use data.table (#11) 
    
  
    

      Package: MSstatsResponse

      Commit: 198ef4e0f10a6440ad2655b8ae4ce1f642b2c469

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2026-07-20 21:46:31 -0400

      Commit message:


	  
		
 Update README to include TMT in workflows 
    
  
    

      Package: MSstatsResponse

      Commit: 38de4ce71cd92ad5067245b3b1cf70db7bcad569

      Author:  Tony Wu <wu.anthon@northeastern.edu> 

      Date: 2026-07-20 21:45:31 -0400

      Commit message:


	  
		
 update README with remotes::install
 
    
  
    

      Package: MSstatsResponse

      Commit: 16a19e9a7df3b234e472c2bb1a0dcc296ffceb55

      Author:  Tony Wu <wu.anthon@northeastern.edu> 

      Date: 2026-07-20 21:34:30 -0400

      Commit message:


	  
		
 docs(readme): Update README with up-to-date information
 
    
  
    

      Package: MSstatsResponse

      Commit: 04b021d73d6788991695c1d92da42efa187031f2

      Author:  Tony Wu <wu.anthon@northeastern.edu> 

      Date: 2026-07-20 15:43:05 -0400

      Commit message:


	  
		
 fix(turnover): handle scenarios where L_frac is NA for all timepoints
 
    
  
    

      Package: scrapbook

      Commit: 8d330d15f9cc8a340af13a9a95ee2feb21bcc25a

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-09-11 03:17:10 +1000

      Commit message:


	  
		
 More minor wording changes in the marker detection chapter.
 
    
  
    

      Package: CLAMP

      Commit: 2cefda5f95f2938cb077ed21c298a6116712daa8

      Author:  msubirana <mb2subi@gmail.com> 

      Date: 2026-09-10 10:06:49 -0600

      Commit message:


	  
		
 Bump to 0.99.8: fix normalized whole-blood examples
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: 5ce8b4ed6f5357b860bcffb984bce1e7eb3b6865

      Author:  Andrew Jaffe <andrewejaffe@gmail.com> 

      Date: 2026-08-18 14:17:35 -0400

      Commit message:


	  
		
 Fix reference-data access to preserve minfi::estimateCellCounts compatibility

The initial migration exposed FlowSorted.DLPFC.450k as a plain callable
function. minfi::estimateCellCounts() (and likely other downstream
consumers) accesses reference packages via the historical lazy-data
pattern: data(list = pkg); get(pkg). With a plain function, get(pkg)
returned the function object itself rather than the RGChannelSet,
silently breaking estimateCellCounts.

FlowSorted.DLPFC.450k is now an active binding installed in .onLoad,
so referencing the bare name (matching the old data() usage) downloads
and returns the actual object, caching it for the session. Verified
against a live estimateCellCounts(..., compositeCellType = "DLPFC") run.
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: f6aaf8bede6db56d6cffef2b3064d63a5d3f333b

      Author:  Andrew Jaffe <andrewejaffe@gmail.com> 

      Date: 2026-08-18 13:55:42 -0400

      Commit message:


	  
		
 Move large data object to Zenodo, download via BiocFileCache

The bundled FlowSorted.DLPFC.450k.rda (130MB) exceeded GitHub's file
size limit ahead of Bioconductor's migration off its own git server.
It is now hosted on Zenodo (doi:10.5281/zenodo.21998569) and
downloaded on first use via BiocFileCache, which caches it locally
afterwards. FlowSorted.DLPFC.450k() replaces the former data(...) call.

