fixed a redundant code
 

 update NEWS.md
 

 avoid requesterpays errors with true public dataset in examples
 

 shQuote all args in gsutil_pipe
 

 protect against multiple length result in gsutil_requesterpays
 

 fix function name to match actual value for gcloud_project
 

 add compress_json.sh script
 

 bump
 

 Bump version
 

 Bump version
 

 bugfix

Signed-off-by: xuz1 <xuz@niehs.nih.gov>
 

 Removing R/zzz.R from Collate
 

 Removing deprecat ion notification
 

 Merge remote-tracking branch 'upstream/devel'
 

 Version bump devel to 1.44.1
 

 Removing deprecation notification
 

 Just use MulticoreParam and its fallback
 

 register snowparam
 

 no more multithreading in vignet buiilding on windiows
 

 Switch off multithreading on windows in vignette
 

 docs: link yamtk and pitch scan_sequences2() in the vignette

- vignettes/SequenceSearches.Rmd: add a "A faster alternative:
  scan_sequences2()" subsection with a baked-in four-way speed
  comparison (yamtk scan, motifmatchr matches, motifmatchr positions,
  scan_sequences2, scan_sequences with calc.pvals=TRUE) on a 50-motif
  HOCOMOCOv11 fixture at p=5e-5. Numbers are not recomputed at
  vignette build time; the source scripts live under benchmarks/.

- R/scan_sequences.R: add a one-line note in the function title
  pointing DNA/RNA users at scan_sequences2().

- R/scan_sequences2.R, R/dedup_hits.R: link the yamtk URL
  (https://github.com/bjmt/yamtk) at the first descriptive mention,
  add @references entries for yamtk, and tighten the docstring
  wording.

Regenerated man/*.Rd via devtools::document().
 

 add dedup_hits(): yamtk-style greedy overlap dedup

dedup_hits() removes overlapping motif hits within each
(sequence, motif, strand) group using the same algorithm as
`yamtk dedup` (yamtk/src/yamdedup.c): a single linear sweep
identifies clusters by running max-end, then within each cluster
hits are sorted by priority (descending) with ties broken by
input order, and a greedy pass keeps the first hit plus any
later hit that does not overlap an already-kept hit.

This is intentionally different from scan_sequences()'s existing
no.overlaps argument, which uses hierarchical clustering on the
full pairwise overlap matrix and collapses every connected-
overlap component to a single survivor. The greedy approach
implemented here keeps legitimately distinct hits even when a
noisy intermediate bridges them. Worked example:

  [1-5, p=1e-10], [3-7, p=1e-8], [6-9, p=1e-9]

  scan_sequences (CC): keeps {1-5}
  dedup_hits (greedy): keeps {1-5, 6-9}

scan_sequences's existing no.overlaps is untouched.

API:

  dedup_hits(hits,
             by            = "pvalue",   # or "score"
             reverse       = FALSE,
             ignore.strand = FALSE,
             ignore.motif  = FALSE,
             ...)

Auto-detects priority direction from column name (pval* ->
lower is better; everything else -> higher is better). Accepts
both data.frame and GRanges; returns the same shape.

scan_sequences2() gains four optional arguments that wire up to
dedup_hits():

  no.overlaps           = FALSE
  no.overlaps.by        = c("pvalue", "score")
  no.overlaps.by.strand = FALSE  # TRUE -> +/- compete
  no.overlaps.by.motif  = FALSE  # TRUE -> motifs compete

Implementation: ~140 lines of C++ (src/dedup_hits.cpp). One Rcpp
export, dedup_hits_cpp(); no threading -- the sweep is fast
enough that thread setup would dominate.

Complexity: O(N log N) overall (dominated by the index sort);
O(K log K) per cluster (K = cluster size, typically 1 or 2);
O(1) extra memory beyond the index permutation. Compared with
scan_sequences's O(N^2 log N) hclust-based implementation.

Verification:
- 16 unit tests in test_dedup_hits.R: hand-computed greedy
  semantics (incl. the disambiguator above), ties, ignore-flag
  combinations, GRanges round-trip, touching/adjacent coord
  edges, empty input, integration with scan_sequences2.
- Cross-check vs `yamtk scan | yamtk dedup` on 50 HOCOMOCO
  motifs x 100 x 5kb random DNA at p=5e-5: 94.6% hit-set
  overlap, same as the un-deduped baseline (the residual is the
  documented PCM-rounding drift in PWM construction).
- Negligible runtime overhead vs scan_sequences2 without dedup
  (1.69s vs 1.64s on the same fixture).
 

 batch the dynamic motif_pvalue path into a single C++ call

motif_pvalue(method="dynamic") previously dispatched per-motif via
mapply(motif_pvalue_dynamic_single_cpp, ...) in R, leaving the
documented `nthreads` argument as a no-op on this path (TODO at
R/motif_pvalue.R:497).

Add two new Rcpp exports in src/motif_pvalue.cpp:

  motif_pvalue_dynamic_batch_cpp(motifs, bkgs, scores,  nthreads)
  motif_score_dynamic_batch_cpp (motifs, bkgs, pvalues, nthreads)

Both pre-extract Rcpp list/matrix inputs into plain std types
serially, then parallelise across motifs with RcppThread::parallelFor
using new plain-std workers (get_pdf_internal, motif_cdf_internal,
pvalue_from_cdf, score_from_cdf). The existing single-motif exports
are left untouched, so any caller still pointing at them continues
to work.

The R helpers motif_pvalue_dynamic() / motif_score_dynamic() are
rewritten as thin wrappers around the new batched entry points and
now accept nthreads, which the motif_pvalue() top-level forwards
through. No public API change.

Results are bit-identical to the previous per-motif path
(`identical()` on a small fixture, both nthreads=1 and nthreads=4)
-- new regression tests in tests/testthat/test_motif_pvalue.R lock
this in.

Performance on 50 HOCOMOCO motifs x 100 x 5kb random DNA
(scan_sequences2, end-to-end):

  pre-batch:  3.77s (nthreads=1)   3.56s (nthreads=4, no scaling)
  post-batch: 1.64s (nthreads=1)   0.48s (nthreads=4, 3.4x)

i.e. 2.3x faster single-threaded and 7.4x faster at 4 threads.
The same speedup applies to scan_sequences(calc.pvals=TRUE) which
shares the same code path.
 

 Bump version
 

 Bump version
 

 Allow oversized chunks (with a warning)

As required by, e.g., anndataR for their nullable arrays
 

 Minor UI changes to `mergeByHMP()` and `addDiffStatus()`
 

 Updated the vendored version of singlepp.
 

 make vignettes chunks runable
 

 Acceleration.
 

 chore: auto-update internal data in sysdata.rda
 

 support shinysever #3
 

 update bioc version
 

 added buffer size for io in cellCounts
 

 added buffer to temp_fp.
 

 prevent general user from using the devel cellCounts
 

 Merge branch 'devel' of https://github.com/gallardoalba/TSENAT into devel
 

 Merge branch 'stable' into devel 

 Increase coverage
 

 Fix name of Xenium example in fetch_data() calls
 

 update NEWS

Co-authored-by: Gemini 3.5 Flash <gemini-assistant@google.com>
 

 update NEWS.md

Co-authored-by: Gemini 3.5 Flash <gemini-assistant@google.com>
 

 v1.25.1 -- `vis_*()` functions and `run_app()` now support visualizing Xenium data. `fetch_data()` now includes example Xenium data.
 

 Update fetch_data() for the spe_xenium_example data
 

 Fix several things about the Xenium support in
vis_clus(), vis_gene() and related functions.

Fix examples.
 

 vis_gene already inherits params from vis_clus
 

 get datatype arg in app_ui and app_server
 

 Add datatype as param to run_app - update docs
 

 fix spe_xenium_example name
 

 Add xenium example, fix auto_crop
 

 Fix typo
 

 Update docs
 

 Bump date and version
 

 Fix cross link in docs (vis_gene_c not defined yet)
 

 fix example, redefine d
 

 use vis_clus_c for xenium datatype
 

 clean up vis_clus_c example
 

 Add xenium example to experimenthub metadata for LFF ERC
 

 Update desciptions for vis_clus_*() functions
 

 Add datatype param, check for correct input formats
 

 Fix codefactor style
 

 Increase test coverage
 

 Bioconductor submission review
 

 Add zenodo example
 

 igblastr 1.3.3: Update the built-in C-region dbs

This follows major updates of the artificially spliced exons sets for IG
and TR constant genes by the IMGT folks in Dec 2025. Note that these sets
are available here: https://www.imgt.org/vquest/refseqh.html#constant-sets

With this update, the new set of built-in C-region dbs is:

    > list_c_region_dbs()
     db_name                                      C
     _IMGT.human.IGH+IGK+IGL.202605             180
     _IMGT.human.TRA+TRB+TRG+TRD.202605          23
     _IMGT.mouse.IGH+IGK+IGL.202605              64
     _IMGT.mouse.TRA+TRB+TRG+TRD.202605          13
     _IMGT.rabbit.IGH+IGK+IGL.202605             50
     _IMGT.rabbit.TRA+TRB+TRG+TRD.202605          6
     _IMGT.rat.IGH+IGK+IGL.202605                25
     _IMGT.rhesus_monkey.IGH+IGK+IGL.202605      44
     _IMGT.rhesus_monkey.TRA+TRB+TRG+TRD.202605  10

The old set was:

    > list_c_region_dbs()
     db_name                                  C
     _IMGT.human.IGH+IGK+IGL.202412          76
     _IMGT.human.TRA+TRB+TRG+TRD.202509      12
     _IMGT.mouse.IGH.202509                  55
     _IMGT.mouse.TRA+TRB+TRG+TRD.202509       9
     _IMGT.rabbit.IGH.202412                 28
     _IMGT.rat.IGH.202508                    18
     _IMGT.rhesus_monkey.IGH+IGK+IGL.202509  40

CONDITIONS OF USE AND LICENSE: The IMGT data is provided to the academic
users and NPO's (Not for Profit Organization(s)) under the CC BY-NC-ND 4.0
license. See https://creativecommons.org/licenses/by-nc-nd/4.0/. Any other
use of IMGT material, from the private sector, needs a financial arrangement
with CNRS.
 

 simplify .cord_blood code
 

 run air on CITEseq.R
 

 updated SCMM package doc from roxygen2 v8
 

 update to roxygen2 v8
 

 Set noRd on internal function
 

 Mention deprecated v3 structured type in NEWS
 

 Implement deprecated v3 structured data type
 

 version bump
 

 Merge pull request #140 from csoneson/set-nthreads

Pass on `nthreads` to `xgboost` functions in `scDblFinder` 

 version bump for bug correction
 

 Bumped-up version and updated NEWS.md
 

 Avoid irrelevant lintrs in data-raw/
 

 Bump version
 

 Use list approach for parsing v3 datatypes
 

 Remove now unused C code
 

 Use parse_npy_datatype() directly
 

 Convert v2 structured types to v3 structured types
 

 Avoid wrapping config in one extra string
 

 Replace (mostly) .parse_datatype by grumpy::parse_npy_datatype()
 

 Merge pull request #8 from BorchLab/bioc-review2

Bioc review2 

 Update documentation
 

 vignette eval
 

 Bump version
 

 Use spec-defined v3 names for S and U types
 

 Mention read_metadata refactor in NEWS
 

 Set s3_client default to NULL
 

 Use %||% in more places
 

 Merge pull request #25 from drake69/refactor/enrichment-ctd-symmetric-dispatch

refactor: unified output schema + symmetric dispatch architecture 

 refactor: unify enrichment output schema across ORA/GSEA/CAMERA

Builds on the symmetric-dispatch refactor by also harmonizing the
public column schema across the three data-frame-returning methods.
Pre-1.0 + pre-Bioconductor-acceptance is the right moment to land a
breaking rename; doing it later would force a real API break.

Architecture
------------

* .format_enrichment_result() is now the single source of truth for
  the engine -> canonical mapping. Each runner declares a
  `rename = c(old = "New")` + `drop = c(...)` and the formatter
  handles all post-processing: padj recomputation, metadata merge,
  column ordering, sort, row-name reset, plus the new Method column.
* gsea() and ora() engines emit native fgsea / clusterProfiler
  column casing (pval / pvalue / ES / NES / size / leadingEdge etc.)
  but lift their primary-key column (pathway / ID) to the
  semantically correct "ChemicalID" right at the engine boundary so
  internal callers never see a misleading generic name.
* The Method column ("ORA" / "GSEA" / "CAMERA") is stamped by the
  formatter so result frames can be rbind / bind_rows'd across
  methods without losing provenance.

Public schema (breaking)
------------------------

Shared front columns (all three methods):
    ChemicalID, ChemicalName, Method, PValue, PValueAdjusted

Input column rename (ORA / GSEA data frame):
    entrez_ids  -> EntrezID

Cross-method canonical aligns:
    pval / pvalue            -> PValue
    padj / p.adjust          -> PValueAdjusted
    size (GSEA) / NGenes (CAMERA) -> GeneSetSize
    geneID (ORA) / Enriched_GENE (GSEA) -> EnrichedGenes
    ES / NES                 -> EnrichmentScore / NormalizedEnrichmentScore
    BgRatio / qvalue / foldEnrichment / leadingEdge ->
        BackgroundRatio / QValue / FoldEnrichment / LeadingEdge

Removed: Description (ORA, was always == ID), FDR (CAMERA,
PValueAdjusted is recomputed under the requested pAdjustMethod).

