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Package: methylclock
Commit: 2f1a002aa4432b374f74eba932e7abcc5ea769ec
Author: dpelegri <43083225+dpelegri@users.noreply.github.com>
Date: 2026-10-18 18:18:28 +0200
Commit message:

 Correct catalog labels and bump version to 1.99.3

Adds an optional `estimates` field to the clock registry: the NEOage clocks now read in weeks and Levine as phenotypic age. Also documents the arrays column as native platforms, corrects the NEOage reference and adds a vignette note on input normalization. Details in NEWS.md.
Package: ClustIRR
Commit: 4bb2099d8e491acae6a0f01a519d5c2df22be6d2
Author: snaketron <snaketron@users.noreply.github.com>
Date: 2026-10-18 15:11:22 +0200
Commit message:

 Fix dataset Rd usage entries to remove stray str() calls from data object documentation.
Package: ClustIRR
Commit: be65fe4f2af5af8ed51f211d525dd52e6e0dc3ee
Author: snaketron <simo.kitanovski@proton.me>
Date: 2026-10-18 14:37:53 +0200
Commit message:

 eval=F
Package: ClustIRR
Commit: 4b31490cdaef9d7f41de466f58b35db715f3982a
Author: snaketron <simo.kitanovski@proton.me>
Date: 2026-10-18 14:23:43 +0200
Commit message:

 README + int G -> array
Package: ClustIRR
Commit: 6073875bd5b954814a7e61f12fa46fd636899e00
Author: snaketron <simo.kitanovski@proton.me>
Date: 2026-10-18 14:12:21 +0200
Commit message:

 Merge branch 'main' of github.com:snaketron/ClustIRR
Package: ClustIRR
Commit: 1059822156de8b25394359d14152cc11a51059a1
Author: snaketron <simo.kitanovski@proton.me>
Date: 2026-10-18 14:09:37 +0200
Commit message:

 stan update vector -> array
Package: ClustIRR
Commit: cb448ae916efa09944778184c7fe1e006149dabc
Author: snaketron <snaketron@users.noreply.github.com>
Date: 2026-10-18 13:59:42 +0200
Commit message:

 Update README overview to reflect the eLife paper and ClustIRR workflow described in the abstract
Package: ClustIRR
Commit: 3b34699e1e23d6a18bc51d46c5553cae26885645
Author: snaketron <simo.kitanovski@proton.me>
Date: 2026-10-18 13:55:17 +0200
Commit message:

 int > array in data
Package: ClustIRR
Commit: 3cbe48f1b2eeb5aeacbb5780350f5e388eb0700d
Author: snaketron <simo.kitanovski@proton.me>
Date: 2026-10-18 13:36:33 +0200
Commit message:

 fix citation
Package: ClustIRR
Commit: c8729af0f94f390df2fe4524685734ad0e00d913
Author: snaketron <simo.kitanovski@proton.me>
Date: 2026-10-18 13:28:55 +0200
Commit message:

 news and citations added
Package: ClustIRR
Commit: fd64157facd3d2e1013e136aa409b6ad8fd9c8db
Author: snaketron <simo.kitanovski@proton.me>
Date: 2026-10-18 13:18:37 +0200
Commit message:

 updated vignette, no delta
Package: ClustIRR
Commit: 2678de6320d1ef9e16a2e3a800771514511fe9c6
Author: snaketron <simo.kitanovski@proton.me>
Date: 2026-10-18 13:15:19 +0200
Commit message:

 delta out
Package: ClustIRR
Commit: a8b19acfc81c3d3b1198990f5db0b41510d56615
Author: snaketron <simo.kitanovski@proton.me>
Date: 2026-10-18 13:14:43 +0200
Commit message:

 model with new array syntax
Package: ClustIRR
Commit: 16707a173a8b2d8977ab2e9efc38958c697b9d7d
Author: snaketron <simo.kitanovski@proton.me>
Date: 2026-10-18 13:14:22 +0200
Commit message:

 community ID to motif
Package: ClustIRR
Commit: 5404c4e36c2d1eb4b364f2611e3c640f2d3f96fe
Author: snaketron <simo.kitanovski@proton.me>
Date: 2026-10-18 13:13:22 +0200
Commit message:

 default gmi=0.9
Package: ClustIRR
Commit: 5f3094945ccb986c809ecf6a6882ecc880f2db93
Author: snaketron <simo.kitanovski@proton.me>
Date: 2026-10-18 13:11:56 +0200
Commit message:

 blast checks and exports
Package: ClustIRR
Commit: 7d4fcc683fc74ac793fca4db19eb841436dac4b4
Author: snaketron <simo.kitanovski@proton.me>
Date: 2026-10-18 13:10:55 +0200
Commit message:

 merge_clustirrs export added
Package: ClustIRR
Commit: 3c3c0695edc6134501a6fe35e353a2ce4f4a7c5d
Author: snaketron <simo.kitanovski@proton.me>
Date: 2026-10-18 13:10:35 +0200
Commit message:

 bump v
Package: ClustIRR
Commit: 96a5b9590a3dfb06234aa00675711b0d23ffaf2c
Author: snaketron <simo.kitanovski@proton.me>
Date: 2026-10-18 13:10:00 +0200
Commit message:

 merging clustirr objects
Package: cellmig
Commit: dcece92c0ed7f3e0f89250b6e20ce9f8a5b87771
Author: snaketron <simo.kitanovski@proton.me>
Date: 2026-10-18 13:32:55 +0200
Commit message:

 merge
Package: cellmig
Commit: b9808ea56f20cc371cbf0275b0c865601d31cf7b
Author: snaketron <simo.kitanovski@proton.me>
Date: 2026-10-18 13:30:09 +0200
Commit message:

 citation fixed, version bump
Package: cellmig
Commit: f806472dd9933e6b2ec9d459a032c24cd0b6a3c4
Author: snaketron <simo.kitanovski@proton.me>
Date: 2026-09-13 22:16:28 +0200
Commit message:

 citation
Package: cellmig
Commit: 49955917963c6c0db854419f359ba49cb4b5ce58
Author: snaketron <simo.kitanovski@proton.me>
Date: 2026-09-13 22:16:07 +0200
Commit message:

 bump
Package: PinPath
Commit: a3bac715cc43639efc8329f93c86cc9129204949
Author: Jarno Koetsier <jarno.koetsier@gmail.com>
Date: 2026-10-18 12:01:52 +0200
Commit message:

 Update to version 0.99.6

+ Improved ID mapping for KEGG pathways.
+ Darker color palette for the default qualitative color scale.
Package: clusterProfiler
Commit: bec51e53d2fddc753d9c6a755549bc486dc0232f
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2026-10-18 16:32:23 +0800
Commit message:

 fixd kegg organism source
Package: clusterProfiler
Commit: 265968cd3d1a797f4e00053364cc4bdc2f635e9e
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2026-10-18 15:18:48 +0800
Commit message:

 perf(enrichGO): stop scanning the whole mapping for each input id

`hybrid_ids_for_input()` looked up each input id with
`mapping$entrez[mapping$source == id]`, a linear scan of the full
keytype-to-Entrez mapping per id. A single `split()` plus a named lookup keeps
every Entrez match (a source can map to several), preserves the input order and
the `E:`/`N:` labelling, and is no longer quadratic in the mapping size. A test
pins multi-match, duplicate-id and unmapped-id behaviour.

Honest measurement note: at cluster-sized inputs (600 ids against a 20k-row
mapping) the old scan is ~0.1 s, so this is a robustness/readability change, not
a wall-clock win; the profile attribution that suggested otherwise did not
reproduce in a microbenchmark. The NEWS entry for the restore-path
vectorisation is corrected to report the measured 140 s -> ~70 s range
(69-78 s run-to-run) rather than a single 70.6 s figure.

`make check`: 0 errors, 0 warnings, 0 notes.

Co-Authored-By: Claude <noreply@anthropic.com>
Package: clusterProfiler
Commit: ae9e17d3d9128dab697c92bebeb45441f4c899b0
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2026-10-18 14:42:19 +0800
Commit message:

 perf(enrichGO): map gene-set IDs back in one pass

`restore_hybrid_result()` and `restore_entrez_result_ids()` translated every
gene set with its own `labels[as.character(ids)]` + `unname()` call. Per set
that is tiny; in aggregate it dominated the restore step: on a BP result with
~5,900 tested sets and 390k ID slots it took 7.5 s per call (2026-10-18), and
`compareCluster()` calls it once per cluster.

The new internal `map_gene_set_labels()` concatenates the ids, maps them once,
and splits the result back by the original set lengths. It preserves the list
names (GO ids), the per-set order, the first-occurrence de-duplication and
empty sets, so the output is byte-identical to the loop; a test pins that,
including an empty input. Measured on the 13-cluster PBMC 10k SYMBOL
`compareCluster()` together with the enrichit fixes: 140 s -> 70.6 s, with
7,489 rows, p-values (difference 0), Counts and geneID sets identical.

`make check`: 0 errors, 0 warnings, 0 notes.

Co-Authored-By: Claude <noreply@anthropic.com>
Package: clusterProfiler
Commit: 64e712737da5043ecd7e54993c1548202210919e
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2026-10-18 11:37:19 +0800
Commit message:

 perf(enrichGO): cache the hybrid GSON when no universe is supplied

For a non-ENTREZID keyType with at least one unmappable input ID,
`enrichGO()` builds a hybrid GSON: every OrgDb key mapped to Entrez plus the
native annotations of IDs that have no Entrez mapping. With no `universe`, the
source ids are `AnnotationDbi::keys(OrgDb, keytype)` -- independent of the gene
list -- so the result depends only on (organism, ont, keyType). It was rebuilt
once per call, and `compareCluster()` calls `enrichGO()` once per cluster:
7.7 s per call on human GO BP (PBMC 10k, 13 clusters, 2026-10-18).

The hybrid GSON is now cached in the existing `GO_Env`, keyed by
(organism, ont, keyType), with a deliberately exact ontology match (unlike the
Entrez annotation cache, the hybrid object is already built and has no later
ontology filter). A universe-scoped call builds from gene + universe and neither
reads nor writes the cache; an `evidence`-filtered call is never cached, the
same rule `get_GO_data()` already applies. An unidentifiable organism (NA) never
matches, so it rebuilds rather than serving another organism's annotation.

The hybrid path itself is unchanged and still fires only when an input ID lacks
an Entrez mapping: all-mappable input keeps the existing fast path and never
builds hybrid data or writes the cache. Tests pin both directions:

- all-mappable symbols -> enrichResult, and NO hybrid cache entry is created;
- mixed IDs -> hybrid cache entry exists, is byte-identical across calls, and
  the results agree; a universe-scoped and an evidence-filtered run leave the
  cache untouched;
- `hybrid_cache_usable()` unit test for organism/ont/keytype mismatches.

Measured after enrichit 64f370a (which removed the identity intersect):
13-cluster SYMBOL compareCluster 197 s -> 143 s. `make check`: 0 errors,
0 warnings, 0 notes. Residual, recorded rather than hidden:
`restore_hybrid_result()` still costs ~7 s per cluster and is not cached.

Co-Authored-By: Claude <noreply@anthropic.com>
Package: systemPipeR
Commit: e3a4f7341146f2477fb0addeb299a127ad08e56f
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-10-17 20:30:25 -0700
Commit message:

 Version bump 2.19.7
Package: systemPipeR
Commit: 64383de65e6d669fb9651050dbb6d045f63fcf99
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-10-17 20:30:25 -0700
Commit message:

 Address BiocCheck notes: R dependency, BugReports, chunk labels, sessionInfo

- Depends: R (>= 4.6.0); add BugReports field
- systemPipeR.Rmd: label all chunks in BiocCheck's {r label, ...} form
- systemPipeR_workflows.Rmd: add sessionInfo() chunk
- Fix stray ']' in the NSF funding link of both vignettes
- man: add missing final newline to 12 Rd files
Package: systemPipeR
Commit: 02a46b1b5b50c94fadc3f54e88f599f566527a06
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-10-17 18:14:56 -0700
Commit message:

 Version bump 2.19.6
Package: systemPipeR
Commit: d809922b97f224730666387bd4dd62e52b9e1415
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-10-17 18:14:56 -0700
Commit message:

 man: fix BiocCheck \value and \format warnings

- catmap.Rd, sysargs.Rd: remove \docType{data}. Both document accessor
  methods (catDB, SYSargs), not datasets - the package has no data/ - so
  BiocCheck wanted a \format section. Replace the placeholder "various
  outputs" \value with what each accessor returns.
- Add \value sections to add-methods, config.param, configWF,
  cwlFilesUpdate, moduleload, olRanges, subsetWF, trimbatch,
  LineWise-class, SYSargsList and SYSargsList-class, written from each
  function's return statements.