Also removes the stray external_data_store.txt, adds Authors@R, and
title-cases the Title field to clear R CMD check NOTEs.
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: 15cb32f55d0d0bd6b99a5030439c07f57beed86d

      Author:  Andrew Jaffe <andrewejaffe@gmail.com> 

      Date: 2026-08-18 10:52:09 -0400

      Commit message:


	  
		
 Update maintainer email

andrew.jaffe@libd.org is no longer reachable.
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: 69ad7300d9f0f280e95865454e355cf93442b331

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-04-28 08:26:58 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: 6573f0236eafa54a498b8c197e1c27f750b3b92b

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-04-28 08:26:58 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: 230a32332e5ba239f1d92ca735864eb8ea88f487

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2025-10-29 09:55:00 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: b3477a40f62e534fa140f26fe19c648c035b074c

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2025-10-29 09:55:00 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: c4d4188ac41085ff47770a00c0f8517db07efa24

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2025-04-15 09:54:52 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_21 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: 155abe4459ccb8cef2e154c280bb931260357037

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2025-04-15 09:54:52 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_21 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: dbb60629439a588a927ef4fec379d541786867f3

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2024-10-29 09:38:58 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_20 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: 9c6932ecc057bc697a6a885b183c3e82fd60c144

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2024-10-29 09:38:58 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_20 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: 19e2ad12d0f1cf9625008b3bd0a88b79d2f8284c

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-30 10:41:39 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_19 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: 3d2f4748f5601fee18ec5648cb3bea738763af20

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-30 10:41:39 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_19 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: bbb9c584eaed6a0a80a1e5c0e340bb78df01bbc5

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2023-10-24 09:08:00 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_18 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: e232946696892dd250e0767ed98fbd0c4dba3431

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2023-10-24 09:08:00 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_18 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: a7338c3480ec1e2845bda6056a70389d2b8ffdd2

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2023-04-25 10:35:41 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_17 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: 819f6baee3293feb6d26f05c47f4891d440d2fef

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2023-04-25 10:35:41 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_17 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: f5da622b24a83b927277b660426e3069aae956be

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2022-11-01 11:01:01 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_16 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: fce417de061b6985f751d00064e58b5c23529d3a

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2022-11-01 11:01:01 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_16 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: ced8387cb470d2d816a969fc758e552560afd474

      Author:  J Wokaty <jwokaty@users.noreply.github.com> 

      Date: 2022-04-26 17:14:09 +0000

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_15 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: 587379588d03178cc0a68db27ce15db5151144e4

      Author:  J Wokaty <jwokaty@users.noreply.github.com> 

      Date: 2022-04-26 17:14:09 +0000

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_15 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: fd9fa33cdfccf5cd968e17d74fcddc308adb8cc5

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2021-11-21 21:39:37 -0500

      Commit message:


	  
		
 Pass serialized S4 instances thru updateObject()
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: 781b9c024c05e14f907af1a6409541b6c5a422e9

      Author:  J Wokaty <jwokaty@users.noreply.github.com> 

      Date: 2021-10-26 12:09:04 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_14 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: 289925a5485a096d29961f972577e58a85fdaad0

      Author:  J Wokaty <jwokaty@users.noreply.github.com> 

      Date: 2021-10-26 12:09:04 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_14 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: b2b6ec5f5297e14d7a379fddee6909dce9def734

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2021-05-19 11:47:06 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_13 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: 69c5d4d5663d875e0941039ff4cce43dcf39cc02

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2021-05-19 11:47:05 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_13 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: 22af035a567acd8feb52992ba97385f652d0189c

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2020-10-27 10:08:55 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_12 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: df7716bc207b7474b7904541e1ebeac332bef6ac

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2020-10-27 10:08:55 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_12 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: ceecd951e0e3a49ee53128f4c70f8c5f8e2dc242

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2020-04-27 15:28:21 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_11 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: 42e7ccf42e20af52e034107c4ed91f35e77f98c5

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2020-04-27 15:28:21 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_11 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: 623273a5a370199df1e4e36169ec688210f0fa5e

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2019-10-29 13:37:02 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y after creation of RELEASE_3_10 branch
 
    
  
    

      Package: FlowSorted.DLPFC.450k

      Commit: 8374a96ecf60eb64840ffc34b4425076fa86aaf8

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2019-10-29 13:29:42 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_10 branch
 
    
  
  


</div>

</div>