Other changes
-------------

* Vignette restructured: new "Shared output schema" section listing
  the five common columns; per-method sub-sections now show only
  method-specific extras.
* NEWS.md expanded with the full breaking-change rename table.
* plot_CTD updated to read PValueAdjusted / GeneSetSize / FoldEnrichment.
* .run_camera() shrank to 45 lines (was 57). BiocCheck "function
  length > 50" NOTE is now satisfied for the enrichment-table
  pipeline (plot_CTD / .plot_camera remain over the limit but are
  unrelated to this refactor; tracked for a separate PR).
* Full test suite: 123 PASS / 0 FAIL.
 

 Merge pull request #24 from drake69/fix/ci-bioccheck-devel-and-shell-guard

fix(ci): close BiocCheck gap (devel BiocCheck + shell guard) 

 fix(ci): assert BiocCheck >= 1.49.0 after install

If Bioconductor renames version = "devel" or the BiocManager mirror
falls back to a release version, the previous install step would
silently succeed with an older BiocCheck that lacks the tracked-system-
files check — exactly the regression this PR was created to prevent.

Add an explicit compareVersion() guard that aborts the job with a clear
error if the resolved BiocCheck is < 1.49.0.
 

 Merge pull request #22 from drake69/chore/biocheck-notes-cleanup

chore: address BiocCheck notes (R 4.6.0 dep, roxygen line widths) 

 Merge pull request #21 from drake69/fix/biocheck-rproj-tracked

fix: untrack ctdR.Rproj and add BiocCheckGitClone to CI 

 need  in cpp
 </pre>
    </div>
  
    

      Package: scran

      Commit: 569d2f89d928451efa912f52f213af2f47c3a695

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

      Date: 2026-05-20 15:24:08 +1000

      Commit message:


	  
		
 Removed the deprecated convertTo function and its dependencies.
 
    
  
    

      Package: scran

      Commit: a6f180625067e4cab7ce240673f0b12c977b0518

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

      Date: 2026-05-20 15:21:14 +1000

      Commit message:


	  
		
 Minor fixes to stop roxygen from complaining.

Also bumped version and date for a new release.
 
    
  
    

      Package: scran

      Commit: 8499bb86f879afa0f47341066e554e635bcaf880

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

      Date: 2026-05-20 14:08:26 +1000

      Commit message:


	  
		
 List deprecated functions in NEWS, added missing deprecation warnings.
 
    
  
    

      Package: igblastr

      Commit: d4c5a0002c765574554db402c42ccac925ad8753

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

      Date: 2026-05-19 22:41:43 -0700

      Commit message:


	  
		
 Add combine_c_region_dbs() to combine two existing C-region dbs
 
    
  
    

      Package: mastR

      Commit: 1e1d3c67119589e38a251e1316ba92d4acc6e4d8

      Author:  Gene233 <chen_jj97@163.com> 

      Date: 2026-05-20 11:58:30 +1000

      Commit message:


	  
		
 version bump.
 
    
  
    

      Package: mastR

      Commit: 59cd91a5401d3911452b583190a2f0d0be27c19c

      Author:  Gene233 <chen_jj97@163.com> 

      Date: 2026-05-20 11:27:23 +1000

      Commit message:


	  
		
 Update vignette name.
 
    
  
    

      Package: igblastr

      Commit: 156fdceaab25278ec7d22449376d2b187dc434b5

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

      Date: 2026-05-19 16:26:12 -0700

      Commit message:


	  
		
 Fix "inconsistent counts" issue

With this fix, the following counts are now correct:

    db_name <- install_IMGT_germline_db("202614-2", "Homo_sapiens",
                                        tcr.db=TRUE)
    all_counts <- list_germline_dbs(long.listing=TRUE)  # long listing
    colSums(all_counts[[db_name]])
    #   V   D   J
    # 355   6 101

More generally speaking, this fix makes sure that the counts reported
by list_germline_dbs()'s and list_c_region_dbs()'s long listings are
consistent with the counts reported by their short listings.
 
    
  
    

      Package: GSVA

      Commit: 6e03805de6899da4a82ef1a069f554177a68930c

      Author:  Robert Castelo <robert.castelo@upf.edu> 

      Date: 2026-05-19 19:07:39 +0200

      Commit message:


	  
		
 Fixed typo
 
    
  
    

      Package: GSVA

      Commit: 401c519027a90a88539737d838fbed387ec436e9

      Author:  Robert Castelo <robert.castelo@upf.edu> 

      Date: 2026-05-19 18:46:39 +0200

      Commit message:


	  
		
 Fixed memory usage
 
    
  
    

      Package: CellMentor

      Commit: 4a5f4ff1b6db6f4265c3f0bf688b09634d90df4f

      Author:  Petrenko Kate <petrenko.kate@icloud.com> 

      Date: 2026-05-19 17:07:24 +0300

      Commit message:


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

# Conflicts:
#	DESCRIPTION
 
    
  
    

      Package: CellMentor

      Commit: d784aaf0af55e22f36a6962c1ffa99d827d54fae

      Author:  Petrenko Kate <petrenko.kate@icloud.com> 

      Date: 2026-05-19 17:04:01 +0300

      Commit message:


	  
		
 Fix vignette build failure on Bioconductor build farm; bump to 1.1.1

The Bioconductor build farm vignette was hitting a cryptic
"switch() EXPR must be a length 1 vector" error because cluster_nmf()
fails on the low-dimensional NMF embeddings produced during grid
search (Seurat 5 Assay5 validation rejects 1-row inputs, and the
kmeans fallback failed its own range check on tiny test splits).
The error was being swallowed by evaluate_params()'s tryCatch, then
which.max(c(NA, NA)) cascaded to a 0-length init_method passed to
switch().

* cluster_nmf(): handle small h_project gracefully (fall back to
  kmeans when n_features < 10 or n_cells < 10, clamp centers to
  feasible range, return trivial clustering when n_cells <= 1).
* CellMentor(): stop with a clear error if every grid configuration
  fails, instead of cascading to the cryptic switch() error.
* evaluate_params(): include conditionMessage(e) in the warning so
  build logs surface the real cause of any future failure.
* initialize_wh(): validate that method is a single character string.
* Update citation to the published Nat Commun 2026 paper
  (doi:10.1038/s41467-025-67088-7) in vignette, README, and a new
  inst/CITATION file.
* Refresh README "Expected Output" blocks to be illustrative (the
  underlying scRNAseq Baron/Muraro snapshot has drifted, so the
  hardcoded counts and k=80 no longer reflect current behavior).
* Add subset-scope disclaimer to the vignette: every downstream
  result (rank, NMI, UMAP) is computed on the 30-cells-per-type
  subset, not the full datasets.
* .gitignore: ignore local vignette HTML previews.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: GSEAlens

      Commit: e6a780fd24ed59d48df8a479bfbdb2c7af31fda0

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-05-19 21:36:52 +0800

      Commit message:


	  
		
 Bump version to 0.99.3 for BiocCheck push trigger
 
    
  
    

      Package: GSEAlens

      Commit: 46e860d90bc969396675c0533dec9d5cff296a99

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-05-19 21:35:18 +0800

      Commit message:


	  
		
 Remove GSEAlen.Rproj from Git tracking (BiocCheck fix)
 
    
  
    

      Package: GSEAlens

      Commit: b968bbf7a6890c2465be5167b91d67d05c3746c4

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-05-19 21:22:14 +0800

      Commit message:


	  
		
 Bump version to 0.99.2
 
    
  
    

      Package: GSEAlens

      Commit: f7b7d6a157b30d50b5b4067afdb5147a3842c713

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-05-19 20:33:23 +0800

      Commit message:


	  
		
 Change UI back
 
    
  
    

      Package: GSEAlens

      Commit: 64103fcc0646ca3179446c8dc789e4e3061e9b6b

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-05-19 20:27:26 +0800

      Commit message:


	  
		
 UI: simplify Gene Expression Table title in quadrant module
 
    
  
    

      Package: GSEAlens

      Commit: d0e603faecf0be33b54adcc5bbf85b448ab32a45

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-05-19 20:20:24 +0800

      Commit message:


	  
		
 Fix: use enrichit instead of enrichplot for gseaScores

enrichit is the source package that actually contains gseaScores function
 
    
  
    

      Package: GSEAlens

      Commit: e0ef3fa13769a110955b6385004f52128062ba81

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-05-19 17:08:27 +0800

      Commit message:


	  
		
 Fix: use enrichplot instead of DOSE for gseaScores

enrichplot >= 4.5.1 reexports gseaScores from enrichit package
 
    
  
    

      Package: GSEAlens

      Commit: 1792a2d5a474c9ec59f47faa0cedda9379acdf03

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-05-19 15:52:46 +0800

      Commit message:


	  
		
 fix RPROJ formatting UTF8
 
    
  
    

      Package: GSEAlens

      Commit: a6ab696218b9dd598ca7b254e631de615126c27a

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-05-19 15:48:26 +0800

      Commit message:


	  
		
 Fix GSEAlens.Rproj formatting
 
    
  
    

      Package: GSEAlens

      Commit: e785e9f0a4540b2fc215be3a9a7e6846529e6d47

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-05-19 15:44:01 +0800

      Commit message:


	  
		
 Restore GSEAlens.Rproj with correct encoding, remove from .gitignore
 
    
  
    

      Package: GSEAlens

      Commit: 724a5686d3fd9ce4fa147405ebd9e858ab2449bc

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-05-19 15:29:05 +0800

      Commit message:


	  
		
 Fix get_sample_meta undocumented obj param, fix .gitignore trailing newline
 
    
  
    

      Package: pathRender

      Commit: 5704b22fb890696a1253eef2e1e6e7067b3b9dfd

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

      Date: 2026-05-19 08:28:26 -0400

      Commit message:


	  
		
 deprecate
  - requested see #questions on team slack channel
 
    
  
    

      Package: limma

      Commit: dd95cdf2b2c8b4e60dc8934acc5a7e47b90eb441

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

      Date: 2026-05-19 22:17:52 +1000

      Commit message:


	  
		
 limma 3.69.1

- Fix filtering error in Agilent rat case study in User's Guide.
- Update references in User's Guide and help pages.
- Update URLs in help pages.
 
    
  
    

      Package: lemur

      Commit: 376f2f91309a5b15c19d6eb5e37ac6d99a2d3b88

      Author:  Wolfgang Huber <wolfgang.huber@embl.org> 

      Date: 2026-05-19 11:42:28 +0200

      Commit message:


	  
		
 version number bump
 
    
  
    

      Package: lemur

      Commit: 3fe72f47abe042060183e3ccc3605907d891ef68

      Author:  Wolfgang Huber <wolfgang.huber@embl.org> 

      Date: 2026-05-19 11:41:38 +0200

      Commit message:


	  
		
 Renaming things
 
    
  
    

      Package: lemur

      Commit: 13c7a9eea7769a81f04beeee8a006631d4192d8d

      Author:  Wolfgang Huber <wolfgang.huber@embl.org> 

      Date: 2026-05-19 11:40:11 +0200

      Commit message:


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

      Package: lemur

      Commit: 18f1d2b2c2157ea799947de395d40e173c532261

      Author:  Wolfgang Huber <wolfgang.huber@embl.org> 

      Date: 2026-05-14 12:42:03 +0200

      Commit message:


	  
		
 Merge pull request #28 from Bisaloo/citation

Update CITATION to published paper 
    
  
    

      Package: lemur

      Commit: 36e4d162a7d8088af0cee847edc783ff850c7946

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-26 17:54:34 +0100

      Commit message:


	  
		
 Update CITATION to published paper
 
    
  
    

      Package: lemur

      Commit: fae5c9e36ec573036c9160d0bc5ed9d0729889b8

      Author:  Wolfgang Huber <wolfgang.huber@embl.org> 

      Date: 2026-03-20 15:59:53 +0100

      Commit message:


	  
		
 Fixed some typos and wordings in the vignette
 
    
  
    

      Package: lemur

      Commit: c07d940244cb1402331789edc5924d1c84f082dd

      Author:  Wolfgang Huber <wolfgang.huber@embl.org> 

      Date: 2026-03-20 14:18:17 +0100

      Commit message:


	  
		
 Missed these two from the previous commit
 
    
  
    

      Package: lemur

      Commit: 1a19cd631ea3c45efab2fca3d41405176ebbb61b

      Author:  Wolfgang Huber <wolfgang.huber@embl.org> 

      Date: 2026-03-20 14:17:21 +0100

      Commit message:


	  
		
 adding the name compute_contrasts for a function that has been called test_de
 
    
  
    

      Package: lemur

      Commit: 931731f9cd0293ad982694a52967d7ec1b394630

      Author:  Wolfgang Huber <wolfgang.huber@embl.org> 

      Date: 2026-03-20 10:25:48 +0100

      Commit message:


	  
		
 more wording improvements
 
    
  
    

      Package: lemur

      Commit: 01a946511046e567cd67e93af073b590ea49e64e

      Author:  Wolfgang Huber <wolfgang.huber@embl.org> 

      Date: 2026-03-20 10:13:21 +0100

      Commit message:


	  
		
 Wording refinements
 
    
  
    

      Package: lemur

      Commit: e3e2769c909df5b3130051a05066bbbda5df29e4

      Author:  Wolfgang Huber <wolfgang.huber@embl.org> 

      Date: 2026-03-20 09:35:48 +0100

      Commit message:


	  
		
 Fixed Intro
 
    
  
    

      Package: mesa

      Commit: ec003e99afbe1f85c5aa644a2ac6d43e4513e067

      Author:  Felipe <92517493+fpmartinez10@users.noreply.github.com> 

      Date: 2026-05-18 17:23:17 +0100

      Commit message:


	  
		
 Fixes Bioconductor Package Builder TIMEOUT in R CMD check and bump to version 0.99.2 (#74)

* fix: wrap slow examples in donttest, convert dontrun to donttest

- Wrap all slow @examples (>5s) in \donttest{} to fix R CMD check TIMEOUT:
  PCA.R, makeQset.R, qseaExtra.R, plotting.R, analyseDMRs.R,
  calculateEnrichment.R
- Convert \dontrun{} to \donttest{} per BiocCheck NOTE:
  qseaCNV.R, utilityFunctions.R, alterQset.R, mixQsets.R,
  calculateEnrichment.R
- Remove duplicate @examples block in plotRegionsHeatmap (plotting.R)

* bump version to 0.99.2, update NEWS for #74

* docs: donttest changes documented in man/ files

* Remove editor options from NEWS.md

Removed editor options for markdown wrapping.