Documentation only; no R code changed.
Package: edgeR
Commit: aeaebafc6dd4fdd029bf1895cfc03040af650659
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2026-10-18 13:28:51 +1100
Commit message:

 edgeR 4.99.10
- Adjustments to "moderate" filtering settings, making more stringent
Package: systemPipeR
Commit: 932a4796663ab537ad40cfc80a9eab299e9d76de
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-10-17 18:01:39 -0700
Commit message:

 Version bump 2.19.5
Package: systemPipeR
Commit: 99a3cf91e6973cafe6b6fc0d7304fa4d65a5b828
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-10-17 18:01:39 -0700
Commit message:

 makeCATdb(lib=): drop require(), fix GO map lookup for current annotation packages

.sampleDFgene2GO() attached the annotation package with require() so a
bare get("GO") could find its GO map (BiocCheck warning). It now
uses requireNamespace() and get(..., envir = asNamespace(lib)), so nothing
is attached, and stops with a clear message if the package is missing.

The same lines walked the map with eapply(), which needs an environment.
Current annotation packages provide an AnnDbBimap instead, so
makeCATdb(lib = ...) failed for all of them ("argument must be an
environment"). as.list() on the Bimap gives the same named per-gene GO
lists; lapply() replaces eapply().

Tested with org.At.tair.db: MF/BP/CC tables 43203/48404/54685 rows, all
GO IDs in their own ontology; makeCATdb() -> catDB in 1.6 min;
GOHyperGAll() returns 10123 rows.
 </pre>
    </div>
  
    

      Package: systemPipeR

      Commit: 588f4e4d3fe47f69dcaa614f8aaf5e5544c9546c

      Author:  tgirke <tgirke@citrus.ucr.edu> 

      Date: 2026-10-17 17:20:53 -0700

      Commit message:


	  
		
 Vignette: fix two broken links

- [here](appendstep) -> [here](#appendstep); the missing '#' made it a
  relative link to a nonexistent page.
- edgeR link: drop a leftover LaTeX '\href{' from the markdown URL.
 

    

  
    

      Package: systemPipeR

      Commit: 76ddba76a0212409860c8d477eb342db7a40d970

      Author:  tgirke <tgirke@citrus.ucr.edu> 

      Date: 2026-10-17 17:09:14 -0700

      Commit message:


	  
		
 README: add TUTORIAL button linking to the rendered vignette on gh-pages
 

    

  
    

      Package: systemPipeR

      Commit: 4fcee8b6f873de78f91e7758a1a3111af5228b24

      Author:  tgirke <tgirke@citrus.ucr.edu> 

      Date: 2026-10-17 16:59:02 -0700

      Commit message:


	  
		
 Version bump 2.19.4
 

    

  
    

      Package: systemPipeR

      Commit: 2d699d0e35ec8b66001d7224d30f6700407bb4ec

      Author:  tgirke <tgirke@citrus.ucr.edu> 

      Date: 2026-10-17 16:59:02 -0700

      Commit message:


	  
		
 Fix BiocCheck T/F and class() == / != warnings

- T/F: simplify = F -> FALSE (chipseq.R), stdout = T -> TRUE
  (utilities.R). In seeFastq's per-base quality block (fastqQuality.R),
  rename the local variables A/C/G/T to qA/qC/qG/qT; T masked TRUE.
- class(x) == / != "..." (49 places) replaced by type:
  - S4 classes (SYSargs, SYSargs2, VENNset, INTERSECTset, GRanges,
    IRanges, TxDb, BamFileList, DNAString, DNAStringSet): is(x, "Class").
  - "list": inherits(x, "list"), which keeps the old result for
    data.frames (is(data.frame(), "list") is TRUE).
  - "data.frame" / "character" / "matrix": is.data.frame() /
    is.character() / is.matrix().
  For multi-class objects (e.g. tibbles) the old comparisons returned a
  vector, which errors inside if() in R >= 4.2.

Old and new builds give identical output on a 21-case smoke test
(olRanges, predORF, overLapper/vennPlot/olBarplot, run_edgeR, and the
argument checks).
 

    

  
    

      Package: systemPipeR

      Commit: 462ad88f6e32c7d54a16a25a0bc86f6e8e527d33

      Author:  tgirke <tgirke@citrus.ucr.edu> 

      Date: 2026-10-17 16:40:26 -0700

      Commit message:


	  
		
 Version bump 2.19.3
 

    

  
    

      Package: systemPipeR

      Commit: 686bc08092cac4dc1d6b0cba85622a03f1206d7a

      Author:  tgirke <tgirke@citrus.ucr.edu> 

      Date: 2026-10-17 16:32:15 -0700

      Commit message:


	  
		
 Fix the three BiocCheck errors

- DESCRIPTION: replace Author/Maintainer with Authors@R (Girke aut/cre;
  Zhang, Cassol, Gongol, Backman aut, matching inst/CITATION).
- NAMESPACE: delete the commented-out exportPattern line; BiocCheck
  matches it as text. Also drop the now-unused download.file/unzip
  imports.
- cwlFilesUpdate(): copy cwl/ and docopt.R/ from the installed package
  (system.file) instead of downloading them from GitHub. The bundled
  copy is the same version (cwl_version 1.0.43) as the cwl_collection
  repo, which has not changed since 2022. Same signature and messages.
 

    

  
    

      Package: pathlinkR

      Commit: 392f330295465ce495f2063936ab86a3a1d03027

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-10-17 16:31:17 -0700

      Commit message:


	  
		
 Drop a direction if not present in the data.
 

    

  
    

      Package: systemPipeR

      Commit: cb3817998d7a6ef62a4a399e2920a3fdde3a0a24

      Author:  tgirke <tgirke@citrus.ucr.edu> 

      Date: 2026-10-17 16:21:00 -0700

      Commit message:


	  
		
 Version bump 2.19.2
 

    

  
    

      Package: systemPipeR

      Commit: 7446c751c359bd9dca184ce9bc8e7a04c4fb2062

      Author:  tgirke <tgirke@citrus.ucr.edu> 

      Date: 2026-10-17 16:21:00 -0700

      Commit message:


	  
		
 Skip command-line tool tests by default; fix docopt test failure

r-universe's site Rprofile unsets CI, so skip_on_ci() never fired there
and tests calling hisat2, bowtie2, trimmomatic and macs2 ran and failed.
Add skip_if_no_cmdline() (tests/testthat/helper-skip.R): these tests now
run only with SPR_TEST_CMDLINE=true and when the tools are in PATH.
Existing skip_on_bioc()/skip_on_ci() guards are unchanged.

check_catDB queries plants.ensembl.org; also skip it on CRAN-like checks.

test.doc.R loaded docopt without using it; docopt is not in Suggests, so
the script failed wherever it is not installed (check_SYSargs2_test).
 

    

  
    

      Package: pathlinkR

      Commit: 82d617399fd4fbf0e8dfa97d2104bd2a34b8355d

      Author:  Travis <travis.m.blimkie@gmail.com> 

      Date: 2026-08-25 15:04:31 -0700

      Commit message:


	  
		
 Merge pull request #22 from hancockinformatics/mouse

Support for mouse data and analysis 

    

  
    

      Package: pathlinkR

      Commit: a43a1642ad402ef5a93c41f3858c7e6b5dbf4b2a

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-25 10:58:26 -0700

      Commit message:


	  
		
 Consistent whitespace in vignette
 

    

  
    

      Package: pathlinkR

      Commit: d72e134a7929e65f2a67e041f26fb4fe43341f54

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-24 08:48:11 -0700

      Commit message:


	  
		
 Added more tests of mouse data.
 

    

  
    

      Package: pathlinkR

      Commit: bd003ced5e697613c9ea6e12c54066d236557a8b

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-21 15:32:21 -0700

      Commit message:


	  
		
 Tests now run in parallel
 

    

  
    

      Package: pathlinkR

      Commit: b6803b4bb32d0bf622aad2f1e02e118a12039247

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-21 11:12:00 -0700

      Commit message:


	  
		
 Added to NEWS.md
 

    

  
    

      Package: pathlinkR

      Commit: bb3e0643f52077c515435457db520295ea33fdec

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-21 11:03:40 -0700

      Commit message:


	  
		
 gpsRepo is now passed as an object, not character, to pathwayEnrichment. Consistent documentation for species argument throughout.
 

    

  
    

      Package: pathlinkR

      Commit: d09ebcb00110a83adfe70c09ae63fa56f8d46bd6

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-20 14:44:12 -0700

      Commit message:


	  
		
 Added gpsLevel argument to ppiEnrichNetwork. Mouse tests for ppiEnrichNetwork
 

    

  
    

      Package: pathlinkR

      Commit: 87b3a97337aec53493150ce7d26e0bd213d9ef10

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-20 14:33:08 -0700

      Commit message:


	  
		
 Added mouse test for ppiBuildNetwork
 

    

  
    

      Package: pathlinkR

      Commit: cc4381045d86f1a693b1363c7f5c6765b4158893

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-20 14:27:20 -0700

      Commit message:


	  
		
 Added mouse test for .runSigora
 

    

  
    

      Package: pathlinkR

      Commit: 2d0f33c09770c1979ee65892d3f30da2bcb18ee9

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-20 13:56:46 -0700

      Commit message:


	  
		
 Added test for mouse data to plotFoldChange
 

    

  
    

      Package: pathlinkR

      Commit: 94c50ea8741d8677af14f6d0a10ae7a1f43381e8

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-20 13:52:21 -0700

      Commit message:


	  
		
 Added mouse tests for pathwayPlots
 

    

  
    

      Package: pathlinkR

      Commit: 14baa5974f415338742fbf86ae6add57a65ab974

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-20 13:48:59 -0700

      Commit message:


	  
		
 Fixed pathwayEnrichment and added tests for mouse
 

    

  
    

      Package: pathlinkR

      Commit: bd84f2359145f171526dc4c8517a7f4cb244c7ab

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-20 13:34:22 -0700

      Commit message:


	  
		
 Test for mouse data in pathnetFoundation
 

    

  
    

      Package: pathlinkR

      Commit: 7fe4250e1bd711854f74bcc9bd4a8e65f6a63ac6

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-20 13:28:02 -0700

      Commit message:


	  
		
 Added check for format of gpsRepo argument
 

    

  
    

      Package: pathlinkR

      Commit: 4fe2b986c1af0708b9bff5939444fcde90f65d2b

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-20 13:27:40 -0700

      Commit message:


	  
		
 Added sigora example in mice
 

    

  
    

      Package: pathlinkR

      Commit: a42cc6a95b2fe10c55b780531a09846acc6957e2

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-20 13:05:23 -0700

      Commit message:


	  
		
 Changed name of example DESeq results object
 

    

  
    

      Package: pathlinkR

      Commit: 0cab8d51e288c91b8e475ad5e3920f79d5aaeb3b

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-19 15:16:53 -0700

      Commit message:


	  
		
 Added example results for mice
 

    

  
    

      Package: pathlinkR

      Commit: b1fb302b0a37230977786c6b07edb7c76b5a1a7b

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-19 14:35:43 -0700

      Commit message:


	  
		
 Added new pathwayCategories mouse support.
 

    

  
    

      Package: pathlinkR

      Commit: 99a96986d70c901bd3894a9db4443d358c723bf9

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-19 14:28:15 -0700

      Commit message:


	  
		
 Streamlined data loading.
 

    

  
    

      Package: pathlinkR

      Commit: 45240433206e492974401785fcf3c3bb66ae9dc7

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-19 13:53:05 -0700

      Commit message:


	  
		
 Removed print() from pathwayEnrichment. Tests for pathwayEnrichment are all non-verbose.
 

    

  
    

      Package: pathlinkR

      Commit: baf1bf9a90a0e16adb8929b6fc01453beca05b28

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-19 13:47:55 -0700

      Commit message:


	  
		
 Finalized pathway categories for mice.
 