---------

Co-authored-by: fperezmartinez <felipe.perezmartinez@manchester.ac.uk> 
    
  
    

      Package: scrapper

      Commit: defe76d3933ce25103f33e82d79745398f63d912

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

      Date: 2026-05-19 19:34:26 +1000

      Commit message:


	  
		
 Bumped version and date, updated NEWS.
 
    
  
    

      Package: scrapper

      Commit: aac7d6e99cc9a1b6f464126a6ec8a305270c2c54

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

      Date: 2026-05-19 19:34:02 +1000

      Commit message:


	  
		
 Protect C++ code against NA values in the factors.

Otherwise we'd get a segfault from attempting to access -2^31.
 
    
  
    

      Package: scrapper

      Commit: 158e1f607240299b02e245da6461f80e9c59e16c

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

      Date: 2026-05-19 17:50:52 +1000

      Commit message:


	  
		
 Overwrite existing columns in *.se() functions instead of using cbind.

The latter just adds more columns of the same name, which leads to weird
results when trying to extract the most recent results as the $ operator
will fetch the first occurrence of each column name.

Now, by overwriting columns, functions that generate multiple result columns
are consistent with those that just add a single column.
 
    
  
    

      Package: scrapper

      Commit: 52ccd13606a18655cbe1793f10ae567e2cd0898e

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

      Date: 2026-05-19 16:41:43 +1000

      Commit message:


	  
		
 Officially make analyze() and convertAnalyzeResults() defunct.

They weren't being tested anyway, so might as well remove them.
 
    
  
    

      Package: BgeeCall

      Commit: 9561289df106767f63ca3b9e5dbde5a563ce7951

      Author:  Julien Wollbrett <julien.wollbrett@unil.ch> 

      Date: 2026-05-19 09:58:51 +0200

      Commit message:


	  
		
 update import of rslurm package
 
    
  
    

      Package: BgeeCall

      Commit: 3b6f317b4fcce35fd858ce4a9e674a1dd8cca4c7

      Author:  Julien Wollbrett <julien.wollbrett@unil.ch> 

      Date: 2026-05-19 09:58:21 +0200

      Commit message:


	  
		
 update documentation for galaxy wrapper function
 
    
  
    

      Package: GSEAlens

      Commit: f390b28a56b3e53500ad1e9db4efe140e4feb5ca

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-05-19 08:38:05 +0800

      Commit message:


	  
		
 Bump version to 0.99.1
 
    
  
    

      Package: GSEAlens

      Commit: 56e6ccd7e419f9eef2825b9b21b298413d5f2b15

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-05-19 08:30:37 +0800

      Commit message:


	  
		
 更新内容清理
 
    
  
    

      Package: GSEAlens

      Commit: b7f338607b361dfcee9e61b50fba9a2abee8aa1f

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-05-19 08:17:22 +0800

      Commit message:


	  
		
 Fix BiocCheck issues: add runnable examples, remove inst/doc HTML, fix DESCRIPTION"
 
    
  
    

      Package: GSEAlens

      Commit: 7afc091bd70078a140b9068ca2d8860eaea3fd41

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-05-19 06:10:37 +0800

      Commit message:


	  
		
 2026_05_19_update_2
 
    
  
    

      Package: GSEAlens

      Commit: 8bc3625c9574da1fba812c45c6b1a2247a754b14

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-05-19 06:02:40 +0800

      Commit message:


	  
		
 2026_05_19_update_1
 
    
  
    

      Package: GSEAlens

      Commit: 13ee0b7fa343b09e03c03834485c0d339f5f809b

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-05-19 05:45:27 +0800

      Commit message:


	  
		
 Merge branch 'master' of https://github.com/DDL095/GSEAlens
 
    
  
    

      Package: GSEAlens

      Commit: 1f4b12ab0599fb9c1d511f6a277e9ff36c807e23

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-03-21 02:54:40 +0800

      Commit message:


	  
		
 2026-03-21-025435 提交忽视文件
 
    
  
    

      Package: dnaEPICO

      Commit: 79c65e2dee8e17946b72db4a0210d1b972c86d1e

      Author:  Paul Ruiz <ruizpint@qut.edu.au> 

      Date: 2026-05-19 09:34:51 +1000

      Commit message:


	  
		
 Bioconductor 0.99.18 Makefile
 
    
  
    

      Package: VisiumIO

      Commit: 3380deea052655fa60fbbd181304e66ba8d0af45

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-18 16:20:50 -0400

      Commit message:


	  
		
 version bump 1.9.5
 
    
  
    

      Package: VisiumIO

      Commit: 4e88893151e6f595c0cb3f643e9a35f842930134

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-18 16:20:44 -0400

      Commit message:


	  
		
 minor update to binSize slot doc
 
    
  
    

      Package: VisiumIO

      Commit: 14ccf79f4a3da98d53b08f9a9db2a021bc82396b

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-18 16:20:25 -0400

      Commit message:


	  
		
 allow empty strings for tissuePos slot instead of NULL
 
    
  
    

      Package: VisiumIO

      Commit: c339286816a2593df15e854358a0b932d3241c9b

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-18 15:40:32 -0400

      Commit message:


	  
		
 version bump 1.9.4
 
    
  
    

      Package: VisiumIO

      Commit: 74dd629fbe927464391014233e08729036067b98

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-18 15:40:27 -0400

      Commit message:


	  
		
 check that bin_size is a three digit string when provided
 
    
  
    

      Package: motifbreakR

      Commit: d7c85a36e867742616f9a234f4b295f3820cf37c

      Author:  Simon-Coetzee <coetzee@uthscsa.edu> 

      Date: 2026-05-18 14:40:42 -0500

      Commit message:


	  
		
 Bump for build
 
    
  
    

      Package: motifbreakR

      Commit: 01d43e4be7abc8591c036d297e11f71ae977b467

      Author:  Simon-Coetzee <coetzee@uthscsa.edu> 

      Date: 2026-05-18 14:38:09 -0500

      Commit message:


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

      Package: motifbreakR

      Commit: c883eaab4a05a1f8a3418ed48adfede6d0a6b45e

      Author:  Simon-Coetzee <coetzee@uthscsa.edu> 

      Date: 2026-05-18 14:34:04 -0500

      Commit message:


	  
		
 Add reference to BSgenome hg19
 
    
  
    

      Package: ChIPQC

      Commit: 1ba474cc16525104a5074882c7bdf382ce814ac3

      Author:  Rory Stark <bioconductor@starkhome.com> 

      Date: 2026-05-18 20:22:31 +0100

      Commit message:


	  
		
 1.49.3: add package anchors to Rd cross-references

Doc-only fix for the "Found Rd file(s) with Rd \link{} targets
missing package anchors" R CMD check NOTE. Mirrors the
RELEASE_3_23 fix (commit 3324b04, version 1.48.3). 9 man/*.Rd
files updated. No code change.
 
    
  
    

      Package: VisiumIO

      Commit: 8b7129588727f115271e98d68c931fa6d9c0c353

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-18 15:18:07 -0400

      Commit message:


	  
		
 version bump 1.9.3
 
    
  
    

      Package: VisiumIO

      Commit: ef8ea6601b8491f22adb65331db4b25233c69c40

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-18 14:35:42 -0400

      Commit message:


	  
		
 update to roxygen2 v8
 
    
  
    

      Package: VisiumIO

      Commit: 21e6bad0bebfba773172ead82609e76dcc27fb5f

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-18 14:29:23 -0400

      Commit message:


	  
		
 set bin_size default to "" or character(1) and allow custom resolutions
 
    
  
    

      Package: barmixR

      Commit: 263669ca2e12b031d900505004161000042b1356

      Author:  Mohammad Darbalaei <125902532+MohammadDarbalaei@users.noreply.github.com> 

      Date: 2026-05-18 17:04:34 +0200

      Commit message:


	  
		
 Fix timeout issues and update to 0.99.1
 
    
  
    

      Package: smoothclust

      Commit: 76b863ed5ef27dd6503d036912716f43dfd8c75c

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-04-28 15:55:46 -0400

      Commit message:


	  
		
 Merge branch 'apr2026-updates' into devel
 
    
  
    

      Package: smoothclust

      Commit: 9e39e901da35886d8ce9f773ad39a7c4875f3a00

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-04-28 15:50:29 -0400

      Commit message:


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

      Package: smoothclust

      Commit: b4a37d4e3c0bd88930ed4868fe3522e6c32cced9

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-04-26 17:13:51 -0400

      Commit message:


	  
		
 version
 
    
  
    

      Package: smoothclust

      Commit: f161057fe056dc1f79200e3eda2a533713191c7f

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-04-26 17:13:39 -0400

      Commit message:


	  
		
 update NEWS
 
    
  
    

      Package: smoothclust

      Commit: b2d4b92a0c71faba2e37fe93815fb0cd6dd7f3b8

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-04-26 17:08:46 -0400

      Commit message:


	  
		
 add n_threads argument for neighbor searches
 
    
  
    

      Package: smoothclust

      Commit: e7e93ae9b157778bba8d32ac23dd4d1b31f62592

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-04-26 17:04:56 -0400

      Commit message:


	  
		
 speed update - sparse aggregation for kernel weight sums
 
    
  
    

      Package: smoothclust

      Commit: fa0520d6168b9f87f33403bd33430814738d1f60

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-04-26 17:01:40 -0400

      Commit message:


	  
		
 speed update - use transposed kNN indices
 
    
  
    

      Package: smoothclust

      Commit: 2ce775300803d2d0261c44a40f7d44c6a23f1051

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-04-26 16:49:30 -0400

      Commit message:


	  
		
 improve input validation and add tests
 
    
  
    

      Package: smoothclust

      Commit: 3d1a75250c71de6fea5ee8c3104e49eb334dea6e

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-04-26 16:43:51 -0400

      Commit message:


	  
		
 fix kernel weight normalization if no neighbors
 
    
  
    

      Package: smoothclust

      Commit: c991476d3127962a7df1e67e7cc538b88fd351e3

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-04-26 16:34:48 -0400

      Commit message:


	  
		
 fix self-neighbor handling
 
    
  
    

      Package: smoothclust

      Commit: 28a453f19548d6ca3df2d23ab73d2301d86ec1ab

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-04-26 15:16:28 -0400

      Commit message:


	  
		
 add AGENTS.md
 
    
  
    

      Package: smoothclust

      Commit: fdbdd080609e90bc82672f4e6c5ebe7dd418e070

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-04-26 15:11:41 -0400

      Commit message:


	  
		
 ignore AGENTS.md for R build
 
    
  
    

      Package: smoothclust

      Commit: 95b64bd6404e641638c26d6ac1f0dd170393295e

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-04-26 15:10:11 -0400

      Commit message:


	  
		
 auto-update .Rbuildignore
 
    
  
    

      Package: smoothclust

      Commit: e760cd867566cdddb6693c73e90580b4a560fddc

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-04-26 15:09:22 -0400

      Commit message:


	  
		
 auto-update .gitignore
 
    
  
    

      Package: cellmig

      Commit: 09424afd6fce5090bd50929f3f0a3a81e3677906

      Author:  sktron <simo.kitanovski@uni-due.de> 

      Date: 2026-05-18 18:56:47 +0200

      Commit message:


	  
		
 update minor changes
 
    
  
    

      Package: lcmsPlot

      Commit: 5c2346c608e73e87ee12b284432d815444e62496

      Author:  Ossama Edbali <ossedb@gmail.com> 

      Date: 2026-05-18 16:36:22 +0100

      Commit message:


	  
		
 refactor: move lp_get_plot after msPurity layer functions

Reorder lp_get_plot to appear at the end of the file, after the msPurity
layer functions, and normalise argument indentation in lp_purity_overlay,
lp_isolation_window, lp_purity_timeline, and lp_purity_distribution.
 
    
  
    

      Package: lcmsPlot

      Commit: 9eb10156c297d49972a42c57cddb91747cfc393b

      Author:  Ossama Edbali <ossedb@gmail.com> 

      Date: 2026-05-18 15:38:29 +0100

      Commit message:


	  
		
 ci: pin Docker image to bioconductor_docker:3.23

The :devel tag is a rolling image whose pre-installed packages can be
mismatched against the current Bioconductor devel release, causing
packages like MSnbase and xcms to fail to load. Pinning to 3.23 gives
a stable, consistent environment where installed package versions are
known to be compatible.
 
    
  
    

      Package: lcmsPlot

      Commit: 2e7a6fd0b3a2d5cf5aad7f382ae377ba98e3a1eb

      Author:  Ossama Edbali <ossedb@gmail.com> 

      Date: 2026-05-18 15:12:45 +0100

      Commit message:


	  
		
 ci: use BiocManager with update=TRUE to fix stale image packages

The bioconductor_docker:devel image ships pre-installed but potentially
outdated versions of MSnbase and xcms. The previous approach (diff filter
or remotes::install_deps) skipped them because they appeared installed,
but the outdated versions failed to load against the current Bioconductor
devel release.

Follow the biocthis standard pattern: pass all dep package names to
BiocManager::install with update=TRUE so stale packages in the image are
updated, not skipped.
 
    
  
    

      Package: lcmsPlot

      Commit: bc89e6469396fe4f46981967b89a9c9997a3b573

      Author:  Ossama Edbali <ossedb@gmail.com> 

      Date: 2026-05-18 14:49:42 +0100

      Commit message:


	  
		
 ci: fix dependency installation step to use remotes::install_deps

Replace the custom dev_package_deps/diff-based install logic with
remotes::install_deps, which reliably installs all missing dependencies
regardless of cache state. The previous approach could be fooled by a
stale partial cache restore, causing MSnbase and xcms to appear satisfied
(diff = 0) while not actually being loadable.
 
    
  
    

      Package: lcmsPlot

      Commit: 01defe46cc4622730d04043e6ccb615f9dd31ec5

      Author:  Ossama Edbali <ossedb@gmail.com> 

      Date: 2026-05-18 14:40:53 +0100

      Commit message:


	  
		
 chore: Fix README.md, bump version, and add NEWS.md item
 
    
  
    

      Package: lcmsPlot

      Commit: f97165ed8b3f21785be811410d8504dba017d464

      Author:  Ossama Edbali <ossedb@gmail.com> 

      Date: 2026-05-18 14:26:28 +0100

      Commit message:


	  
		
 feat: Enable support for msPurity
 
    
  
    

      Package: smoppix

      Commit: 5682328e71554092dca1512e17d1523d8ac74202

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2026-05-18 17:46:39 +0200

      Commit message:


	  
		
 Merge conflict

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

# Conflicts:
#	DESCRIPTION
 
    
  
    

      Package: smoppix

      Commit: f1f99e0229f47298c133e3232871df7c5dbaea4a

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2026-05-18 17:14:34 +0200

      Commit message:


	  
		
 bpnworkers in doc
 
    
  
    

      Package: smoppix

      Commit: ea6055f17bc72432f298c989bf181b3d712ce1b4

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2026-05-18 17:08:58 +0200

      Commit message:


	  
		
 with canonical bpnworkers function
 
    
  
    

      Package: smoppix

      Commit: 2298e4fa4fe63ce5b69356f44c1d6a0edefed26c

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2026-05-04 15:35:53 +0200

      Commit message:


	  
		
 Modern roxygen versioning
 
    
  
    

      Package: smoppix

      Commit: 98a1a08e00d3a13673aaffb70a392ca5fcc6399e

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2026-03-17 15:13:04 +0100

      Commit message:


	  
		
 version bump for bugfix
 
    
  
    

      Package: smoppix

      Commit: 989d81d2b29f8e39332b7d2c89a05309e9540073

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2026-03-05 10:48:40 +0100

      Commit message:


	  
		
 devel

Merge branch 'devel'
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.
 
    
  
    

      Package: smoppix

      Commit: 73e8a2e7c5cea50d7f9cff75f214b37cdbc22bf4

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2026-03-05 10:48:21 +0100

      Commit message:


	  
		
 Update news file
 
    
  
    

      Package: smoppix

      Commit: 89a6604b2a5e1fe8c3c7b97dd4ad9dbbe71e3e55

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2026-03-05 10:47:34 +0100

      Commit message:


	  
		
 Fixed drop=FALSE results
 
    
  
    

      Package: smoppix

      Commit: 41b004ba51e8ea206aaabb295acfbc71ff6059cb

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2026-03-04 09:10:59 +0100

      Commit message:


	  
		
 Pull in test changes
 
    
  
    

      Package: OmniAgeR

      Commit: dba85006e4f6e09da4f7318ef97e7cd1930229a6

      Author:  Zhaozhen Du <duzhaozhen@inspur.com> 

      Date: 2026-05-18 23:43:07 +0800

      Commit message:


	  
		
 Fix: Prevent devtools::check timeout; bump version
 
    
  
    

      Package: scuttle

      Commit: 88a483825ee583c0f15f88dab95e36384af8d1c5

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

      Date: 2026-05-18 15:49:17 +1000

      Commit message:


	  
		
 List deprecated functions and their replacement in the NEWS.
 
    
  
    

      Package: scuttle

      Commit: 83b3bdbb45d266e062799bc261ec0bc754217eed

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

      Date: 2026-05-18 15:33:30 +1000

      Commit message:


	  
		
 Added GitHub links to the description, bumped version and date.
 
    
  
    

      Package: OmniAgeR

      Commit: dfba20e4ac7f7227a4b9c98302d4d5aebcb1cdbd

      Author:  Zhaozhen Du <duzhaozhen@inspur.com> 

      Date: 2026-05-18 10:43:48 +0800

      Commit message:


	  
		
 Bump version to re-trigger Bioconductor build due to 500 server error
 
    
  
    

      Package: OmniAgeR

      Commit: 9d58737454f6cc735184f9996f2875a3bef39f99

      Author:  Zhaozhen Du <duzhaozhen@inspur.com> 

      Date: 2026-05-18 10:35:30 +0800

      Commit message:


	  
		
 Fix: Prevent devtools::check timeout; bump version
 
    
  
    

      Package: Rsubread

      Commit: 15e8f2346b471ff48de7d808c3589c932b68636a

      Author:  Yang Liao (Monash University) <yliao@m3-login2.massive.org.au> 

      Date: 2026-05-18 11:48:37 +1000

      Commit message:


	  
		
 Fixed a bug in cellCounts not reporting read numbers in meta info output.
 
    
  
    

      Package: SEMPLR

      Commit: fcecf410ed0390191b132ba9d8370eb4c9c3e7c5

      Author:  Grace Kenney <kenney.grace6@gmail.com> 

      Date: 2026-05-16 20:12:20 -0400

      Commit message:


	  
		
 fix headings
 
    
  
    

      Package: SEMPLR

      Commit: c9435b9db95687280e6af43a3e51e4c344a5fa9c

      Author:  Grace Kenney <kenney.grace6@gmail.com> 

      Date: 2026-05-16 19:55:00 -0400

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: SEMPLR

      Commit: c29e250b12cf463037d1aa7150306a76d251deae

      Author:  Grace Kenney <kenney.grace6@gmail.com> 

      Date: 2026-05-16 19:54:22 -0400

      Commit message:


	  
		
 update the news
 
    
  
    

      Package: SEMPLR

      Commit: fb4bc50f4306d45b952fc60419aad225926890f8

      Author:  Grace Kenney <kenney.grace6@gmail.com> 

      Date: 2026-05-16 19:54:06 -0400

      Commit message:


	  
		
 update documentation for columns of scoreVariants
 
    
  
    

      Package: SEMPLR

      Commit: f38147d2ba10de0149fa9c99aec8beb5482c1be5

      Author:  Grace Kenney <kenney.grace6@gmail.com> 

      Date: 2026-05-16 19:53:17 -0400

      Commit message:


	  
		
 only consider the orientation with the highest binding score in enrichment analysis
 
    
  
    

      Package: extraChIPs

      Commit: 876144433dcc5f5321bb197fd3f84fcdd555bb24

      Author:  Stevie Ped <stephen.pederson.au@gmail.com> 

      Date: 2026-05-16 22:27:31 +0930

      Commit message:


	  
		
 Version bump after bugfix
 
    
  
    

      Package: extraChIPs

      Commit: 93bf833aa6d1f7bfd523af6b0ed755cd04c1e558

      Author:  Stevie Ped <stephen.pederson.au@gmail.com> 

      Date: 2026-05-16 22:04:38 +0930

      Commit message:


	  
		
 Corrected deprecation test
 
    
  
    

      Package: extraChIPs

      Commit: 051996fc65c360bacb0a27ef19eb1cbcb804b33b

      Author:  Stevie Ped <stephen.pederson.au@gmail.com> 

      Date: 2026-05-16 19:26:40 +0930

      Commit message:


	  
		
 Revised dualFilter to cut RAM usage
 
    
  
    

      Package: pipeComp

      Commit: 9a5c7c29204953249115aa691df30b57a1bb6af0

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

      Date: 2026-05-16 09:58:20 +0200

      Commit message:


	  
		
 fix aricode function rename
 
    
  
    

      Package: DelayedArray

      Commit: 09b534c4eeeb05c257ac68c6670dbb0fb186a46b

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

      Date: 2026-05-15 22:10:45 -0700

      Commit message:


	  
		
 DelayedArray 0.39.2: Use new table() signature in method definition
 
    
  
    

      Package: IRanges

      Commit: edb3e7763f5ba5631c35ec1773bebbff8676b487

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

      Date: 2026-05-15 22:09:53 -0700

      Commit message:


	  
		
 IRanges 2.47.1: Use new table() signature in method definitions
 
    
  
    

      Package: S4Vectors

      Commit: 5a0ff09c210147117e9216f43f3107b1eb45105b

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

      Date: 2026-05-15 22:08:52 -0700

      Commit message:


	  
		
 S4Vectors 0.51.2: Use new table() signature in method definitions
 
    
  
    

      Package: BiocGenerics

      Commit: 235a41a41a3ba1639f77c5a061541a44d540dbed

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

      Date: 2026-05-15 21:23:27 -0700

      Commit message:


	  
		
 BiocGenerics 0.59.2: Change interface of table() generic to table(x, ...)

The table() S4 generic now uses the table(x, ...) interface instead of
table(...), with dispatch on 'x' instead of dispatch on the ellipsis.

This should make it easier for package developers to implement table()
methods that take additional arguments. So, for example, they'll be able
to make things like 'table(x, i=2)' work on their objects. Note that this
specific use case comes from the SpatialData developers and is the main
motivation behind this change.

But it's not all roses:

1. This change will require adjusting all the table() method definitions
   defined in Bioconductor. The good news is that, to my knowledge, the
   only packages that define table() methods are S4Vectors, IRanges,
   DelayedArray, and R453Plus1Toolbox. I'll take care of them soon.

2. Unfortunately this new interface makes it harder for developers to
   implement table() methods that do cross tabulation (a.k.a. n-ary
   table()). In particular, to make something like 'table(y=Y, z=Z)' work
   on S4 objects 'Y' and 'Z' (e.g. Rle objects) has many challenges. So
   more work will be needed to smooth that path.
 