    

  
    

      Package: pathlinkR

      Commit: 24ee652f9e7c0894eace721be1c0a4580c1a8fd3

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-19 13:47:28 -0700

      Commit message:


	  
		
 Updated data object and documentation
 

    

  
    

      Package: pathlinkR

      Commit: b02f3f9d568ce108eb54f077a1a71f76d5f9dd4f

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-18 12:37:14 -0700

      Commit message:


	  
		
 Updated vignette.
 

    

  
    

      Package: pathlinkR

      Commit: d86ca8a88d7088916e3c69f86a13e4185a57a05e

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-18 12:11:02 -0700

      Commit message:


	  
		
 Code formatting to match bioconductor specs.
 

    

  
    

      Package: pathlinkR

      Commit: 405cd44d8aff3f09163b6f1d0256d7776fa06039

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-18 11:34:52 -0700

      Commit message:


	  
		
 Updated ppiExtractSubnetwork
 

    

  
    

      Package: pathlinkR

      Commit: 5e71a46d16a36f3fd3047c9b41115255c87405a3

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-18 11:27:42 -0700

      Commit message:


	  
		
 Updated function ppiEnrichNetwork
 

    

  
    

      Package: pathlinkR

      Commit: 722fef697f9c3595a7df164a95f71be8b7f62b1f

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-18 11:15:34 -0700

      Commit message:


	  
		
 Updated example in ppiPlotNetwork
 

    

  
    

      Package: pathlinkR

      Commit: e7316c7171e12c31a765347727f3d42925c2eec7

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-18 11:10:02 -0700

      Commit message:


	  
		
 Updated ppiBuildNetwork
 

    

  
    

      Package: pathlinkR

      Commit: 9b9641d3d03d8e20435bb29745739592e43f9082

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-18 10:53:16 -0700

      Commit message:


	  
		
 Updated function plotFoldChange
 

    

  
    

      Package: pathlinkR

      Commit: ae4e05d51f11ede5797ea40265f37942e22234aa

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-18 10:33:34 -0700

      Commit message:


	  
		
 Fixed test for pathwayPlots
 

    

  
    

      Package: pathlinkR

      Commit: 35fd218949c9e600cfd8941cc6b6e9834a7256f4

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-18 10:33:19 -0700

      Commit message:


	  
		
 Partial first update to pathwayEnrichment
 

    

  
    

      Package: pathlinkR

      Commit: cb31d47a67b26d0882a6d8d2de9f5071c0394d5d

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-18 10:32:37 -0700

      Commit message:


	  
		
 Fixed example in documentation
 

    

  
    

      Package: pathlinkR

      Commit: 6c29f32ad62acadadd42acbac5a78b90dd734197

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-17 15:22:39 -0700

      Commit message:


	  
		
 Updated example and two documentation pages.
 

    

  
    

      Package: pathlinkR

      Commit: 9a62b32e3028eb5efc7358928f07d0a2212249ac

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-17 15:20:46 -0700

      Commit message:


	  
		
 Fixed more examples.
 

    

  
    

      Package: pathlinkR

      Commit: 763713a9a413ced753f04a02ab869c9c7df5994d

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-17 15:20:27 -0700

      Commit message:


	  
		
 Fixed eruption example.
 

    

  
    

      Package: pathlinkR

      Commit: 332702bdc3d9f38e92200325b1767ecadc36f816

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-17 15:20:12 -0700

      Commit message:


	  
		
 Added global variable.
 

    

  
    

      Package: pathlinkR

      Commit: a12e5f7bbb8bd1c5d561f8746b88119d2c96a049

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-17 15:19:55 -0700

      Commit message:


	  
		
 Updated documentation.
 

    

  
    

      Package: pathlinkR

      Commit: d3fdc86806248985de67c920a114d548f3a3e3ea

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-17 15:08:12 -0700

      Commit message:


	  
		
 Added species support to pathnetFoundation.
 

    

  
    

      Package: pathlinkR

      Commit: d9abf2f5dc05947700b982c5e5a09f2752baacbc

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-17 14:59:10 -0700

      Commit message:


	  
		
 Species support for pathnetCreate
 

    

  
    

      Package: pathlinkR

      Commit: c22412658f55dd7a4cb31e23d0f3baff9515a791

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-17 14:58:44 -0700

      Commit message:


	  
		
 Added new variables to 'globals.R'
 

    

  
    

      Package: pathlinkR

      Commit: de3e8b3085ab59cf87992517f994e0bbdc669edb

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-17 14:57:25 -0700

      Commit message:


	  
		
 Species support to getPathwayDistances
 

    

  
    

      Package: pathlinkR

      Commit: f068c103e5d67bec28e556d49ea4e59f9dc92831

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-17 14:45:05 -0700

      Commit message:


	  
		
 Function 'eruption' now supports human or mouse. Tests updated.
 

    

  
    

      Package: pathlinkR

      Commit: 20a4cfaaa1a5facf14cafd0112528d755228258c

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-11 13:42:58 -0700

      Commit message:


	  
		
 New mouse data objects and documentation.
 

    

  
    

      Package: pathlinkR

      Commit: b6c7782e1de6f7df4a1f3c0796a325ebe91df0b4

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-11 13:42:39 -0700

      Commit message:


	  
		
 Version bump for upcoming release
 

    

  
    

      Package: pathlinkR

      Commit: d26a0df9180d2c40289b62d034b9a0803f10cc4d

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-08-10 16:12:10 -0700

      Commit message:


	  
		
 Named data objects to be specific to human.
 

    

  
    

      Package: GExPipe

      Commit: 8cc75d6ed3bfdb0d27cd75ad0c0c87f35f9e1119

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-10-17 17:53:37 +0500

      Commit message:


	  
		
 Sync with GitHub main: GExPipe 0.99.115
 

    

  
    

      Package: Statial

      Commit: 8092dca62e41ee029732cfe7ba77571f8be00f00

      Author:  EllisPatrick <ellis.patrick@sydney.edu.au> 

      Date: 2026-10-17 22:55:52 +1100

      Commit message:


	  
		
 kontextualTest: labelClustering = FALSE by default, matching spicyR 1.99.31

Without the label clustering term the p-values are calibrated under
relabelling of the images. Version 1.15.5.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
 

    

  
    

      Package: spicyR

      Commit: fb0a5388a92594bde2c6a8bcd9d2c32b698c5936

      Author:  EllisPatrick <ellis.patrick@sydney.edu.au> 

      Date: 2026-10-17 22:02:07 +1100

      Commit message:


	  
		
 1.99.31: kontextualEngine() defaults to labelClustering = FALSE (psi off); the option is kept

With psi, the weight concentrates on a few images and a few triples came up too often when the conditions were
shuffled; without it every cohort stayed at or below nominal (any-BH 0/150 against 1/150) with more observed calls.
Matches spicy(), where psi has been off since 1.99.8. Only the Kontextual references change.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
 

    

  
    

      Package: spatialdataR

      Commit: 00e7596c8d72bd9514fc54c7098b1eb8402ce4c0

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2026-10-17 12:47:45 +0200

      Commit message:


	  
		
 resolve version conflicts
 

    

  
    

      Package: spatialdataR

      Commit: c1f9da73e4530f2485cc3dcd8e0c9faafffc5717

      Author:  Helena L. Crowell <helena@crowell.eu> 

      Date: 2026-10-17 12:08:12 +0200

      Commit message:


	  
		
 fix crop & add 'drop=TRUE/FALSE' arg (#282)

* Drop element without content last
* Create tables directly in SpatialData call
* Let elements with different coordinate space untouched
* Unlist intersect() result
* add crop(..., drop=TRUE/FALSE) argument)
* add crop,drop tests

---------

Co-authored-by: Hugo Gruson <git@hugogruson.fr> 

    

  
    

      Package: spatialdataR

      Commit: dd3f4262189c3e5b7ad904b31d8a3794ae933381

      Author:  Helena L. Crowell <helena@crowell.eu> 

      Date: 2026-10-16 09:15:19 +0200

      Commit message:


	  
		
 simplify show method for inf. elements (#277) 

    

  
    

      Package: spatialdataR

      Commit: 8090c4a49c794ec1ccb6ef67152700de989b0596

      Author:  Helena L. Crowell <helena@crowell.eu> 

      Date: 2026-10-15 21:56:46 +0200

      Commit message:


	  
		
 affine coord.trans. for points/shapes (#276)

* affine coord.trans. for points/shapes
* add affine,point/shape tests 

    

  
    

      Package: spatialdataR

      Commit: 6422a4e87bc9ce7010cdd824809e8dfa14f84b56

      Author:  Helena L. Crowell <helena@crowell.eu> 

      Date: 2026-10-15 14:31:40 +0200

      Commit message:


	  
		
 more explicit error for unsupported transformations (#274) 

    

  
    

      Package: spatialdataR

      Commit: 623485dd4bff66f76fc4ffaebc7e44460810bdc7

      Author:  Helena L. Crowell <helena@crowell.eu> 

      Date: 2026-10-15 13:35:40 +0200

      Commit message:


	  
		
 fix #256 (#273) 

    

  
    

      Package: spatialdataR

      Commit: db1f01a3402fa7a1137b3f828104a7d940bd9b05

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

      Date: 2026-10-15 11:56:14 +0200

      Commit message:


	  
		
 pull table attr from zarr attr instead (#270) 

    

  
    

      Package: spatialdataR

      Commit: cafce21f8b5f1a5084633dee78bacaa16d2a22d7

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2026-10-15 11:51:29 +0200

      Commit message:


	  
		
 Merge branch 'ome' into devel
 

    

  
    

      Package: spatialdataR

      Commit: 289082145eaf86afb0b36ff429b8e0d2a35e04d0

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2026-10-15 11:51:22 +0200

      Commit message:


	  
		
 v0.99.46
 

    

  
    

      Package: spatialdataR

      Commit: 72e07e152ab83ef161985fb5ef31f96ffa0b6f69

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2026-10-15 11:49:13 +0200

      Commit message:


	  
		
 code formatting
 

    

  
    

      Package: spatialdataR

      Commit: 388621e9655a80f1bbddeb1f8acc08104c5420cf

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2026-10-15 11:44:32 +0200

      Commit message:


	  
		
 Merge branch 'readme' into devel
 

    

  
    

      Package: spatialdataR

      Commit: 0952a417563786a932b21ad27097e3df5edd5d4c

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2026-10-15 11:44:27 +0200

      Commit message:


	  
		
 update installation instructions & hyperlinks to other resources
 

    

  
    

      Package: spatialdataR

      Commit: ecc97c6f935753cfbabede6d609f5477ac054952

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-15 10:18:22 +0200

      Commit message:


	  
		
 Define .ome_root() & .ome_root<-() helpers
 

    

  
    

      Package: spatialdataR

      Commit: 7769a6dab414854411ccbb254e565f65cc093d8c

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-15 10:13:26 +0200

      Commit message:


	  
		
 Use multiscales() helper
 

    

  
    

      Package: spatialdataR

      Commit: 04db1a3223aafe2e1ec3cecf6e15ab7bba61a87c

      Author:  Helena L. Crowell <helena@crowell.eu> 

      Date: 2026-10-14 23:05:26 +0200

      Commit message:


	  
		
 +CTunit() (#264)

* fix 261

* document CTunit

* test ctunit

* Document CTunit() return value

* Mention CTunit in NEWS

---------

Co-authored-by: Hugo Gruson <git@hugogruson.fr> 

    

  
    

      Package: spatialdataR

      Commit: b332000fca92ac39ed1fe5184d9fd90d29e83b7a

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-14 14:15:09 +0200

      Commit message:


	  
		
 Update install instructions
 

    

  
    

      Package: spatialdataR

      Commit: fc1c8cfc0fd75d31a4aa9ed51bccfe7a20b459a0

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-13 15:14:38 +0200

      Commit message:


	  
		
 Run workflows on devel
 

    

  
    

      Package: spatialdataR

      Commit: 9070d0e9808d4058492ab45224a140b11363f0f8

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2026-10-13 20:15:42 +0200

      Commit message:


	  
		
 merge NEWS items
 

    

  
    

      Package: spatialdataR

      Commit: 5134add05438f6920a43f387a4e96e22c9548b23

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-13 20:13:34 +0200

      Commit message:


	  
		
 Fix addCT() dispatch on OME versions (#265) 

    

  
    

      Package: spatialdataR

      Commit: 78f97693783934c5c8a23b6eb2635796d404ca2c

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-13 15:19:41 +0200

      Commit message:


	  
		
 Enable reading on s3 (#263)

* Document how to install the duckdb httpfs extension
* Make data readable from S3
* Run devtools::document()
* Restore multiscale path validation on s3
* Normalize path before attempting to read anything
* Ensure individual read functions still work
* Silence false positive lint
* Add minimal test for S3 reading
* Skip S3 reading test where unavailable
* Add NEWS item
* Bump version
* Force use of BioC devel in pkgdown workflow
* text formatting
* code formatting

---------

Co-authored-by: HelenaLC <helena@crowell.eu> 

    

  
    

      Package: OMA

      Commit: a33442b2c643b1194d87945f2478cdb28cf1d675

      Author:  Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

      Date: 2026-10-17 11:41:56 +0300

      Commit message:


	  
		
 version bump (#905) 

    

  
    

      Package: OMA

      Commit: bdd73e125b0843bd3aec51da4f559ef180a57ed6

      Author:  Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

      Date: 2026-10-17 11:35:51 +0300

      Commit message:


	  
		
 Decrease size of tar ball (#904) 

    

  
    

      Package: spicyR

      Commit: f122809181db750945c2e53312b6b776504d687e

      Author:  EllisPatrick <ellis.patrick@sydney.edu.au> 

      Date: 2026-10-17 18:16:20 +1100

      Commit message:


	  
		
 1.99.30: a radius is not tested when a condition's effective patients fall below min(3, m_g/2)

m_g is the number of that condition's patients that contribute at the radius; the bound was 3. Unchanged for
conditions of 6 or more patients. Applies to count, allocation, Kontextual, adjusted designs, each level with more
than two conditions, and Hartung-Knapp; the label stays few_effective_units. Small studies: grid tests run go from
78% to 95%, and conditions of 3 patients can be tested. diabetesData: 167 allocation pairs tested (110 before);
kontextualEngine's example uses alpha again.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
 

    

  
    

      Package: edgeR

      Commit: 516e21d5d65d48c230ac5a06ecb9ccddcc9bb561

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

      Date: 2026-10-17 18:02:12 +1100

      Commit message:


	  
		
 edgeR 4.99.9
- sumTechReps() now supports 'offset` and 'offset.prior' matrices.
- estimateTxExpr() now supports multiple columns of equivalence class counts.
 

    

  
    

      Package: spicyR

      Commit: 3fb1369deb55f76be692dc3cefa6d5391b733ce6

      Author:  EllisPatrick <ellis.patrick@sydney.edu.au> 

      Date: 2026-10-17 09:18:37 +1100

      Commit message:


	  
		
 1.99.29: one dispersion shared by the conditions and at least 3 effective patients per condition; images with no condition left out of the side and tau2_image

Three changes approved on 17 Oct 2026 (ProjectSpicyRCell docs/DECISIONS.md), ported from scratch/sorin_cords/remedy.R
("phipool + neff3"), for both effects and Kontextual (count effect approved after its remedy table,
scratch/sorin_cords/count/):

- neff3: the core's test_rules() asks for kMinEffectiveUnits = 3 effective units per condition, Kish's
  (sum a J)^2 / sum (a J)^2 at the test's tau2 (ExcessResult::n_eff; effective_units() for more than two conditions).
  pair_tests(): after no_information, a radius with fewer is not tested (p and unadjusted p NaN, design 2
  "few_effective_units", left out of davies/maxT/cauchy). R's .cell_rows_test() and .cell_pair_test_levels() do the
  same. Order: no_variation, no_information, few_effective_units.
- phipool: excess_test(pooled_dispersion) with CR2 gives V = phi (1/B0 + 1/B1), phi = sum_g m_g V_g / EV_g / sum m_g,
  df those of CR2; influences unchanged. design_tests(n_groups) extends it to the adjusted design and to more than
  two conditions: per condition the CR2 / model variance ratio of its indicator coefficient, pooled by units, scales
  every contrast's model variance (exactly remedy.R's phi with only the indicators). Hartung-Knapp keeps its variance
  (neff3 applies). Survival is unchanged.
- allocation_image_rows() / excess_image_rows() take image_group: an image with a missing condition gives no row, so
  it has no say in the side or tau2_image; the result equals that with the images removed.

Checks: on the 11 analyses of the remedy tables (31 labellings each) the package's omnibus and single-radius p equal
remedy.R's phipool + neff3 to <= 7.9e-13 (allocation) and <= 7.1e-13 (count), NA patterns identical; the tables'
rows are reproduced (allocation any-BH sorin .033, cords .033, controls .030, 510 calls; count .033, 0, .030, 546).
On the 12 worst-calibrated analyses any-BH falls 10.8% -> 1.7% (allocation) and 10.0% -> 0.8% (count). References
(fresh 25efbe3 install): survival identical(); every other configuration changes in se and p; small-sample ones lose
pairs to few_effective_units (diabetesData 69 of 179 allocation pairs; the Kontextual example triple, now delta).
testthat: 473 passed (the new tests fail on 1.99.28). R CMD check: only the src/concaveman.hpp warning; every
vignette check passes.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
 

    

  
    

      Package: gdscloud

      Commit: 094075f4ac082d668147f88d5f532fd6f7a04c39

      Author:  Xiuwen Zheng <zhengxwen@gmail.com> 

      Date: 2026-10-16 23:47:10 -0500

      Commit message:


	  
		
 HTML redirect
 

    

  
    

      Package: drugTargetInteractions

      Commit: bf6616552e125642ac04d795dec153c00ca63000

      Author:  tgirke <tgirke@citrus.ucr.edu> 

      Date: 2026-10-16 19:36:23 -0700

      Commit message:


	  
		
 Add runnable examples to the two hand-written man pages

downloadChemblDb.Rd and getUniprotIDs.Rd are among the 15 man pages
written by hand rather than generated from roxygen, so the pass that
added runnable examples to the other pages never reached them.

downloadChemblDb() now shows where the download is cached and that a
small sample of the same database ships with the package, which is what
the examples of the functions querying it use - so trying those needs no
download. That also surfaces the "this is a very large file" warning
that was previously only an Rd comment, invisible to readers.

getUniprotIDs() shows the shape of its two result tables from the
snapshot already shipped in inst/extdata, which is useful on its own
given the live UNIREF path depends on UniProt being reachable. The live
query stays under \donttest.

Exported-object man pages with a runnable example: 57 of 64 (89%), up
from 55. The threshold BiocCheck errors below is 80%, so this widens the
margin from three pages to five. The remaining seven are REST getters
with no local data to demonstrate on.
 

    

  
    

      Package: drugTargetInteractions

      Commit: 704b5bb0bdd22a7c0e8a0533edaf3b55a93cd056

      Author:  tgirke <tgirke@citrus.ucr.edu> 

      Date: 2026-10-16 16:35:34 -0700

      Commit message:


	  
		
 Give the UniChem cache-lookup tests databases with a real layout

.unichemLatestCachedDb() now checks a cached database's tables and
columns before returning it, so the two fixtures this test registered -
empty files created with file.create(), carrying only the right name -
are correctly rejected and the lookup returns NA.

Build them as minimal databases with the layout buildUnichemDb() writes,
so the test goes back to asserting what it is about: that the most
recently added unichem_*.db wins regardless of the date in its name.

Added the complementary case while here: a cached database whose layout
is two columns short of the current one is skipped rather than returned.
Unlike most of this suite these tests touch no network, so they run
under R CMD check.
 

    

  
    

      Package: drugTargetInteractions

      Commit: 88328aed70775452ccefca69a1a98439bffda973

      Author:  tgirke <tgirke@citrus.ucr.edu> 

      Date: 2026-10-16 16:06:43 -0700

      Commit message:


	  
		
 Reuse a cached database only if its layout is the one we build

The local-SQLite builds cache a ready-to-query database under a name
carrying the upstream release (gtopdb_2026.3.1.db, ttd_.db, ...)
and, on rerun = FALSE, return whatever is cached under that name rather
than rebuilding.

The upstream release alone is not a safe cache key. When this package
changes a table's columns, a database built by an older version of the
package - same upstream release, so the same cache name - is still
sitting there and was returned, after which the query functions failed
on columns they expect and cannot find:

  buildGtoPdbDb(rerun = FALSE)
    columns returned: ..., selectivity, refIds
  gtoPdbTargetAnnot(...)
    Error: undefined columns selected

Renaming gtp_interactions' refIds to pubmedId in this release is exactly
that case, and it escaped notice only because GtoPdb published 2026.3.1
at the same time, so the stale gtopdb_2026.2.db copies were never
consulted. Had GtoPdb not republished, every rerun = FALSE call would
have returned a database with the old layout. This is not hypothetical
on a build machine: BiocFileCache persists between runs on the
Bioconductor builders by design, so such a database outlives an upgrade
there and is found first.

.dtiCachedDbIfCurrent() reuses a cached database only when every
expected table is present with exactly the expected columns; an older
layout, or a truncated or half-written file, counts as a cache miss and
the caller rebuilds. Wired into the TTD, Repurposing Hub, GtoPdb and
UniChem builds through one layout constant per source.

Validation rather than a hand-bumped version suffix in the name because
it is self-healing, and because its failure mode is fail-safe: a
constant that drifts out of date costs an unnecessary rebuild, never a
wrong answer. That is what makes it safe to apply to UniChem, whose
rebuild takes about an hour. Checked against this machine's real cache -
all four layouts are accepted, and the three cheap builds still
short-circuit in well under a second.

For GtoPdb the constant is now also the single description of the table:
the build derives its column selection from it, so builder and validator
cannot disagree.

UniChem needed a different shape, since .unichemLatestCachedDb() takes
the newest unichem_* entry regardless of name: it now walks candidates
newest-first and returns the first whose layout matches.

Also, buildGtoPdbDb() returned a bfcrpath()-named vector from the
fresh-build path and a plain string from the cached-reuse path while
documenting character(1), so identical() on two paths naming the same
file was FALSE. Unnamed in both now.
 </pre>
    </div>
  
    

      Package: drugTargetInteractions

      Commit: 1dd8e60ba7ca23b0c99e68bc563d40de54bf9f83

      Author:  tgirke <tgirke@citrus.ucr.edu> 

      Date: 2026-10-13 19:45:32 -0700

      Commit message:


	  
		
 Bump to 1.21.15; run the r-universe build on every push

.github/workflows/r-universe.yml calls the r-universe build workflow
with universe: bioc and organization: bioconductor, so a push runs the
same build and checks r-universe does rather than waiting for its next
scheduled run. ^\.github$ keeps it out of the tarball.

Also, from BiocCheck's notes: GeneTarget and Network added to biocViews,
and the Description expanded past the 3-sentence minimum, fixing two
typos in it along the way.
 

    

  
    

      Package: drugTargetInteractions

      Commit: cef6e72c36af824e85b20041b3c46bde1aae4c82

      Author:  tgirke <tgirke@citrus.ucr.edu> 

      Date: 2026-10-13 19:45:32 -0700

      Commit message:


	  
		
 Fix the r-universe build: GtoPdb's REST API now requires an API key

r-universe starts from an empty BiocFileCache every run, where BBS keeps
its cache between runs. That had been masking a real failure: GtoPdb
began requiring a registered API key for every /services/ endpoint, and
an unauthenticated request returns HTTP 401 ("API key is missing"), so
buildGtoPdbDb() could not run on any machine without a key - including
the build machines. The vignette's gtopdb_build chunk was the reported
error, as an opaque "bfcadd() failed".

GtoPdb still publishes the same data as public bulk downloads needing no
registration, so build from those: /DATA/interactions.tsv (the whole
~25,000-row table) joined against GtP_to_HGNC_mapping.tsv as before.
Those files carry the same release and more columns than the REST
payload did.

The authenticated route stays available via
downloadGtoPdb(useServices = TRUE, apiKey = ...), defaulting to the
GTOPDB_API_KEY environment variable, and a missing or rejected key is
now reported as an authentication failure.