    
  
    

      Package: TCGAutils

      Commit: a4bd3f718f41a252f1bffe5fd696fb3060ff4b5e

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-15 14:37:44 -0400

      Commit message:


	  
		
 version bump 1.33.1
 
    
  
    

      Package: TCGAutils

      Commit: bba797b48b4054deae1c52ac87b60c866359b143

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-15 16:02:01 -0400

      Commit message:


	  
		
 minor formatting
 
    
  
    

      Package: TCGAutils

      Commit: dd6d501bde1795985ecea7a65ef4e4d68de6906b

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-15 14:37:39 -0400

      Commit message:


	  
		
 update to changes in roxygen
 
    
  
    

      Package: TCGAutils

      Commit: cd2de765709f05947db3c2d4ccb4ecb2f0d73e9e

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-15 14:36:37 -0400

      Commit message:


	  
		
 remove lifeCycle import from BiocBaseUtils
 
    
  
    

      Package: TCGAutils

      Commit: 9c6bd34879af3fed62314868d979754d05e6768d

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-15 14:35:59 -0400

      Commit message:


	  
		
 update package Authors and fnd with roxygen doc
 
    
  
    

      Package: TCGAutils

      Commit: e355e1ea3ba2cd38fe4af8f5e4402f4350f82177

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-15 14:35:17 -0400

      Commit message:


	  
		
 update .get_hsa_url function to not download unspecified current genome
 
    
  
    

      Package: cellmig

      Commit: 1ea1db706ea8991f0383559f2f888d4305eca5d0

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

      Date: 2026-05-15 15:59:47 +0200

      Commit message:


	  
		
 volcano plot
 
    
  
    

      Package: scTypeEval

      Commit: 33e37ac9513de2bd02ebdd1ff20449f1c7d2ae36

      Author:  JGarnica22 <j.garnica22@gmail.com> 

      Date: 2026-05-15 15:20:47 +0200

      Commit message:


	  
		
 rm: deprecated functions for benchmarking. Now found and maintnated in repo for reproducibility
 
    
  
    

      Package: MSTree

      Commit: 08cdc1833921fa67b40aaaa275cd641f8a8f02e0

      Author:  abedkurdi <abed_kurdi@hotmail.com> 

      Date: 2026-05-15 13:44:33 +0300

      Commit message:


	  
		
 pushing 0.99.7 typos correction
 
    
  
    

      Package: mia

      Commit: fafaeb560e7d693fe41f500692cbd6cd223be0f2

      Author:  Leo Lahti <leo.lahti@iki.fi> 

      Date: 2026-05-15 11:14:50 +0300

      Commit message:


	  
		
 Fixed PC explained vars in joint-RPCA (#826)

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

      Package: RnBeads

      Commit: 97064d762063fa4cf9eb29f59e574693e93b9c97

      Author:  Fabian Müller <fmueller@mpi-inf.mpg.de> 

      Date: 2026-05-15 08:33:35 +0200

      Commit message:


	  
		
 Reupdated Version
 
    
  
    

      Package: RnBeads

      Commit: e8c35b33c1884661dd25e68def8d4708c84ff6cc

      Author:  Fabian Müller <fmueller@mpi-inf.mpg.de> 

      Date: 2026-05-15 08:32:22 +0200

      Commit message:


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

# Conflicts:
#	DESCRIPTION
 
    
  
    

      Package: RnBeads

      Commit: 599fbf843132dde8e9a6f099786eaf4b3f58df99

      Author:  Fabian Müller <fmueller@mpi-inf.mpg.de> 

      Date: 2026-05-15 08:30:40 +0200

      Commit message:


	  
		
 Updated version to be constistent with bioC
 
    
  
    

      Package: RnBeads

      Commit: 7362133709f6b072af56287a05b4a61065933617

      Author:  Fabian Müller <fabian.mueller@uni-saarland.de> 

      Date: 2026-05-15 08:26:34 +0200

      Commit message:


	  
		
 Merge pull request #73 from Staminima/fix/disable-nv-probe-table

added enable-disable option for nv-probe tables 
    
  
    

      Package: RnBeads

      Commit: 7f6f20ba776fafe9fc0f7587d805ed5e6c643772

      Author:  Nima Amini <nima@dhcp134-96-90-80.icbb.uni-saarland.de> 

      Date: 2026-05-13 15:58:37 +0200

      Commit message:


	  
		
 added enable-disable option for nv-probe tables
 
    
  
    

      Package: RnBeads

      Commit: ef0e8576dcfb1936a7a4b662c6dbe70e14618e60

      Author:  Fabian Müller <fabian.mueller@uni-saarland.de> 

      Date: 2026-03-16 10:07:30 +0100

      Commit message:


	  
		
 Merge pull request #72 from schmic05/master

Implemented XenoMix 
    
  
    

      Package: BiocPkgTools

      Commit: 16b8797072953cdf7ab0d0f1eb6f278df7efb0bb

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-14 18:33:36 -0400

      Commit message:


	  
		
 version bump 1.31.6
 
    
  
    

      Package: BiocPkgTools

      Commit: 2463f0aecfcdcc2eea1803223f24c6dcaed4636a

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-14 18:32:26 -0400

      Commit message:


	  
		
 remove defunct arguments and options
 
    
  
    

      Package: BiocPkgTools

      Commit: 05c61e11819024f3e45d1c00e58471fe502fe985

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-14 18:31:54 -0400

      Commit message:


	  
		
 add chunk labels to vignette
 
    
  
    

      Package: BiocPkgTools

      Commit: 1aa9d1f21e95c14ac9b01bd842731d6feac1cdb9

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-14 18:31:38 -0400

      Commit message:


	  
		
 use TRUE instead of T
 
    
  
    

      Package: BiocPkgTools

      Commit: 41f53fbd82727630b6aff0f6d754c0c10686b3e7

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-14 18:31:25 -0400

      Commit message:


	  
		
 add examples to exported functions
 
    
  
    

      Package: BiocPkgTools

      Commit: ef81b56f52502d7b1876cbab2aba90953f0cdb6b

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-14 18:30:43 -0400

      Commit message:


	  
		
 use R 4.6 and resolve NOTE
 
    
  
    

      Package: BiocPkgTools

      Commit: 139a9e392bd44b446da30c9765f7980a7ab02b13

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-14 18:30:29 -0400

      Commit message:


	  
		
 add maintainer ORCID
 
    
  
    

      Package: augere.solo

      Commit: 51e31e9991745bcabbb31b2e9fa25407216f9546

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

      Date: 2026-05-15 08:32:53 +1000

      Commit message:


	  
		
 Added links to the BioC build status.
 
    
  
    

      Package: augere.screen

      Commit: 295a1bd64f84a65e9730d5453caf003e191324a4

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

      Date: 2026-05-15 08:30:59 +1000

      Commit message:


	  
		
 Added links to the BioC build status.
 
    
  
    

      Package: augere.gsea

      Commit: a7cb67d5db8416d6ffe5e1387eb2a13d57c10d7c

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

      Date: 2026-05-15 08:20:48 +1000

      Commit message:


	  
		
 Added links to the BioC build status.
 
    
  
    

      Package: augere.de

      Commit: 9c39bb43f273502229031d890db102cf306b972b

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

      Date: 2026-05-15 08:19:21 +1000

      Commit message:


	  
		
 Added links to the BioC build status.
 
    
  
    

      Package: augere.core

      Commit: 892e35cd9e777f8a1b3a59daef63b6c227b906b4

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

      Date: 2026-05-15 08:17:52 +1000

      Commit message:


	  
		
 Added links to the BioC build reports.
 
    
  
    

      Package: curatedOvarianData

      Commit: 42c144dc6d65a8b2455dcc873da923105282837e

      Author:  Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com> 

      Date: 2026-05-14 21:14:55 +0000

      Commit message:


	  
		
 Add CITATION.cff 
    
  
    

      Package: bugsigdbr

      Commit: 5d737b34139920fc877d3f706331e463ec6c790a

      Author:  Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com> 

      Date: 2026-05-14 21:12:58 +0000

      Commit message:


	  
		
 Add CITATION.cff 
    
  
    

      Package: GSEABenchmarkeR

      Commit: 21b3ef8ac091f8d7864bc94a32ff828a45b5754f

      Author:  Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com> 

      Date: 2026-05-14 21:12:09 +0000

      Commit message:


	  
		
 Add CITATION.cff 
    
  
    

      Package: curatedCRCData

      Commit: ffde61eac7c5703e94400becafc83e0acb60c589

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-14 17:10:42 -0400

      Commit message:


	  
		
 version bump 2.45.2
 
    
  
    

      Package: curatedCRCData

      Commit: 63f1bac26e33f35880037804466856763ce859c7

      Author:  Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com> 

      Date: 2026-05-14 21:03:09 +0000

      Commit message:


	  
		
 Add CITATION.cff 
    
  
    

      Package: curatedCRCData

      Commit: 8894a7cd3be70cd00057f03e34d5bac4ced23453

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

      Date: 2026-05-14 20:54:50 +0000

      Commit message:


	  
		
 Update CITATION bibentry with full author names

Agent-Logs-Url: https://github.com/waldronlab/curatedCRCData/sessions/95c4fd2a-7732-407e-887d-7d3b80329236

Co-authored-by: LiNk-NY <4392950+LiNk-NY@users.noreply.github.com>
 
    
  
    

      Package: cBioPortalData

      Commit: a9714e8ab9fde119c1516b0915bc15d2a26d989c

      Author:  Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com> 

      Date: 2026-05-14 21:04:14 +0000

      Commit message:


	  
		
 Add CITATION.cff 
    
  
    

      Package: SingleCellMultiModal

      Commit: 1aa5ea5dc047101283cc0552c849b78f17b646dc

      Author:  Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com> 

      Date: 2026-05-14 21:03:45 +0000

      Commit message:


	  
		
 Update CITATION.cff 
    
  
    

      Package: curatedTCGAData

      Commit: d235c1b30eb79e5a83068f95c6052fb70d13edf2

      Author:  Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com> 

      Date: 2026-05-14 20:52:04 +0000

      Commit message:


	  
		
 Add CITATION.cff 
    
  
    

      Package: lefser

      Commit: a0a8ddd4c8818b5c93a6b67bf75b3eee145526b4

      Author:  Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com> 

      Date: 2026-05-14 20:51:03 +0000

      Commit message:


	  
		
 Add CITATION.cff 
    
  
    

      Package: doppelgangR

      Commit: 94a7be768e3f585b129d104f3c94806b8bb5a3ea

      Author:  Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com> 

      Date: 2026-05-14 20:43:30 +0000

      Commit message:


	  
		
 Add CITATION.cff 
    
  
    

      Package: doppelgangR

      Commit: b9c2a10ed023cc1da4de2eaa366a2b1f9947eb21

      Author:  Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com> 

      Date: 2026-03-26 14:20:48 -0400

      Commit message:


	  
		
 Migrate pr_check.yml to ci.yml (#23)

* Add ci.yml reusable-workflow wrapper

* Remove pr_check.yml (replaced by ci.yml) 
    
  
    

      Package: doppelgangR

      Commit: c58a88cc7e9935df02f94eadc866bfdc2f350ff7

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 17:11:35 -0500

      Commit message:


	  
		
 update README.md
 
    
  
    

      Package: HMP16SData

      Commit: a9807c3ed97f24c94d40fc4e62329a2d83a7e673

      Author:  Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com> 

      Date: 2026-05-14 20:39:19 +0000

      Commit message:


	  
		
 Add CITATION.cff 
    
  
    

      Package: curatedMetagenomicData

      Commit: cecdfeca42d0f6cda6bad3f5c755c5c4ba4da858

      Author:  Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com> 

      Date: 2026-05-14 20:37:12 +0000

      Commit message:


	  
		
 Add CITATION.cff 
    
  
    

      Package: BiocPkgTools

      Commit: ff832b31bd41787358f92437f6f8f26125cc75b6

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-14 16:02:44 -0400

      Commit message:


	  
		
 version bump 1.31.5
 
    
  
    

      Package: BiocPkgTools

      Commit: 4f961881960b95f1cb18ca92b6fe1c5ce324e5ae

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-14 15:47:19 -0400

      Commit message:


	  
		
 remove httr dependency completely
 
    
  
    

      Package: BiocPkgTools

      Commit: 726169edb744adb88e9cb922a763298a947df03f

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-14 15:46:48 -0400

      Commit message:


	  
		
 remove duplicate function generateBiocPkgDOI_REST
 
    
  
    

      Package: BiocPkgTools

      Commit: 9cbd5e0b2c74b1e1d41309a2ea7c2771e1aba190

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-12 15:12:24 -0400

      Commit message:


	  
		
 clean up quoted names in lists
 
    
  
    

      Package: tkWidgets

      Commit: d06dbb88cb687fd9c37f294e8188cee7fc35e483

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-14 12:21:19 -0400

      Commit message:


	  
		
 version bump 1.91.1
 
    
  
    

      Package: tkWidgets

      Commit: 66aa5d255dff63e56210df19b49a1a444e2f9804

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-12 17:48:07 -0400

      Commit message:


	  
		
 remove hgu95av2 from Suggests
 
    
  
    

      Package: scrapbook

      Commit: bf019be31f4205c25fd87bc42731437f1563267e

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

      Date: 2026-05-15 02:06:02 +1000

      Commit message:


	  
		
 Updated roxygen flags, minor rewording.
 
    
  
    

      Package: scrapbook

      Commit: a10a8ecded6e1700bb2ca7ef554f53f178930b90

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

      Date: 2026-05-15 01:24:17 +1000

      Commit message:


	  
		
 Sprinkle in some more rewording and cynical wisdom, fixed links.

Bumped version for a new release.
 
    
  
    

      Package: scrapbook

      Commit: 71064c9eb7008dfc32689bb16db8293f07228dd1

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

      Date: 2026-05-14 22:28:11 +1000

      Commit message:


	  
		
 Restore the multi-condition section into its own chapter.
 
    
  
    

      Package: scrapbook

      Commit: d44a6629f1e83be3a4818c090c889d21496dfb4f

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

      Date: 2026-05-13 21:26:35 +1000

      Commit message:


	  
		
 Reorganized the batch correction chapter.

Mostly to clarify wording and eliminate redundant explanations.

Also start moving multi-sample analyses to its own chapter.
 
    
  
    

      Package: scrapbook

      Commit: af84f9b0763f3528e5ecab8a36b34391d0cf5598

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

      Date: 2026-05-13 16:08:36 +1000

      Commit message:


	  
		
 Ignore the auto-generated markdown files during testing.
 