Two consequences of the flat file's shape:

- refIds, GtoPdb's internal reference IDs, has no equivalent there. The
  file carries the reference's PubMed ID instead, so gtp_interactions
  and gtoPdbTargetAnnot() now report pubmedId in its place. The REST
  route cannot populate it.
- The affinity string is rebuilt from the file's separate low/median/
  high columns: a range where the bounds differ, else the single value,
  each to one decimal since the file stores single-precision floats.
  Checked against a cached /services/interactions response - 90.7% exact
  agreement joining on (targetId, ligandId, type, action), the remainder
  explained by that key not being unique (up to 23 rows share one) and
  by the two releases differing.

Rows whose Target ID, Target and Target Gene Symbol are all empty carry
no target identity and cannot form a (target, drug) edge, so they are
dropped at build time.

buildGtoPdbDb() gained a paths argument for building from local copies
of the two files, writing to a tempfile rather than the cache so a small
build can never shadow the real gtopdb_.db. A 12 KB extract of
both files now ships in inst/extdata, regenerated byte-for-byte by
inst/scripts/generate_gtopdb_example.R. The GtoPdb examples and tests
use it, and the vignette falls back to it only if GtoPdb cannot be
reached, so the section still demonstrates the real download.

Also fixed, found while reproducing the above from an empty cache:

A documented field request no longer fails when a source is unreachable.
.dtiSelectFields() validated the names passed through 'fields' against
the columns the current response happened to carry, so when ChEMBL was
intermittently returning HTTP 500 the response came back without its
optional columns and documented field names looked like typos:

  Error in .dtiSelectFields(): Unknown field(s) requested:
    molecule.molecule_type, target.organism.

That alone failed a vignette build. Each source now passes its
documented field list, the one listDrugTargetFields() reports; a field
on that list which the response does not carry comes back as an NA
column, and a name no source documents is still an error. This also
covers the case the docs already warned about, where a field appears
only for certain record types.

BiocCheck's two warnings are gone. getSymEnsUp() loads its EnsDb package
namespace instead of attaching it with require(), and says so if the
package is missing. The Repurposing Hub's supplemental CA retry no
longer sets CURL_CA_BUNDLE for the session - repo-hub.broadinstitute.org
still serves its leaf certificate alone, so the workaround is still
needed, but the bundle now travels as a per-request curl option. Full
chain verification still happens; the bundle only adds the one
legitimate InCommon intermediate.

BiocCheck's runnable-examples ERROR is gone too. It comments out both
\dontrun and \donttest when deciding, so a page whose examples live
entirely inside \donttest counts as having none; 18 of 64 pages passed,
now 55. Where a function can do real work offline the example does it;
for the REST getters the runnable part lists the columns that source
returns, which is what the reader needs before choosing 'fields'; for
the download and build functions it names the cache directory.

The test helpers now download when nothing is cached, rather than
erroring, so the suite runs on a cold cache.
 </pre>
    </div>
  
    

      Package: SeqArray

      Commit: c0e0c0dd2ad9605f71b098fd1f0e4f24ee0a160c

      Author:  Xiuwen Zheng <zhengxwen@gmail.com> 

      Date: 2026-10-16 21:51:27 -0500

      Commit message:


	  
		
 optimize memory usage
 

    

  
    

      Package: spicyR

      Commit: 25efbe3f8fa9282781eac22ce634677bd09f13c1

      Author:  EllisPatrick <ellis.patrick@sydney.edu.au> 

      Date: 2026-10-17 06:55:25 +1100

      Commit message:


	  
		
 1.99.28: images with a missing condition are left out of the unadjusted test

The core's excess_test() split image rows with `group == 0 ? g0 : g1`, so a row with a missing condition (R's
NA_integer_, Python's -1) was counted in the second condition: the unadjusted test (no adjustment, or the unadjusted_*
columns) included those images, while the adjusted design (pair_design_test's keep, .cell_design's keep) left them
out. split_groups() now skips negative groups, which fixes excess_test() and excess_tau2() for both front ends (one
change in the shared core). availability_test() leaves those rows out too. With more than two conditions,
.cell_pair_test_levels() built Zg from NA groups, so every pair failed ("no pair could be tested"); it now fits the
unadjusted design on the rows with a condition. informative_units() and no_variation already skipped negative groups.
R encodes a missing condition as NA_integer_ (match() - 1L), which reaches the core as INT_MIN, a negative group.

The adjusted test is unchanged except where its tau2 is held at the unadjusted value (an added column that varies
within patients, e.g. adjustAbundance with several images per patient). The pooled steps that use every image, the
allocation side and tau2_image, are not changed.

Checks: refs.R 26 of 26, maxt_refs.R 11 of 11 and memref identical() to 1.99.27 (none has a missing condition).
Missing-condition cases (scratch/missing_cond_dev/mc_refs.R): with one image per patient the results now equal those
with the images removed; R and Python agree to <= 6e-13. testthat: 357 passed, 0 failed (the three new tests fail on
1.99.27). R CMD check: only the src/concaveman.hpp warning.

Closes #83

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
 

    

  
    

      Package: SparseArray

      Commit: 6614ff6e4a00ec0bfa4605690aa0b3d1d3ad82b2

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

      Date: 2026-10-16 11:28:14 -0700

      Commit message:


	  
		
 small tweak to unit tests
 

    

  
    

      Package: thyroidBRS

      Commit: b05a43b5dbe986c9ef2bfeff4eab0b18f5a4b543

      Author:  Camila Barrios <151900030+camilasauria@users.noreply.github.com> 

      Date: 2026-10-16 12:00:32 -0600

      Commit message:


	  
		
 Merge pull request #4 from camilasauria/bioc-zenodo-badges

Add Bioconductor and Zenodo badges, cite the Zenodo DOI (0.99.8) 

    

  
    

      Package: thyroidBRS

      Commit: d6195ca72ee933565f2f78f79cf851f4d13dbafc

      Author:  Hugo Tovar <hatovar@inmegen.gob.mx> 

      Date: 2026-10-14 23:25:58 -0600

      Commit message:


	  
		
 Add Bioconductor and Zenodo badges, cite the Zenodo DOI

Badges for the Bioconductor devel build and years in Bioconductor, and
the Zenodo concept DOI in the README, which gets a Citation section.
inst/CITATION carries the same DOI. Bump to 0.99.8. No code changed.

Assisted-by: Claude Haiku 5.5 (Anthropic)
Co-Authored-By: Claude Haiku 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: StatescopeR

      Commit: 0c00f58d630d66adb103364933562895c1b3ec75

      Author:  MSteketee <m.f.b.steketee@amsterdamumc.nl> 

      Date: 2026-10-16 17:44:54 +0200

      Commit message:


	  
		
 same as 1.0.2 but for dev branch actual deprecation warning of aggregrateAcrossCells and fitTrendVar fix & citation update to published manuscript
 

    

  
    

      Package: ADAPT

      Commit: 85b835f558a1d769b8bc7204c356042367e7a165

      Author:  Mukai Wang <wangmk@umich.edu> 

      Date: 2026-10-16 11:21:35 -0400

      Commit message:


	  
		
 Merge branch 'devel' of github.com:mkbwang/ADAPT into devel
 

    

  
    

      Package: ADAPT

      Commit: ba9da13f335fa6da96bfd05412b877fbbaca3504

      Author:  Mukai Wang <wangmk@umich.edu> 

      Date: 2026-10-16 11:18:49 -0400

      Commit message:


	  
		
 Use portable 'strip -S' in Makevars to fix macOS install

Apple's strip does not accept the GNU-only --strip-debug flag, which broke
installation on Bioconductor macOS builders. -S is accepted by both GNU and
Apple strip and is equivalent to --strip-debug in GNU binutils.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
 

    

  
    

      Package: ADAPT

      Commit: 78cdfd52fd12bdb67bea1fbb623378a5fdd852ed

      Author:  Mukai Wang <wangmk@umich.edu> 

      Date: 2024-08-21 14:55:15 -0400

      Commit message:


	  
		
 Merge pull request #21 from mkbwang/debug

Address reviewer's requests 

    

  
    

      Package: ADAPT

      Commit: e2288702a60550c6f917a3e8ba1fbade34325476

      Author:  Mukai Wang <wangmk@umich.edu> 

      Date: 2024-07-28 17:13:03 -0400

      Commit message:


	  
		
 Merge pull request #20 from mkbwang/debug

Two bugs fixed.  

    

  
    

      Package: spicyR

      Commit: f197332bf485d7fb4fc16cb70f68b22d65e70c31

      Author:  EllisPatrick <ellis.patrick@sydney.edu.au> 

      Date: 2026-10-17 01:55:02 +1100

      Commit message:


	  
		
 1.99.27: a radius where a condition has no informative patient is not tested (adjusted_for "none (no_information)")

The allocation effect is bounded: an image of an avoiding pair with no `to` cell next to a `from` cell has y = -1
exactly, and one of an attracting pair with every `to` cell next to one +1. When every patient of a condition is at the
bound, that condition's CR2 variance is exactly 0, the se rests on the other condition's few informative patients and
the Satterthwaite df stay at 9-14 (t of -44 to -63 under relabelling). The core's informative_units() counts, per
condition, the units with at least one image row whose (O - E) / n is not exactly -1 or +1 (the omni_calib engine's
definition). pair_tests(): allocation, se > 0 and a condition with none -> p and the unadjusted p NaN, with adjustment
design 2 "no_information" (no design fitted), and the radius does not enter the davies, maxT or cauchy combination.
R's .cell_rows_test() does the same, and .cell_pair_test_levels() (more than two conditions) leaves the pair untested
(reason "no_information") when any level has none. The count effect and Kontextual have no bound and are not touched;
survival has no condition groups (a response with no variation is already not tested). The printed summary counts the
pairs not tested; the vignette's checks count BH calls with na.rm = TRUE.

Checks: refs.R 24 of 26 identical() to 1.99.26 (omni_davies_allocation_t40: 156 of 40000 radius tests, all r = 2 on
the avoid side, now NA, and the combined p of 131 of 1600 pairs; kontextual$diab/diab_adj: 14 of 193 three-stage
pairs no longer tested, the same 14 that the engine's definition finds); maxt_refs.R 11 of 11 identical; memref.R
identical except diabetes (the same 14 pairs). Every count result and Kontextual is identical. On the investigation's
worst cases (HCC shuffle 14, Metabric 25, Vannan min3 15) and on all 31 labellings of the 12 worst-calibrated real-data
analyses, the package's omnibus and single-radius p equal the engine's inf1 p exactly for every pair; any-BH over
those 12 falls from 36.1% to 10.8% (omnibus) and from 8.3% to 5.0% (single radius). New tests: a constructed pair with
every image of one condition at -1 at r = 4 (not tested, labelled, left out of davies/maxT/cauchy with and without
adjustment, count unaffected, three conditions). Tests pass; R CMD check: the src/concaveman.hpp WARNING only.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
 

    

  
    

      Package: exploreSE

      Commit: f040a0537d3d18e8e61af9489382b8799aa9ef1b

      Author:  Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com> 

      Date: 2026-10-16 16:41:10 +0200

      Commit message:


	  
		
 added the adding of context to the app, with testing, vignette changes, etc
 

    

  
    

      Package: BgeeDB

      Commit: 00ac7cda111c66cecd316dd8fef900ae723bef05

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

      Date: 2026-10-16 16:41:35 +0200

      Commit message:


	  
		
 bump version
 

    

  
    

      Package: MsBackendParquet

      Commit: e24075795b4d9aa3f1fc97642a275a1001de04a0

      Author:  Ossama Edbali <ossedb@gmail.com> 

      Date: 2026-10-16 15:02:24 +0100

      Commit message:


	  
		
 chore: Update authors list in DESCRIPTION
 

    

  
    

      Package: BreastSubtypeR

      Commit: 962c9e1715fa4c5ae5e0e70bd4436ae52122b0ea

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-16 10:49:28 +0200

      Commit message:


	  
		
 Merge pull request #151 from JohanHartmanGroupBioteam/docs/release-sync-after-1.5.6

Prepare BreastSubtypeR 1.5.7 development maintenance update 

    

  
    

      Package: BreastSubtypeR

      Commit: 3ff2e032ef74741f370f5193123dfeca02abad0d

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-16 10:33:01 +0200

      Commit message:


	  
		
 Clarify regression-test and browser-validation provenance
 

    

  
    

      Package: BreastSubtypeR

      Commit: e33928ff045028ff0525abccc4134bdd1968a94f

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-16 10:33:00 +0200

      Commit message:


	  
		
 Make installation and distribution-channel documentation durable
 

    

  
    

      Package: BreastSubtypeR

      Commit: b90028767a9d15d54f97e773895bc250fa69b146

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-16 10:01:30 +0200

      Commit message:


	  
		
 Align roxygen and help pages with validated behavior
 

    

  
    

      Package: BreastSubtypeR

      Commit: 54e487f7b4a9539c7616ffec01a35535b07030f4

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-16 10:01:30 +0200

      Commit message:


	  
		
 Synchronize installation and workflow documentation
 

    

  
    

      Package: BreastSubtypeR

      Commit: 79634a88ca8a961862c407f2544bd7608512575e

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-16 10:01:29 +0200

      Commit message:


	  
		
 Document AIMS and Shiny maintenance corrections in NEWS
 

    

  
    

      Package: BreastSubtypeR

      Commit: 06c603bd871ea623f84b24dfbcaab10a31f9b121

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-16 10:01:29 +0200

      Commit message:


	  
		
 Prepare version 1.5.7 development maintenance metadata
 

    

  
    

      Package: BreastSubtypeR

      Commit: 0ec48ec8f44849588525c48cecb707340ad09c49

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-16 09:05:22 +0200

      Commit message:


	  
		
 Merge pull request #150 from JohanHartmanGroupBioteam/fix/shiny-state-validation-1.5.6

Prevent stale Shiny downloads and handle invalid inputs 

    

  
    

      Package: BreastSubtypeR

      Commit: a36cd643b695f181c71af4cc923da1e8c9b0bdbd

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-16 08:39:04 +0200

      Commit message:


	  
		
 Merge remote-tracking branch 'origin/main' into fix/shiny-state-validation-1.5.6
 

    

  
    

      Package: BreastSubtypeR

      Commit: dce60984fc73d8b1970defa18f65fc0db77b790d

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-16 08:38:29 +0200

      Commit message:


	  
		
 Merge pull request #149 from JohanHartmanGroupBioteam/fix/aims-single-sample-1.5.6

Fix AIMS single-sample prediction and output documentation 

    

  
    

      Package: BreastSubtypeR

      Commit: c580d5cc57ca58640dea6037beab2d55b496c681

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-15 22:06:05 +0200

      Commit message:


	  
		
 Prevent stale Shiny downloads and handle invalid inputs
 

    

  
    

      Package: BreastSubtypeR

      Commit: fda1f453c9ef07f17a639768adec32da1a4decd8

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-15 16:45:56 +0200

      Commit message:


	  
		
 Fix AIMS single-sample prediction and document output structure
 

    

  
    

      Package: BreastSubtypeR

      Commit: 6fbb1fb0c47c899d9159141136c481ac283ba644

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-13 11:32:51 +0200

      Commit message:


	  
		
 Merge pull request #146 from JohanHartmanGroupBioteam/maintenance/cihc-itr-1.5.6

Fix cIHC.itr ER balancing and prepare version 1.5.6 

    

  
    

      Package: BreastSubtypeR

      Commit: 445b8b86dde41b29a98a7335f02976e63a06fa85

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-12 19:57:14 +0200

      Commit message:


	  
		
 Clarify the cohorts affected by the cIHC.itr fix; add an AUTO routing test

NEWS.md (1.5.6 entry): the earlier wording limited the affected AUTO runs
to ER+ fractions above 0.39, but get_methods() selects cIHC.itr in both
branches of the eligible mixed cohort (ten methods when the ER+ fraction
is strictly between 0.39 and 0.69, eight methods otherwise). The entry now
says that, with the default ratio = 54 / 64, cohorts with an ER-negative
majority can be affected, in manual BS_Multi() calls that include cIHC.itr
and in AUTO calls that select it under the existing routing and size
gates, and that a changed balancing subset need not change every subtype
call. The routing code and its thresholds are unchanged.

BS_cIHC.itr() roxygen (er_subsample), the regenerated man/BS_cIHC.itr.Rd
and the comment above .cihc_itr_plan(): the statement that both modes give
the same results when ER+ samples are at least as many as ER- samples is
qualified with the default ratio = 54 / 64 and otherwise identical inputs,
seed and settings; "larger" rejects a ratio above n_larger / n_smaller,
which "target" accepts.

tests/testthat/test-auto-cihc-itr-routing.R (new): synthetic phenotype
tables only. AUTO selects cIHC.itr in both mixed-cohort branches for
20/80, 39/61, 40/60, 45/55, 50/50, 68/32, 69/31 and 80/20 ER+/ER- with
the exact method vectors and strict boundaries; a below-minimum cohort
and a HER2+ cohort are not routed to cIHC.itr; the default-ratio plans
for 20/80 are 20 : 17 ("larger") and 20 : 24 ("target"). Existing
assertions and the retained 1.5.5 fixture are untouched.

No executable code changes: the parsed expressions of every R/*.R file
are identical to the previous commit.
 

    

  
    

      Package: BreastSubtypeR

      Commit: 3a4f83d098695564522ab933eddc394dcab12aa8

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-12 19:06:42 +0200

      Commit message:


	  
		
 Prepare maintenance version 1.5.6 with the cIHC.itr ER subsampling fix

Bump the version to 1.5.6 and document the behaviour-changing cIHC.itr
bug fix of the previous commit (db80994) in NEWS.md: target-aware ER
balancing, the retained ceiling() rounding convention, the cohorts whose
results can change (ER- samples outnumbering ER+ samples), and
er_subsample = "larger" for exact reproduction of BreastSubtypeR 1.5.5
and earlier. No code, help-page, README, vignette or test changes in
this commit.
 

    

  
    

      Package: BreastSubtypeR

      Commit: db80994fcf0f630a65f9e85c9c5bb4a016faef2c

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-11 00:45:16 +0200

      Commit message:


	  
		
 cIHC.itr: subsample the ER group over-represented relative to the target

cIHC.itr subsampled the numerically larger ER group to
ceiling(ratio * n_smaller). With the default ratio 54/64 (the ER+ : ER-
distribution of the UNC PAM50 reference set) the balancing subset only
followed that target when ER+ samples were at least as many as ER-
samples; otherwise it was inverted (for example 54 ER+ / 64 ER- was
subsampled to 54 : 46).

- New default er_subsample = "target": ratio is the ER+ : ER- target; the
  ER group over-represented relative to it is subsampled without
  replacement to ceiling(ratio * n_ERneg) ER+ or ceiling(n_ERpos / ratio)
  ER- samples, the other group is kept in full, and a cohort already at
  the target is used in full. Any single positive finite ratio is valid.
- er_subsample = "larger" keeps the previous rule, sampling order and
  outputs exactly; it is also exposed through BS_Multi() and affects only
  cIHC.itr.
- Results are identical to 1.5.5 whenever ER+ samples are at least as
  many as ER- samples (ceiling() rounding is retained for this reason).
- Validates ratio (single, finite, positive) and keeps the empty-ER-group
  error; sizes are computed without integer overflow.
- Tests compare both modes with outputs retained from 1.5.5 (commit
  0dcc0c8) and check that BS_Multi() changes no other method.
 

    

  
    

      Package: BreastSubtypeR

      Commit: 0dcc0c8a846290fcca3f266bd79248bff84fb58b

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-09 12:23:42 +0200

      Commit message:


	  
		
 Merge pull request #145 from JohanHartmanGroupBioteam/maintenance/bioc-devel-1.5.5

Prepare development maintenance version 1.5.5 

    

  
    

      Package: BreastSubtypeR

      Commit: f09b14b99283ab809f9d9d20a5c26ae9e98b0cde

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-09 09:37:53 +0200

      Commit message:


	  
		
 Prepare development maintenance version 1.5.5
 

    

  
    

      Package: BreastSubtypeR

      Commit: ac0f1c20357f4324ee4c9d1e8f2b9fb88d5e3985

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-08 23:00:38 +0200

      Commit message:


	  
		
 Merge pull request #144 from JohanHartmanGroupBioteam/ci/bioccheck

Add an advisory BiocCheck CI workflow (R 4.6, Bioc 3.24) 

    

  
    

      Package: BreastSubtypeR

      Commit: 8201f68a5f68d0b1759567ddfedd4553892ca927

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-08 22:33:30 +0200

      Commit message:


	  
		
 BiocCheck CI: run steps with pipefail and verify it

Without a shell setting, GitHub runs Linux steps with "bash -e", so a
command piped through tee could fail while its step succeeded. In run
37837213404 BiocCheck exited 1 (one Support Site WARNING) but the step
was reported successful; only the summary consistency check failed the
job, and the summary table showed the BiocCheck stage as PASS.

- Set defaults.run.shell: bash for the BiocCheck job, which GitHub runs
  as "bash --noprofile --norc -eo pipefail".
- The self-test step now checks that pipefail is on in its own (the
  job's default) shell and that a producer exiting non-zero after
  writing a clean result fails a "| tee" pipeline in that shell.
- Stage status in the job summary is FAIL whenever the recorded result
  has an ERROR or WARNING, regardless of the step outcome.
- Synthetic controls added for the clean-result-then-failure case and
  for the summary of masked and genuinely failed steps.
 

    

  
    

      Package: BreastSubtypeR

      Commit: ae0fc7cc7369b06ff9d614404786b2aa06589fcd

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-08 22:08:00 +0200

      Commit message:


	  
		
 Add an advisory BiocCheck CI workflow (R 4.6, Bioc 3.24)

New independent workflow with one Linux job, "BiocCheck (R 4.6, Bioc
3.24)". It runs BiocCheckGitClone on the untouched checkout, builds one
source tarball, runs R CMD check --no-manual on it and, only if that has
no ERROR or WARNING, runs BiocCheck in existing-package mode on the same
tarball using the R CMD check installation (install = "check:...").

The job fails on any ERROR or WARNING, on incomplete or malformed
results, on an unresolved tarball/installation identity and on missing
evidence; NOTEs are listed in the job summary. A synthetic self-test
verifies the gate's exit statuses on the runner before the real checks.
Evidence is uploaded on every outcome.

The existing required R-CMD-check workflow, package sources and
dependencies are unchanged; BiocCheck is installed only in the runner
library. No secrets are used, so the Bioc-devel subscription check is
reported as NOT VERIFIED.
 

    

  
    

      Package: BreastSubtypeR

      Commit: 2c67e7086b3bc719c8f716496aa1828d86c06b63

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-08 16:51:08 +0200

      Commit message:


	  
		
 Merge pull request #143 from JohanHartmanGroupBioteam/fix/citation-bioccheck

Fix CITATION reading without package metadata 

    

  
    

      Package: BreastSubtypeR

      Commit: 7d8a4a6e0f4229943d592412c6c6ff13c6b1176e

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-08 14:39:57 +0200

      Commit message:


	  
		
 Fix CITATION reading without package metadata
 

    

  
    

      Package: BreastSubtypeR

      Commit: f474e6bb5cd5822796836483afa018bfee53b5cc

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-07 11:17:15 +0200

      Commit message:


	  
		
 Merge pull request #142 from JohanHartmanGroupBioteam/ci/r-cmd-check

Add minimal R CMD check CI 

    

  
    

      Package: BreastSubtypeR

      Commit: b560657ff8553b99fe1899626a6d23ea30131cfe

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-07 10:25:33 +0200

      Commit message:


	  
		
 Add minimal R CMD check CI
 

    

  
    

      Package: SpectraStash

      Commit: 89ced95d5eb698e4e98233a200a0684e845a9dbe

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

      Date: 2026-10-16 15:39:47 +0200

      Commit message:


	  
		
 Merge pull request #15 from rformassspectrometry/jomain

feat: add plain text stash format for MsBackendOfflineSql 

    

  
    

      Package: SpectraStash

      Commit: 208be98ddf654d7b5fce89470f41e9c59f35f9aa

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

      Date: 2026-10-16 15:14:34 +0200

      Commit message:


	  
		
 Address Gabriele's comments
 

    

  
    

      Package: SpectraStash

      Commit: a35c9f821c8f2553e5f9c5735b117d2e9c25fab4

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

      Date: 2026-10-16 14:47:18 +0200

      Commit message:


	  
		
 fix: try to fix Windows path problems
 

    

  
    

      Package: SpectraStash

      Commit: 575d99ac972e5188d7c1e0946c38b22fbf727ef3

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

      Date: 2026-10-16 12:10:58 +0200

      Commit message:


	  
		
 feat: add plain text stash format for MsBackendOfflineSql

- Add support for the plain text stash format for the `MsBackendOfflineSql`
  backend. This backend is defined in the *MsBackendSql* package, but creating
  yet another stash package (for a single backend) seems not reasonalble. Adding
  the respective packages to *Suggests* instead of *Imports*.
 