    
  
    

      Package: splicelogic

      Commit: c11b5e52fdfa78f6150d5def302a79476329ac8c

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-05-14 09:56:12 -0400

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: splicelogic

      Commit: 0eeb7ee0894fa12c97685c11cf5ab1e10f6affeb

      Author:  Mike Love <mikelove@users.noreply.github.com> 

      Date: 2026-05-13 21:27:06 -0400

      Commit message:


	  
		
 propagate original metadata
 
    
  
    

      Package: splicelogic

      Commit: aaba161bdbde7025794e76d90b5d5229b42c9a2f

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-05-13 16:35:29 -0400

      Commit message:


	  
		
 include info about output format and preprocess function
 
    
  
    

      Package: splicelogic

      Commit: a851f651c7e87c21cf161481492f94e754448aa9

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-05-13 15:43:15 -0400

      Commit message:


	  
		
 fix doc typos
 
    
  
    

      Package: splicelogic

      Commit: 430f8539bdab6d5ab81f659d7471ed404fb4fae8

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-05-13 15:31:20 -0400

      Commit message:


	  
		
 add test for preprocess
 
    
  
    

      Package: splicelogic

      Commit: 30b952630a63f91515ffb53eb811b19765d55342

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-05-13 15:15:30 -0400

      Commit message:


	  
		
 add test for additional_columns in preprocess output
 
    
  
    

      Package: splicelogic

      Commit: 154d31731ae80772924170bee3d89d6cb7728f58

      Author:  Beatriz Campillo <beatrizcampillo29@gmail.com> 

      Date: 2026-05-12 14:41:21 -0400

      Commit message:


	  
		
 typo 
    
  
    

      Package: splicelogic

      Commit: 7539c5b7f80550a494446738a206a57bd673900f

      Author:  Beatriz Campillo <beatrizcampillo29@gmail.com> 

      Date: 2026-05-12 13:38:17 -0400

      Commit message:


	  
		
 typo 
    
  
    

      Package: splicelogic

      Commit: 4ab9fab2cd6943d231b910954fade52cf78eb8f7

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-05-08 18:21:15 -0400

      Commit message:


	  
		
 typo
 
    
  
    

      Package: splicelogic

      Commit: 3b65bc1a17f89a3a6866ae5250a30b5d9a214644

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-05-08 18:14:40 -0400

      Commit message:


	  
		
 add tx_id_col to prepare_exons_by_partition
 
    
  
    

      Package: splicelogic

      Commit: a63eebd8bf83da436f7ebde318b64c75776274aa

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-05-08 18:08:55 -0400

      Commit message:


	  
		
 refactor - update event metadata output event_type event_tx_id, and include additional_columns option with event_<> prefix
 
    
  
    

      Package: splicelogic

      Commit: bf55e1aab3cbb43fe64a81004769c61b35d6598b

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-05-08 15:01:26 -0400

      Commit message:


	  
		
 fix - add prepare_exons_by_partition to index
 
    
  
    

      Package: splicelogic

      Commit: 4909cc341946811632d240345d8ef56aaa6c21bc

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-05-08 14:11:06 -0400

      Commit message:


	  
		
 bump version
 
    
  
    

      Package: splicelogic

      Commit: 07ff9567f696cc7af281247ae5b60d2634ab39dd

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-05-08 13:59:32 -0400

      Commit message:


	  
		
 add tests for preprocess, prepare_exons and prepare_exons_by_partition
 
    
  
    

      Package: splicelogic

      Commit: ee38035f5aaa6a329fc974ec10528aec107f1df3

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-05-08 13:57:52 -0400

      Commit message:


	  
		
 add prepare_exons_by_partition function and documentation
 
    
  
    

      Package: splicelogic

      Commit: 239c6da42c9d3bbed6112b3c5cc24b562caceee9

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-05-06 14:56:24 -0400

      Commit message:


	  
		
 update examples to use n_tx_per_gene and n_exons_per_tx parameter names
 
    
  
    

      Package: splicelogic

      Commit: 3616802c9d2a17df47df2fff85731ff1b44dd636

      Author:  Mike Love <mikelove@users.noreply.github.com> 

      Date: 2026-05-07 14:39:40 -0400

      Commit message:


	  
		
 roll back
 
    
  
    

      Package: splicelogic

      Commit: 4d6126648e1741287ceb5e26c3bb7ac974906c36

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-05-06 14:18:29 -0400

      Commit message:


	  
		
 update examples to use n_tx_per_gene and n_exons_per_tx parameter names
 
    
  
    

      Package: sketchR

      Commit: f1e060bd60002c47e6e326ac314d62a4315fd2c3

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-05-14 11:12:48 +0200

      Commit message:


	  
		
 Merge pull request #19 from fmicompbio/use-scrapper

Use scrapper replacements for deprecated functions 
    
  
    

      Package: sketchR

      Commit: f428be453368217d9780401cb207f06d4af37294

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-05-14 09:59:49 +0200

      Commit message:


	  
		
 Adapt to roxygen2 v8.0.0
 
    
  
    

      Package: sketchR

      Commit: f0002c19408e8bbc8928427eb38f1dc9e837fe04

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-05-14 09:58:55 +0200

      Commit message:


	  
		
 Replace deprecated functions with scrapper equivalents
 
    
  
    

      Package: iCOBRA

      Commit: 88db64687355e49d27c434c3da078ede61508dcd

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-05-14 08:29:43 +0200

      Commit message:


	  
		
 Merge pull request #8 from csoneson/simpleupset

Switch to SimpleUpset 
    
  
    

      Package: iCOBRA

      Commit: 4fc2d9c335fc7140de822a909c06021d458d580a

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-05-13 21:54:29 +0200

      Commit message:


	  
		
 Fix UpSet plot export
 
    
  
    

      Package: iCOBRA

      Commit: 6e4728c1df9453d053bcf35aec53c54550661b10

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-05-13 21:42:41 +0200

      Commit message:


	  
		
 Be more specific with imports from dplyr
 
    
  
    

      Package: iCOBRA

      Commit: 560692452d2b14a921a7417b795e0c2177c61aeb

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-05-13 21:36:32 +0200

      Commit message:


	  
		
 Swap dependency on UpSetR for SimpleUpset
 
    
  
    

      Package: iCOBRA

      Commit: 23fa928b115c64097d293d5c4d37b96e87b0c363

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-05-10 22:01:47 +0200

      Commit message:


	  
		
 Adapt to roxygen2 8.0.0
 
    
  
    

      Package: iCOBRA

      Commit: 15f3b099f70a908aa9c395593d2a81361f3a8aff

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-05-10 21:50:12 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: iCOBRA

      Commit: 23af0e307b3d2a60c41b305f5ee35be6f8f6d128

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-05-10 21:49:42 +0200

      Commit message:


	  
		
 Add _pkgdown.yaml to .Rbuildignore
 
    
  
    

      Package: iCOBRA

      Commit: 4eef180c994cfce62fa31ffd1df9709172f1f161

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-04-28 19:48:15 +0200

      Commit message:


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

      Package: iCOBRA

      Commit: 8cc806c9142b4cd12bb7744bb92d5438cac9f99a

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-03-20 20:13:24 +0100

      Commit message:


	  
		
 Bump cache version
 
    
  
    

      Package: BiocGenerics

      Commit: d03e641dacae49997f07bd56c831e76a91991d84

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

      Date: 2026-05-13 21:50:23 -0700

      Commit message:


	  
		
 BiocGenerics 0.59.1: paste2() now propagates NAs, as it should
 
    
  
    

      Package: SingleCellExperiment

      Commit: 9972b11175aa389e777ca38da4a31491636bb6fe

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

      Date: 2026-05-14 12:13:59 +1000

      Commit message:


	  
		
 Dual-license it under GPL-2, added links to DESCRIPTION.
 
    
  
    

      Package: igblastr

      Commit: 53bbc8e676dba68e6577a245e505b85c22095a0b

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

      Date: 2026-05-13 13:04:12 -0700

      Commit message:


	  
		
 igblastr 1.3.2: Add combine_germline_dbs()

combine_germline_dbs() can be used to combine two existing germline
databases, typically (but not necessarily) from two different organisms,
into a new one.

More testing needed. Man page still needs to be completed and the examples
in it need to be expanded.
 
    
  
    

      Package: TabulaMurisData

      Commit: 40695466cd55f3e300a262790e89a9c83463ce1c

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-05-13 22:05:41 +0200

      Commit message:


	  
		
 Replace deprecated function in vignette
 
    
  
    

      Package: maaslin3

      Commit: a7f224a6d4e20134cba729e92089b8a977e00286

      Author:  Will Nickols <willnickols@college.harvard.edu> 

      Date: 2026-05-13 06:32:13 -0700

      Commit message:


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

# Conflicts:
#	DESCRIPTION
 
    
  
    

      Package: maaslin3

      Commit: a5f86080c27fcbf4c0eaef663f24eb2ef9622348

      Author:  Will Nickols <willnickols@college.harvard.edu> 

      Date: 2026-05-13 06:29:15 -0700

      Commit message:


	  
		
 Bump version to 1.3.2
 
    
  
    

      Package: maaslin3

      Commit: 6cc3789b3b2f9fc9902ed4fd59626f22a0e31793

      Author:  Will Nickols <78048944+WillNickols@users.noreply.github.com> 

      Date: 2026-05-11 13:39:26 -0700

      Commit message:


	  
		
 Merge pull request #45 from biobakery/devel

Remove logging dependency 
    
  
    

      Package: maaslin3

      Commit: 87d751491a622e1dac9d0a95cc507de044d15a49

      Author:  Will Nickols <willnickols@college.harvard.edu> 

      Date: 2026-05-11 12:54:18 -0700

      Commit message:


	  
		
 Reset maaslin log at the end of each example
 
    
  
    

      Package: maaslin3

      Commit: fd58ecaf53df914a60cf24e1c28265f1da0b3438

      Author:  Will Nickols <willnickols@college.harvard.edu> 

      Date: 2026-05-11 12:16:47 -0700

      Commit message:


	  
		
 Remove logging dependency
 
    
  
    

      Package: maaslin3

      Commit: 6c219a0a25234049c539ffe7573fdec480532ab7

      Author:  Will Nickols <78048944+WillNickols@users.noreply.github.com> 

      Date: 2026-04-24 08:49:31 -0700

      Commit message:


	  
		
 Add GitHub installation instructions to README

Added installation instructions for GitHub. 
    
  
    

      Package: msa

      Commit: 97dc2bbeff49e539b554cbb6b3fdbf31ae53a23e

      Author:  UBod <ulrich@bodenhofer.com> 

      Date: 2026-05-13 15:10:41 +0200

      Commit message:


	  
		
 Change of format of inst/NEWS file
 
    
  
    

      Package: kebabs

      Commit: 759f631a608e04f80154923b1b648a22b186b51c

      Author:  UBod <ulrich@bodenhofer.com> 

      Date: 2026-05-13 15:08:26 +0200

      Commit message:


	  
		
 Change of format of inst/NEWS file
 
    
  
    

      Package: podkat

      Commit: a5ee2c46535d6071db4ae2927c3d98390238b392

      Author:  UBod <ulrich@bodenhofer.com> 

      Date: 2026-05-13 15:05:42 +0200

      Commit message:


	  
		
 Change of format of inst/NEWS file
 
    
  
    

      Package: scECODA

      Commit: 4af79f037e3e0613cbcb41be68750e870e342405

      Author:  halterc <chalterbio@gmail.com> 

      Date: 2026-05-13 14:30:00 +0200

      Commit message:


	  
		
 Merge remote-tracking branch 'upstream/devel'
 
    
  
    

      Package: scECODA

      Commit: 3a73b11d4b5ab64a1ab1e5e215482904e0b69fff

      Author:  halterc <chalterbio@gmail.com> 

      Date: 2026-05-13 11:46:51 +0200

      Commit message:


	  
		
 Update examples
 
    
  
    

      Package: scECODA

      Commit: 80f07d8d61781efb4a2a259cb44f53e6cb49c36b

      Author:  halterc <chalterbio@gmail.com> 

      Date: 2026-05-13 11:46:51 +0200

      Commit message:


	  
		
 Update examples
 
    
  
    

      Package: scECODA

      Commit: 09c75d57d9c2b75be6b847ae41b4d4f2812902da

      Author:  halterc <chalterbio@gmail.com> 

      Date: 2026-05-08 10:32:37 +0200

      Commit message:


	  
		
 Update README
 
    
  
    

      Package: scFastDE

      Commit: e9a9d8837ff66391c50318899091367ce82851b9

      Author:  SubhadipJana1409 <subhadipjana1409@gmail.com> 

      Date: 2026-05-13 12:09:07 +0530

      Commit message:


	  
		
 v0.99.2: stability improvements and code refinements
 
    
  
    

      Package: scBatchQC

      Commit: 53175b94d5504a614c97d442536c837d6952e911

      Author:  SubhadipJana1409 <subhadipjana1409@gmail.com> 

      Date: 2026-05-13 11:39:59 +0530

      Commit message:


	  
		
 v0.99.2: stability improvements, updated QC backend and tests
 
    
  
    

      Package: spatialHeatmap

      Commit: 9b077b1ab08aa63474bcb9ab012fc71963d93df5

      Author:  jianhaizhang <jzhan067@ucr.edu> 

      Date: 2026-05-12 20:17:40 -0700

      Commit message:


	  
		
 Fixed errors on Bioc devel.
 
    
  
    

      Package: epigraHMM

      Commit: 17ec9bb8e25b7566427d107100e9ad6da05add40

      Author:  Pedro Baldoni <pedrobaldoni@gmail.com> 

      Date: 2026-05-13 09:38:42 +1000

      Commit message:


	  
		
 version bump in devel
 
    
  
    

      Package: epigraHMM

      Commit: 5486f9d930a3a7491d8df59a78c345e60d2488ac

      Author:  Pedro Baldoni <pedrobaldoni@gmail.com> 

      Date: 2026-05-13 09:37:46 +1000

      Commit message:


	  
		
 Fix plotPatterns function to handle case with a single genomic window/row. Now using 500bp in the case study to speed up vignette build.
 
    
  
    

      Package: goSorensen

      Commit: 2d4ad98447cd238334a353098acc80e2720f5043

      Author:  pablof1988 <pablojfm1988@gmail.com> 

      Date: 2026-05-12 15:55:23 -0500

      Commit message:


	  
		
 version without GO level restrictions
 
    
  
    

      Package: metabom8

      Commit: 45e02263ea363d8cabbf2f437632a487381aee4a

      Author:  tk <tkimhofer@gmail.com> 

      Date: 2026-05-12 23:02:47 +0200

      Commit message:


	  
		
 patch bump v after citatation fix
 
    
  
    

      Package: metabom8

      Commit: b7220a65e026cd4420c1877c4dcd180683d7fb68

      Author:  tk <tkimhofer@gmail.com> 

      Date: 2026-05-12 23:02:01 +0200

      Commit message:


	  
		
 rm packageDescription fun - meta obj natively injected
 
    
  
    

      Package: HuBMAPR

      Commit: 947b3b879e5759035a46b2afa2ba74972883f46d

      Author:  christinehou11 <chou11@jh.edu> 

      Date: 2026-05-12 14:54:26 -0500

      Commit message:


	  
		
 version bump up
 
    
  
    

      Package: HuBMAPR

      Commit: 0e16e69a98b8e0d96401e281965005e4ea66a6e1

      Author:  christinehou11 <chou11@jh.edu> 

      Date: 2026-05-12 14:43:26 -0500

      Commit message:


	  
		
 version bump up in devel
 
    
  
    

      Package: HuBMAPR

      Commit: b7ace14e6c5ebbda7c75ddd968898789da816a1d

      Author:  christinehou11 <chou11@jh.edu> 

      Date: 2026-05-12 14:42:59 -0500

      Commit message:


	  
		
 update affiliation
 
    
  
    

      Package: HuBMAPR

      Commit: 827fc446b2105578725e0a4703d93312445c432a

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

      Date: 2026-04-07 08:52:14 +0200

      Commit message:


	  
		
 Merge pull request #15 from christinehou11/pryr_removed

Pryr removed 
    
  
    

      Package: HuBMAPR

      Commit: 5c48bf675ad33dfa63eb01315951567b03542c70

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

      Date: 2026-04-07 08:50:47 +0200

      Commit message:


	  
		
 Merge branch 'devel' into pryr_removed 
    
  
    

      Package: HuBMAPR

      Commit: 8aeead720f4cb60f75a31a08e0f3fa5694bbdd4d

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

      Date: 2026-04-05 16:29:03 +0200

      Commit message:


	  
		
 version bump, 1.5.1
 
    
  
    

      Package: HuBMAPR

      Commit: 48d167f8fb2d82cc6ee147140a07330df39eef6a

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

      Date: 2026-04-05 16:28:15 +0200

      Commit message:


	  
		
 changing dependency for the vignette
 
    
  
    

      Package: HuBMAPR

      Commit: 5f38b33974c65dddc98722e857680d7549947e31

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

      Date: 2026-04-05 16:28:01 +0200

      Commit message:


	  
		
 pryr got removed from CRAN, functionality superseded in this case via lobstr - pryr::object_size -> lobstr::obj_size
 
    
  
    

      Package: extraChIPs

      Commit: 66c6a95a43f2716d0fb50d120bc6bdacd853f06f

      Author:  Stevie Ped <stephen.pederson.au@gmail.com> 

      Date: 2026-05-13 02:02:32 +0930

      Commit message:


	  
		
 Version bump after bugfix
 
    
  
    

      Package: extraChIPs

      Commit: 5cf536ec43705867fc33493153acc46d0421b307

      Author:  Stevie Ped <stephen.pederson.au@gmail.com> 

      Date: 2026-05-13 01:41:53 +0930

      Commit message:


	  
		
 Added label fill to plotSplitDonut
 
    
  
    

      Package: extraChIPs

      Commit: f8e708cd390f9e51ba0ada8a7702c10f00e03376

      Author:  Stevie Ped <stephen.pederson.au@gmail.com> 

      Date: 2026-05-13 01:00:46 +0930

      Commit message:


	  
		
 Updated to edgeR v4.0 methods for dispersions
 
    
  
    

      Package: scrapbook

      Commit: dbb6f811df42b9f87f928fb59a7dbf8488b06361

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

      Date: 2026-05-12 22:40:12 +1000

      Commit message:


	  
		
 Cleaned up text and explanations in the PCA chapter.
 
    
  
    

      Package: scrapbook

      Commit: ca139a67f336c13cc3b7353ce687d1f4c984e8fc

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

      Date: 2026-05-12 17:38:27 +1000

      Commit message:


	  
		
 Tidied up wording for the feature selection chapter.
 
    
  
    

      Package: looplook

      Commit: d90ff0e6766b82d113a6b714c959a4e4663519be

      Author:  Ying Zhang <12207129@zju.edu.cn> 

      Date: 2026-05-12 16:58:47 +0800

      Commit message:


	  
		
 Remove html
 
    
  
    

      Package: looplook

      Commit: 4e6bdc925a3bc8b99dfcb2985844be0cbc41ac4e

      Author:  Ying Zhang <12207129@zju.edu.cn> 

      Date: 2026-05-12 16:52:19 +0800

      Commit message:


	  
		
 Fix connectivity raincloud regression
 
    
  
    

      Package: looplook

      Commit: 21ed3c970aae2175cfbb015c234619e2f8be7a8f

      Author:  Ying Zhang <12207129@zju.edu.cn> 

      Date: 2026-05-12 16:46:52 +0800

      Commit message:


	  
		
 Fix connectivity raincloud regression and restore p-value subtitles
 
    
  
    

      Package: scRepertoire

      Commit: 0d1fe84ebdca53b9cbac9c75ab7f9cd08def1703

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-05-12 05:32:33 -0500

      Commit message:


	  
		
 better logo handling
 
    
  
    

      Package: ProteinBatcher

      Commit: e4791a576bec6014913b1cd4e56c37f6887e7fc2

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2026-05-12 10:20:05 +0200

      Commit message:


	  
		
 version
 
    
  
    

      Package: ProteinBatcher

      Commit: 1ea4ac369b6ec6c95df17c1026f2b6e9d0df4a78

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2026-05-12 10:13:55 +0200

      Commit message:


	  
		
 Remove ProteinBatcher.Rproj from git tracking (BiocCheck ERROR fix)
 
    
  
    

      Package: Ularcirc

      Commit: 9e0304952edda76ebf11fb86d2fa5a76b092a3be

      Author:  David Humphreys <dth569@gadi-login-09.gadi.nci.org.au> 

      Date: 2026-05-12 16:03:15 +1000

      Commit message:


	  
		
 Remove dependency on Organism.dplyr (package removed in Bioc 3.24)
 
    
  
    

      Package: MSTree

      Commit: cfd81b6b0cd7b00ec852a03ce3bb0c687583a4cc

      Author:  abedkurdi <abed_kurdi@hotmail.com> 

      Date: 2026-05-12 08:39:23 +0300

      Commit message:


	  
		
 pushing 0.99.6 with latest changes
 
    
  
    

      Package: igblastr

      Commit: ab6ea279e82c86f667f8bfbe3289c356cab37357

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

      Date: 2026-05-11 22:12:29 -0700

      Commit message:


	  
		
 igblastr 1.3.1: Fix representation of missing values in custom annotations

We cannot use the string NA to represent missing values in the custom "ndm"
or ".aux" files that we create, because this crashes IgBLAST!
So now we use the following special values instead:
  o "N/A" for missing character values;
  o -1 for missing integer values.
See long comment at the top of R/igdata-IO.R for more information.
 
    
  
    

      Package: spammR

      Commit: 41f8da0c4eb5b55c8d97dae5ee8cce0537d1db87

      Author:  Sara JC Gosline <sara.gosline@pnnl.gov> 

      Date: 2026-05-11 21:12:45 -0700

      Commit message:


	  
		
 updated
 
    
  
    

      Package: growkar

      Commit: f003e382cebb2b87a677a87ccb49cdc97b96ba6d

      Author:  Pooja Sethiya <poojasethiya24@gmail.com> 

      Date: 2026-05-12 13:17:56 +1000

      Commit message:


	  
		
 Bump version to 0.99.1
 
    
  
    

      Package: growkar

      Commit: bed575f69764469ada30086c69024c7311cf7a57

      Author:  Pooja Sethiya <poojasethiya24@gmail.com> 

      Date: 2026-05-06 09:02:32 +1000

      Commit message:


	  
		
 Remove local system files
 
    
  
    

      Package: growkar

      Commit: 6205f8977b86768bbbfaea608f9d17a00dc4a663

      Author:  Pooja Sethiya <poojasethiya24@gmail.com> 

      Date: 2026-05-06 09:00:05 +1000

      Commit message:


	  
		
 Remove local history and system files
 
    
  
    

      Package: growkar

      Commit: 9fbf1c847f38fb874ae02c632e9dbf76882c13f7

      Author:  Pooja Sethiya <poojasethiya24@gmail.com> 

      Date: 2026-05-06 08:56:36 +1000

      Commit message:


	  
		
 Remove local system files from repository
 
    
  
    

      Package: growkar

      Commit: e2e528c1a777035f6f25296bbdcab8cc0bd3827c

      Author:  Pooja Sethiya <poojasethiya24@gmail.com> 

      Date: 2026-05-05 16:03:11 +1000

      Commit message:


	  
		
 R version updated
 
    
  
    

      Package: growkar

      Commit: 362c0e72de9a6ba77369c725261c66ad6580cfdf

      Author:  Pooja Sethiya <poojasethiya24@gmail.com> 

      Date: 2026-05-05 15:55:31 +1000

      Commit message:


	  
		
 root hexasticker removed
 
    
  
    

      Package: growkar

      Commit: 02803555067a2872215873e5d38b12a01d23670e

      Author:  Pooja Sethiya <poojasethiya24@gmail.com> 

      Date: 2026-05-05 15:52:56 +1000

      Commit message:


	  
		
 hexasticker updated
 
    
  
    

      Package: growkar

      Commit: 1a108d6d911225c8a71a01fa6ab42edefa28a672

      Author:  Pooja Sethiya <poojasethiya24@gmail.com> 

      Date: 2026-05-05 15:11:06 +1000

      Commit message:


	  
		
 duplicate hexasticker removed
 
    
  
    

      Package: OmniAgeR

      Commit: e249664a0be261eec15b1be77a579b348931c4f2

      Author:  Zhaozhen Du <duzhaozhen@inspur.com> 

      Date: 2026-05-09 13:33:48 +0800

      Commit message:


	  
		
 Bump version to trigger webhook build
 
    
  
    

      Package: OmniAgeR

      Commit: fd02947845f38c6f60d334be191ec601c60b8b08

      Author:  Zhaozhen Du <duzhaozhen@inspur.com> 

      Date: 2026-05-09 13:24:03 +0800

      Commit message:


	  
		
 Fix TIMEOUT: disable vignette evaluation and update DESCRIPTION version
 
    
  
    

      Package: ontoProc2

      Commit: afb9147c1cd4341a4f5ed2b76d32e4f688b3cf10

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

      Date: 2026-05-11 19:01:49 -0400

      Commit message:


	  
		
 remove swap file
 
    
  
    

      Package: ontoProc2

      Commit: 5631ddd1da6a770d3ccfe6ebf879244016c52899

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

      Date: 2026-05-11 19:01:03 -0400

      Commit message:


	  
		
 solve warnings in BiocCheck
 
    
  
    

      Package: miloR

      Commit: ff744bbb5d793163b59f28483c1ad05192fddc15

      Author:  MikeDMorgan <michael.morgan@abdn.ac.uk> 

      Date: 2026-05-11 22:26:50 +0100

      Commit message:


	  
		
 fix missing semicolon
 
    
  
    

      Package: ontoProc2

      Commit: e0795b9871207118f7eef95af48917f42bae6ee0

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

      Date: 2026-05-11 17:17:14 -0400

      Commit message:


	  
		
 update doc per review, solve bug in cells_with_pmp, and use copy instead of move in bfcadd
 
    
  
    

      Package: ontoProc2

      Commit: b69ee459b53a652bd9870dfc2fd2ba46ece3bdfd

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

      Date: 2026-05-11 15:16:54 -0400

      Commit message:


	  
		
 Merge branch 'devel' of github.com:BiocStaging/ontoProc2 into devel
 
    
  
    

      Package: ontoProc2

      Commit: 12fb61866d5ad9f8a0bce66fa5b38b54d72543df

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

      Date: 2026-05-11 15:16:02 -0400

      Commit message:


	  
		
 use tempdir for file manipulations
 
    
  
    

      Package: ontoProc2

      Commit: 322f270189075d4c2bc4e642dbf9062c85a90583

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

      Date: 2026-04-11 13:54:03 -0400

      Commit message:


	  
		
 Merge remote-tracking branch 'bioc/devel'
 
    
  
    

      Package: ontoProc2

      Commit: 9ce7e66513354152f09576561e8e446cb28f88d7

      Author:  Vince Carey <stvjc@channing.harvard.edu> 

      Date: 2026-03-31 13:53:18 -0400

      Commit message:


	  
		
 Merge pull request #7 from vjcitn/devel

adding vignette 
    
  
    

      Package: CyTOFpower

      Commit: b8a830642677d24e7beccf0a71e3b1f2f56c53ea

      Author:  Anne-Maud Ferreira <anne-maud.ferreira@epfedu.fr> 

      Date: 2026-05-02 16:33:22 -0700

      Commit message:


	  
		
 Merge upstream/devel: resolve version conflict
 
    
  
    

      Package: CyTOFpower

      Commit: dea9871c1aaefd873379854eb57ff33d823f61a9

      Author:  Anne-Maud Ferreira <anne-maud.ferreira@epfedu.fr> 

      Date: 2026-05-02 16:31:30 -0700

      Commit message:


	  
		
 Bump version to 1.17.4
 
    
  
    

      Package: CyTOFpower

      Commit: edd1ce5f104fe679b944f0796e738d8bb9c9c8a8

      Author:  Anne-Maud <anne-maud@Anne-Mauds-MacBook-Neo.local> 

      Date: 2026-05-02 16:28:52 -0700

      Commit message:


	  
		
 Fix: suppress mbest warnings in function_run_cytoGLMM and update test expectations
 
    
  
    

      Package: SEMPLR

      Commit: 0bc12fab3869811db4427761f5c5fbafd5ab72db

      Author:  Grace Kenney <kenney.grace6@gmail.com> 

      Date: 2026-05-11 14:37:02 -0400

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: SEMPLR

      Commit: a1ad81a828cd239fadeb4738cc91c95debd5bcee

      Author:  Grace Kenney <kenney.grace6@gmail.com> 

      Date: 2026-05-11 14:30:53 -0400

      Commit message:


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

      Package: SEMPLR

      Commit: 16f0c313e83bb7268b1b3a8714f0d7683e9b0404

      Author:  Grace Kenney <kenney.grace6@gmail.com> 

      Date: 2026-04-30 12:41:58 -0400

      Commit message:


	  
		
 fix bug that was merging meta data incorrectly
 
    
  
    

      Package: rexposome

      Commit: 2a65b5f87612f67d196aae2a521620654e05ab0a

      Author:  Xavier Escribà Montagut <xavier.escriba.montagut@gmail.com> 

      Date: 2026-05-11 19:35:33 +0200

      Commit message:


	  
		
 fix vignettes
 
    
  
    

      Package: variancePartition

      Commit: 97c8bfeab0be7524803b7b16bf1d4cb59a6df477

      Author:  Gabriel Hoffman <gabriel.hoffman@gmail.com> 

      Date: 2026-05-11 12:49:27 -0400

      Commit message:


	  
		
 update
 
    
  
    

      Package: variancePartition

      Commit: 34a3d47901950ef913e388f6fd86177c07d74c23

      Author:  Gabriel Hoffman <gabriel.hoffman@gmail.com> 

      Date: 2026-05-11 12:49:24 -0400

      Commit message:


	  
		
 update
 
    
  
    

      Package: variancePartition

      Commit: f37a28ed6494ffb2781d5ba9e26df821dca75964

      Author:  Gabriel Hoffman <gabriel.hoffman@gmail.com> 

      Date: 2026-05-11 12:46:25 -0400

      Commit message:


	  
		
 1.43.1
 
    
  
    

      Package: variancePartition

      Commit: c06d832b214f9a753c44565d40844e8c23d7a0d6

      Author:  Gabriel Hoffman <gabriel.hoffman@gmail.com> 

      Date: 2026-03-19 09:20:59 -0400

      Commit message:


	  
		
 1.40.2
 
    
  
    

      Package: looplook

      Commit: 77d09d2a2ab96268a107282188d430a7266fa12e

      Author:  Ying Zhang <12207129@zju.edu.cn> 

      Date: 2026-05-11 22:57:08 +0800

      Commit message:


	  
		
 Reduce SPB runtime and bump version1
 
    
  
    

      Package: looplook

      Commit: f930fd65b40c0799fd3b4759cd8c3a9d44fc8c25

      Author:  Ying Zhang <12207129@zju.edu.cn> 

      Date: 2026-05-11 22:43:19 +0800

      Commit message:


	  
		
 Optimize tests for SPB build time
 
    
  
    

      Package: MSTree

      Commit: f38d5bb8ede4e619123b05282815f662f916da26

      Author:  abedkurdi <abed_kurdi@hotmail.com> 

      Date: 2026-05-11 16:55:36 +0300

      Commit message:


	  
		
 making changes according to the reviewer's suggestions
 
    
  
    

      Package: MSTree

      Commit: 4f6accda8146828dc293d92971ae38dad501483d

      Author:  abedkurdi <abed_kurdi@hotmail.com> 

      Date: 2026-05-11 16:37:17 +0300

      Commit message:


	  
		
 making changes according to the reviewer's suggestions
 
    
  
    

      Package: MSTree

      Commit: 81e743492285fb1ef9728272e7f8772ed542926d

      Author:  abedkurdi <abed_kurdi@hotmail.com> 

      Date: 2026-05-11 16:29:35 +0300

      Commit message:


	  
		
 making changes according to the reviewer's suggestions
 
    
  
    

      Package: looplook

      Commit: 6c6c58544ee386eab25963f6bb221915abd01f92

      Author:  Ying Zhang <12207129@zju.edu.cn> 

      Date: 2026-05-11 20:32:26 +0800

      Commit message:


	  
		
 Reduce SPB runtime and bump version
 
    
  
    

      Package: metabom8

      Commit: af4ecfca7df86b8f6b85dc6b6a57b1430db5ac9c

      Author:  tk <tkimhofer@gmail.com> 

      Date: 2026-05-11 15:01:29 +0200

      Commit message:


	  
		
 upd doi covid ds
 
    
  
    

      Package: metabom8

      Commit: 86cc95ee86eb8f4eaa48ac6b5a79edef6a5017eb

      Author:  tk <tkimhofer@gmail.com> 

      Date: 2026-05-11 14:55:28 +0200

      Commit message:


	  
		
 upd doi cov data
 
    
  
    

      Package: miaDash

      Commit: 27b79e157eb1d07fec74f6235cfcb70d1075d519

      Author:  Giulio <giuliobene2000@gmail.com> 

      Date: 2026-05-11 14:00:00 +0300

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: miaDash

      Commit: 605ab0d250dddaf1a2510e43ddc322759dee71da

      Author:  Giulio <giuliobene2000@gmail.com> 

      Date: 2026-04-23 13:22:54 +0300

      Commit message:


	  
		
 Update docker files
 
    
  
    

      Package: miaDash

      Commit: b96d4c9e34f8b1a4a5e4ece6fc4c36451cadca58

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2026-04-23 13:18:13 +0300

      Commit message:


	  
		
 Use latest instead of devel miadash in dockerfile 
    
  
    

      Package: miaDash

      Commit: 300b7f53cef4d6b7d7b3d321eb6943a351d43852

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2026-04-21 11:24:56 +0300

      Commit message:


	  
		
 Update Rscript command to install packages with remotes 
    
  
    

      Package: miaDash

      Commit: 4d9eef672c7683a0301daed7ed578eb7af1b317e

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2026-04-20 21:50:21 +0300

      Commit message:


	  
		
 Replace remotes with pak for local installation in Docker 
    
  
    

      Package: miaDash

      Commit: 0571930103d945a4287840356e0549a3876ae81a

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2026-04-20 21:41:51 +0300

      Commit message:


	  
		
 Replace devtools with remotes for package installation in Docker 
    
  
    

      Package: miaDash

      Commit: c0532d0f8558d9f25f1eb25b8a2137d9573ee169

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2026-04-20 21:30:44 +0300

      Commit message:


	  
		
 Change Docker Rscript command to use install_local 
    
  
    

      Package: miaDash

      Commit: e0f54848b7f3dfa76fdc15a02f745bf8d73fbbfa

      Author:  Giulio <giuliobene2000@gmail.com> 

      Date: 2026-04-20 20:51:32 +0300

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: miaDash

      Commit: e6de93b67be3a16a52e9a667ba8bb848c29bac47

      Author:  Giulio <giuliobene2000@gmail.com> 

      Date: 2026-04-20 20:48:05 +0300

      Commit message:


	  
		
 Solve conflicts with Bioconductor version
 
    
  
    

      Package: miaDash

      Commit: bbc43dbb7b3762229966ed99172708e262ffe2f3

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2026-04-20 13:33:21 +0300

      Commit message:


	  
		
 Merge pull request #28 from microbiome/tracker

Code tracker, general observers and exports 
    
  
    

      Package: miaDash

      Commit: 31f6e9a09df8622d383d000250a02a9d22df39d9

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2026-04-20 13:07:11 +0300

      Commit message:


	  
		
 Add rbiom to DESCRIPTION dependencies 
    
  
    

      Package: miaDash

      Commit: 87688059997ef007d3e7fc74f9c249b768ef23a5

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2026-04-20 12:45:30 +0300

      Commit message:


	  
		
 Add general observers, code tracker and exports
 
    
  
    

      Package: miaDash

      Commit: 7c7a69dc0e01b4bb80033c511ec6e297ee28c2c5

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2026-04-20 00:16:46 +0300

      Commit message:


	  
		
 Catch warnings and multi-line errors, download output in several formats
 
    
  
    

      Package: miaDash

      Commit: 3d423c6d747ea590681ca900e5c7fab708b68295

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2026-04-19 12:48:07 +0300

      Commit message:


	  
		
 Enable vignettes, citation and session buttons
 
    
  
    

      Package: miaDash

      Commit: 2bed17660e6c0b3c15210ae2b6d249e225a81ed0

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2026-04-18 22:25:54 +0300

      Commit message:


	  
		
 Add philr and improve code tracker
 
    
  
    

      Package: miaDash

      Commit: 9548b7c82993149ce9cac3af3c4ae00619e8b229

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2026-04-17 23:03:54 +0300

      Commit message:


	  
		
 Add tracker prototype
 
    
  
    

      Package: miaDash

      Commit: 83a435f68b9c889909e276a45e6f4c787788f553

      Author:  Giulio <giuliobene2000@gmail.com> 

      Date: 2025-09-10 16:36:39 +0300

      Commit message:


	  
		
 Simplify foreign observers
 
    
  
    

      Package: miaDash

      Commit: da37a962f02e1d833e9502366d03458be94b29f7

      Author:  Giulio <giuliobene2000@gmail.com> 

      Date: 2025-09-10 16:01:28 +0300

      Commit message:


	  
		
 Split landing page definition into multiple functions
 
    
  
    

      Package: scrapper

      Commit: db414924f0dfe17be005f411061c0152ad2b9dd3

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

      Date: 2026-05-11 20:38:29 +1000

      Commit message:


	  
		
 fitVarianceTrend and relatives now default to use.min.width=TRUE.

This improves fitting performance at high abundances for most scRNA-seq
datasets. We explicitly disable this mode for spike-in transcripts where the
dataset probably can't meet the minimum number of points per window.

Also bumped version and date.
 
    
  
    

      Package: scrapper

      Commit: c36f9aa5cd6889e338c264df27acfbfde6fd1f85

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

      Date: 2026-05-10 02:16:27 +1000

      Commit message:


	  
		
 Renamed runPca() arguments for centering scores per block.

We also respect the C++ default (which is now the same as the R default).
 
    
  
    

      Package: scrapbook

      Commit: 6efe5ac927a438ffb2cd003b01c106418ca9926d

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

      Date: 2026-05-11 20:36:04 +1000

      Commit message:


	  
		
 Updated feature selection chapter for the new use.min.width=TRUE default.

Also added back the endogenous trend for comparison to the spike-in trend.

Also bumped version and date.
 
    
  
    

      Package: scrapbook

      Commit: ead9096bb51fd64b994590a959eaf8e9955741d1

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

      Date: 2026-05-11 20:35:27 +1000

      Commit message:


	  
		
 Merge remote-tracking branch 'upstream/devel'
 
    
  
  


</div>

</div>