    

  
    

      Package: BgeeDB

      Commit: da6a0642088daa528d75a385638405791c74862a

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

      Date: 2026-10-16 14:55:23 +0200

      Commit message:


	  
		
 check that a download is complete from its last bytes, read the expression calls with fread as character, and keep the calls of Bgee 16 compressed
 

    

  
    

      Package: BindingSiteFinder

      Commit: 026576dd29b73ebc725014e7f9d0a05c2ca3b2e2

      Author:  Mirko Brüggemann <mirko.brueggemann@mail.de> 

      Date: 2026-10-16 13:44:36 +0200

      Commit message:


	  
		
 Add changes to news and bump version number
 

    

  
    

      Package: BindingSiteFinder

      Commit: 2f2e56cb3ff6c4136881c92bbc0e96b89d0ca640

      Author:  Mirko Brüggemann <mirko.brueggemann@mail.de> 

      Date: 2026-10-16 13:41:35 +0200

      Commit message:


	  
		
 fixed minor ggplot visuals
 

    

  
    

      Package: BindingSiteFinder

      Commit: 1dca290f90ab4afe3833fb484d979ad1b7b7647d

      Author:  Mirko Brüggemann <mirko.brueggemann@mail.de> 

      Date: 2026-10-16 13:31:14 +0200

      Commit message:


	  
		
 bugfix in reproducibilityFilter
 

    

  
    

      Package: BindingSiteFinder

      Commit: db6078a32c86f551934fd10656abb08fb2d0beda

      Author:  Mirko Brüggemann <mirko.brueggemann@mail.de> 

      Date: 2026-10-16 12:07:46 +0200

      Commit message:


	  
		
 Fixed condition variable naming bug
 

    

  
    

      Package: BindingSiteFinder

      Commit: 68ca62ba1af50de9a473e2cf0e3cbda2aeae13a3

      Author:  Mirko Brüggemann <mirko.brueggemann@mail.de> 

      Date: 2026-10-09 14:51:23 +0200

      Commit message:


	  
		
 explicitly call the correct package for the makeTxDbFromGFF function
 

    

  
    

      Package: BindingSiteFinder

      Commit: 27279f5b82b5e94a8a6b3afd98372fc6c0559675

      Author:  Mirko Brüggemann <mirko.brueggemann@mail.de> 

      Date: 2026-10-09 14:22:59 +0200

      Commit message:


	  
		
 fixed missing colors in the targetGeneSpectrumPlot
 

    

  
    

      Package: BindingSiteFinder

      Commit: 9fe0ca285617ede99c1503c12f3e5d4a86373b52

      Author:  Mirko Brüggemann <mirko.brueggemann@mail.de> 

      Date: 2026-10-09 13:49:51 +0200

      Commit message:


	  
		
 Added a test case to check that meta data is kept after background is added
 

    

  
    

      Package: BindingSiteFinder

      Commit: ea56141c4c8f72b163295854a7f9b9a24313b46b

      Author:  Mirko Brüggemann <mirko.brueggemann@mail.de> 

      Date: 2026-10-09 13:49:32 +0200

      Commit message:


	  
		
 removed cbind to avoid duplicated meta columns
 

    

  
    

      Package: BindingSiteFinder

      Commit: c8156366c7191c9664e4c6429773187cc23c919f

      Author:  Mirko Brüggemann <mirko.brueggemann@mail.de> 

      Date: 2026-10-09 13:48:48 +0200

      Commit message:


	  
		
 make explanation of overlap resolve options in assignToTranscriptRegions more clear
 

    

  
    

      Package: BindingSiteFinder

      Commit: fff3badcd9d6e12fac06136fcd1000147f5192ca

      Author:  Mirko Brüggemann <mirko.brueggemann@mail.de> 

      Date: 2026-10-09 13:48:38 +0200

      Commit message:


	  
		
 make explanation of overlap resolve options in assignToTranscriptRegions more clear
 

    

  
    

      Package: BindingSiteFinder

      Commit: 1adc8c99231ab052343f1dffce7ff2a27f06fa2e

      Author:  Mirko Brüggemann <mirko.brueggemann@mail.de> 

      Date: 2026-10-09 13:47:50 +0200

      Commit message:


	  
		
 make explanation of overlap resolve options in assignToTranscriptRegions more clear
 

    

  
    

      Package: gDRcore

      Commit: 29d344f530e03d026be9e29abac4c657fd386e75

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

      Date: 2026-10-16 12:06:39 +0200

      Commit message:


	  
		
 Merge pull request #212 from gdrplatform/GDR-3637

feat: process time-course data in runDrugResponseProcessingPipeline() 

    

  
    

      Package: gDRcore

      Commit: d1393eaa1a583c2a265ca228df756a18f34ce656

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

      Date: 2026-10-15 16:01:18 +0200

      Commit message:


	  
		
 fix: require three time points before treating a plate as time-course

A plate read at time zero and at the end point, or a day 0 plate scanned
twice, met the old rule and lost its end-point metrics. Every Incucyte
plate processed so far has 16 or more time points, so the stricter rule
costs nothing there and keeps such end-point plates on the path they
took before.
 

    

  
    

      Package: gDRcore

      Commit: 688591a31399044952a8b793d942c0a72e450b1b

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

      Date: 2026-10-15 12:36:06 +0200

      Commit message:


	  
		
 fix: warn about plates read repeatedly without a reading at time zero

Such a plate fell back to end-point processing without a word, while
data_model() still called the same table time-course. Both now use one
helper, identify_data_type() names the plates it sends to the end-point
path, and the pipeline documentation states the time-zero requirement.
The NEWS entries for the unreleased time-course processing are merged.
 

    

  
    

      Package: gDRcore

      Commit: 32cdfb8e4eb5b08e874be287aba96f4a71e4c64c

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

      Date: 2026-10-14 09:46:56 +0200

      Commit message:


	  
		
 refactor: stop time-course data at LogFoldChange in the pipeline
 

    

  
    

      Package: gDRcore

      Commit: 12f348a52381e1abc33bfc83e28e238a50fe1260

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

      Date: 2026-10-14 09:00:24 +0200

      Commit message:


	  
		
 fix: keep the drug order of time-course combinations in split_raw_data()
 

    

  
    

      Package: gDRcore

      Commit: 320c5d071bbbb81daa8fd59d4387029bd6a3a9c0

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

      Date: 2026-10-14 08:14:20 +0200

      Commit message:


	  
		
 feat: process time-course data in runDrugResponseProcessingPipeline()
 

    

  
    

      Package: miaViz

      Commit: 4716552cea29f5c56c1af2a6074bca1d9e849c63

      Author:  Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

      Date: 2026-10-16 13:01:14 +0300

      Commit message:


	  
		
 Fix plotBoxplot: duplicated column names (#235) 

    

  
    

      Package: spicyR

      Commit: 5bb8e8d239f77207f426d13acba1fdb0fc2de969

      Author:  EllisPatrick <ellis.patrick@sydney.edu.au> 

      Date: 2026-10-16 20:48:03 +1100

      Commit message:


	  
		
 1.99.26: no adjusted design at a radius with no variation (adjusted_for "none (no_variation)")

Where a pair's response has no variation at a radius (no `to` cell has a `from` neighbour, or every one has), the
unadjusted test is exactly 0 / 0 and the radius is left out. The adjusted design (adjustAbundance, covariates)
turned those zeros into rounding noise (~1e-16), so the radius was kept with t = noise / noise and an arbitrary
influence vector, which moved the davies, maxT and cauchy combinations arbitrarily. Now, when the unadjusted test
has no variation (!(se > 0)), no design is fitted: adjusted_for "none (no_variation)", p NaN, and nothing of the
radius enters the combination (core pair_tests() and R's .cell_rows_test(); Kontextual uses the latter). The core's
design_tests() also reports "no_variation" when the weighted residual sum of squares is at most (64 eps n)^2 times
the weighted sum of squares of the response (more than two conditions, survival, Hartung-Knapp); survival is
adjusted for abundance only where the unadjusted test was done. With several radii, a radius where no pair's design
was fitted gets the other radii's effect columns (combining them stopped with an error before).

Checks: refs.R (26 cases), maxt_refs.R (11) and memref.R (8) are identical() to 1.99.25's. t04 -> t05 of the
10-type synthetic data (r = 5..125, age, abundance, davies) gives 0.772 (0.967; 0.772 with r = 115, 120 dropped),
and with age perturbed by 1e-10 its p no longer moves. The davies_dev perturbation experiments (25 configurations,
Jackson, Keren, Schurch and synthetic): no combined p moves by more than 4e-9 (21-28% moved by > 0.01 before on
the adjusted real-data runs). New tests: empty and saturated radii give "none (no_variation)" for davies, maxT,
cauchy and one radius; the combination equals that without the radius; a perturbed covariate; design_tests() on an
exactly fitted response; three conditions and survival. Tests pass; R CMD check: the src/concaveman.hpp WARNING only.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
 

    

  
    

      Package: spicyR

      Commit: a2b302ce423df29ab42e00f6a25966f12f2f4531

      Author:  EllisPatrick <ellis.patrick@sydney.edu.au> 

      Date: 2026-10-16 19:47:26 +1100

      Commit message:


	  
		
 1.99.25: maxT's multivariate normal probability by Genz-Bretz quasi-Monte Carlo (abs. error 1e-4)

spicy(combine = "maxT") computes P(max |Z_k| > c) for Z ~ N(0, R) with the quasi-Monte Carlo method of Genz (1992)
and Genz & Bretz (2009) in place of recursive Gauss-Legendre quadrature (3.2 million evaluations per pair with six
radii). Separation of variables on the Cholesky factor with the Genz-Bretz variable reordering; Korobov lattice rules
of growing size (parameters from an exhaustive weighted-P2 search, inst/scripts/korobov_search.cpp), baker's
transformation, antithetic points and 12 shifts from a fixed-seed SplitMix64; rules combined by inverse-variance
weights until 3.5 standard errors < 1e-4 (at most 100,000 points per shift). Deterministic: the same inputs give the
same p on every call and at any number of cores. Written from the publications; no mvtnorm code. Two radii keep the
quadrature; it stays in the core as mvn_outside_quadrature() (R: stats_mvn_outside_quadrature(),
stats_mvn_outside_qmc()).

Validation against mvtnorm::pmvnorm (abseps 1e-6): 100 real 10-type calls, max abs diff 6.1e-5 (0.44% rel. at
p < 0.05); 308 random/singular K = 2..6 matrices, max abs 1.0e-4 (4.8% rel. for 0.001 <= p < 0.05). Real calls:
18 ms against 233 ms (pmvnorm at 1e-4: 28 ms). On 4,200 timing pairs 6 p change by > 1e-4 (max 1.4e-4), none
crosses 0.05; only p_value, p_adj and unadjusted_p_* change. Non-maxT results identical(): refs.R 18/18 non-maxT
cases (the 8 that differ all contain maxT), memref 7/8 (radii is maxT), cores 8 = cores 1. Tests pass (258, 2
skip), with a new test against pmvnorm (mvtnorm in Suggests). R CMD check: only the concaveman.hpp WARNING.
Timing, maxT over 6 radii, 50 images x 5,000 cells, 1 core: 80 types 141 s (1,438 s), 40 types 32 s (381 s).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
 

    

  
    

      Package: OMA

      Commit: e18366ecb4b9b5026ddb09f1436a8519536b55fd

      Author:  Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

      Date: 2026-10-16 08:58:13 +0300

      Commit message:


	  
		
 Fix ML chapter build (#903) 

    

  
    

      Package: OMA

      Commit: 5cab63b1fd8baedcb165f344c610eb4f9912e4b7

      Author:  Sadia Zaman <69467219+Sadia12345@users.noreply.github.com> 

      Date: 2026-10-16 08:35:38 +0300

      Commit message:


	  
		
 Change miaverse to OMA in overview, refs #895 (#900)

Co-authored-by: Muluh <127390183+0xMuluh@users.noreply.github.com> 

    

  
    

      Package: spicyR

      Commit: 9c6becb2ca04ce8627648066c619346cec02616e

      Author:  EllisPatrick <ellis.patrick@sydney.edu.au> 

      Date: 2026-10-16 14:37:08 +1100

      Commit message:


	  
		
 1.99.24: every pair at every radius in one core call (pair_tests); writeCellStore() region key categorical

spicy() (cell method, two conditions) runs the image rows, the image random effect, the frailty test, the adjusted
design and the multi-radius combination for all pairs and radii in src/core/src/pairs.cpp (pair_tests,
pair_design_test), bound as stats_pair_tests(); R builds each table column-wise. Results identical() to 1.99.23
(26 reference cases, memref 8/8). Omnibus (25 radii, davies) at 80 types: 263 s -> 8.6 s; single radius at 80
types 10.9 s -> 0.6 s; 10M cells unchanged. Rows bindings return data.frames without as.data.frame().

writeCellStore(): the image column always categorical, instance IDs at least uint16, and the "array" encoding on
nullable values and masks, so Python's spatialdata and anndata read R stores cleanly.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
 

    

  
    

      Package: Rsubread

      Commit: 4337825c3de53b4d57f4b28f2546c7d7ec7e8323

      Author:  Ubuntu <ubuntu@crispr-screening-webservice.novalocal> 

      Date: 2026-10-16 03:34:32 +0000

      Commit message:


	  
		
 added a missing manual page.
 

    

  
    

      Package: SpotSweeper

      Commit: 7e6ebf68c205cf0c102d8ed6b363752d5288d179

      Author:  Michael Totty <mictott@gmail.com> 

      Date: 2026-10-15 22:22:19 -0400

      Commit message:


	  
		
 Fix Windows parallel nearest-neighbor search

Select socket workers automatically on Windows in localOutliers and localVariance while preserving the workers interface. Add native and socket parallel regression coverage and bump to 1.9.3. Fixes #27.
 

    

  
    

      Package: spicyR

      Commit: 99ee1cdf682f6fff878b5182a40c1cc846d34d7d

      Author:  EllisPatrick <ellis.patrick@sydney.edu.au> 

      Date: 2026-10-16 12:04:50 +1100

      Commit message:


	  
		
 1.99.23: writeCellStore() writes the store in chunks of 2^20 rows, in bounded memory

writeCellStore() wrote the cell table with one anndataR call, which writes every array as a single chunk: it failed
at 100 million cells on the row index, and reading any slice of its stores decompressed the whole column. The
table is now written directly, each column, the row index and obsm "spatial" (float64) in chunks of 2^20 rows
compressed with zstd, one chunk at a time. The AnnData layout, data types and attributes are those anndataR wrote;
uns region_key/instance_key are now string scalars and the per-image table has the SpatialData table attributes,
so Python spatialdata reads the stores. spicy() results are identical to the old stores and to the data.frame (100
million cells: write 81 s, +0.4 GB; spicy(r = 25) from the store 1.8 GB on 1 core, 5.2 GB on 8). anndataR is no
longer suggested.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
 

    

  
    

      Package: spicyR

      Commit: 0da2feac1f37331027302568ae1401d062b01bfb

      Author:  EllisPatrick <ellis.patrick@sydney.edu.au> 

      Date: 2026-10-16 10:23:32 +1100

      Commit message:


	  
		
 pkgdown: writeCellStore in the reference index

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
 

    

  
    

      Package: spicyR

      Commit: f3c8096829cd8828868c6a118288ff8dd04ba375

      Author:  EllisPatrick <ellis.patrick@sydney.edu.au> 

      Date: 2026-10-16 10:13:15 +1100

      Commit message:


	  
		
 pkgdown workflow: build against Bioconductor devel (3.24), where spatialdataR and its dependencies are

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
 

    

  
    

      Package: spicyR

      Commit: c3dab2361eb86ca297fbd68e4a3cd1017eff53ec

      Author:  EllisPatrick <ellis.patrick@sydney.edu.au> 

      Date: 2026-10-16 10:08:18 +1100

      Commit message:


	  
		
 1.99.22: images with a missing condition left out of the covariate design (#82); BLAS-thread test skipped where BLAS runs one thread

Fixes #82.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
 

    

  
    

      Package: BiocDuckDB

      Commit: 8b91a688644e71eafdf979ebecb214d7ad1e9c86

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

      Date: 2026-10-15 13:53:25 -0700

      Commit message:


	  
		
 fix: preserve a matrix label's true extent past an all-zero trailing row/column (0.99.26)

writeParquet,ANY only attaches index->label categories (the metadata a
reader uses to recover the true axis size) when the array already has
dimnames at the point it captures them, before it assigns synthetic
seq_len() dimnames for the physical write. A spatialLabels() matrix is
normally dimname-less, so no categories were ever recorded for the
spatial_label_coord path added above, and .readParquetArray() fell back
to inferring the shape from the sparse COO data alone -- undercounting
whenever the dropped (all-zero) entries included a whole trailing row or
column.

Fixed by synthesizing dimnames on the label matrix (the same seq_len()
values ANY would assign internally anyway) before writing it, so
categories are always attached regardless of what the input happened to
have. Added a regression test using a label whose only nonzero entry is
at row 1/col 1; the existing round-trip test has a nonzero in both the
last row and last column, which masked this gap.
 

    

  
    

      Package: Rsubread

      Commit: 9c10478e63a557e9285b5d2864b0d745a9c4065e

      Author:  Ubuntu <ubuntu@crispr-screening-webservice.novalocal> 

      Date: 2026-10-15 20:04:04 +0000

      Commit message:


	  
		
 try fixing slow loading index
 

    

  
    

      Package: BiocDuckDB

      Commit: 8097109a601ed78269d7fc39f268fd79da4370bb

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

      Date: 2026-10-15 11:52:00 -0700

      Commit message:


	  
		
 fix: correct spatial_label_coord write path for matrix-valued labels (0.99.26)

The spatial_label_coord write path for a matrix/array-valued spatialLabels()
entry (writeParquet,MultiAssaySpatialExperiment-method) was broken and had
never been exercised by any test or fixture. The internal
.matrixToCoordLabel() built a COO triples data.frame (row, col, value
columns) and passed it to DuckDBArray::writeCoordArray() along with
row=/col= arguments -- writeCoordArray() has no such parameters (they
belong to the unrelated DuckDBMatrix() constructor), so they were silently
swallowed by ..., and the COO data.frame itself was passed as the array to
write, whose dim() is (nnz, 3) rather than the original matrix's
(nrow, ncol). Separately, the resource dict for this layout carried no
schema field, unlike every other array writer, so .readParquetArray()
could never detect the 2 keycols needed to dispatch to DuckDBMatrix() on
read and silently fell back to DuckDBArray() with no datacol or keycols
at all.

Fixed by writing the label matrix through the existing, already
schema-correct writeParquet,ANY-method (the same path used for every
other array-like object) instead of a bespoke COO assembly, which fixes
both problems by construction. Removed the now-dead
.matrixToCoordLabel(). Added a round-trip regression test (writeParquet()
+ readParquet() a matrix-valued label, asserting it comes back as a
DuckDBMatrix with the original values).
 

    

  
    

      Package: gDRutils

      Commit: 299807bf2a7c45ee414a26c9712d8853f25e907e

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

      Date: 2026-10-15 20:11:54 +0200

      Commit message:


	  
		
 Merge pull request #205 from gdrplatform/GDR-3487

feat: record the recipe of each fit in SE metadata 

    

  
    

      Package: gDRutils

      Commit: d34a07be7c38d2673f8b0449335258daef245276

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

      Date: 2026-10-15 12:48:09 +0200

      Commit message:


	  
		
 test: check max_bytes of record_processing_step()
 

    

  
    

      Package: gDRutils

      Commit: 0228479a6387cbcb17f70b652f8e691f8cb95ff2

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

      Date: 2026-10-15 12:48:09 +0200

      Commit message:


	  
		
 feat: let record_processing_step() store larger settings when asked
 

    

  
    

      Package: gDRutils

      Commit: 84c0dc0858246dea88fcdba794278f78721f7576

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

      Date: 2026-10-14 16:18:25 +0200

      Commit message:


	  
		
 test: check that replace drops recipes of other fit sources
 

    

  
    

      Package: gDRutils

      Commit: 3fb958ad97c271992fd9c48e3cddccb2b6aa55a0

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

      Date: 2026-10-14 16:18:25 +0200

      Commit message:


	  
		
 feat: let record_fit_provenance() drop the recipes of an overwritten assay
 

    

  
    

      Package: gDRutils

      Commit: 944e2b66990761b78a997680f037f70c76a75a5e

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

      Date: 2026-10-14 16:13:24 +0200

      Commit message:


	  
		
 chore: mention the provenance recorders in NEWS
 

    

  
    

      Package: gDRutils

      Commit: fa4d7a37d8256fa73cbd3b0261c874253d06a5d4

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

      Date: 2026-10-14 16:13:24 +0200

      Commit message:


	  
		
 test: cover recipes of SE-level functions and processing steps
 

    

  
    

      Package: gDRutils

      Commit: 5d624d2d8c4bdf5d68e5ada71aa951bf5df9fafc

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

      Date: 2026-10-14 16:13:24 +0200

      Commit message:


	  
		
 feat: add record_fit_provenance() and record_processing_step() for code outside apply_fit()
 

    

  
    

      Package: gDRutils

      Commit: 9802efead077c2c49a7e7abde9fc855e1bf0ec42

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

      Date: 2026-10-14 15:57:21 +0200

      Commit message:


	  
		
 test: check that fitting the same data twice gives an identical object
 

    

  
    

      Package: gDRutils

      Commit: 741a3f40f46dfbcefbe13d2ae5abfe77c95729a0

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

      Date: 2026-10-14 15:57:21 +0200

      Commit message:


	  
		
 docs: list the fit provenance functions in the pkgdown reference
 

    

  
    

      Package: gDRutils

      Commit: d859c8c2c49c288d467d5bccdba37c7c0a2de842

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

      Date: 2026-10-14 15:57:21 +0200

      Commit message:


	  
		
 fix: leave the run time out of the fit recipe so repeated fits give identical objects
 

    

  
    

      Package: gDRutils

      Commit: 0341febf3dc54139d6d5584130ca525afa5e261c

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

      Date: 2026-10-13 17:40:54 +0200

      Commit message:


	  
		
 chore: bump version to 1.11.18 and update NEWS
 

    

  
    

      Package: gDRutils

      Commit: 18c60a8b9a0027c64b59412de6f6cad3332ba241

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

      Date: 2026-10-13 17:40:48 +0200

      Commit message:


	  
		
 test: cover fit provenance and single calls of multi-output functions in apply_fits()
 

    

  
    

      Package: gDRutils

      Commit: 147ca52691552b03795b05d921ff3b97a3929569

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

      Date: 2026-10-13 17:39:22 +0200

      Commit message:


	  
		
 feat: record the recipe of each fit in metadata(se)$provenance
 

    

  
    

      Package: gDRutils

      Commit: d163764559899ff6b480002b19ff4ccd1c703ae8

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

      Date: 2026-10-13 17:39:13 +0200

      Commit message:


	  
		
 fix: stop apply_fits() from writing every row twice for a multi-output function
 

    

  
    

      Package: quantMSImageR

      Commit: d1987f264383c7995d80b8a3679670ddb1d9e366

      Author:  Matthew Smith <matthew.smith@ki.se> 

      Date: 2026-10-15 19:12:57 +0200

      Commit message:


	  
		
 Version 0.99.10: blocking, per-block ion images, stitch overlap

Correct a study for a factor that is not the comparison -- the patient a
paired set of treatments came from, the sex of an animal, the slide an
acquisition sat on.

* `block:` names that factor per sample, beside the `group:` being compared.
  `parameters: block_centre:` decides what to do about it: `center` divides
  each feature by the block's own geometric mean, `baseline` by its
  `baseline_group` arm so a value reads as a fold change against its own
  control. `off` is the default, so declaring a block changes no number on
  its own. The correction is multiplicative, so a block's gain goes and the
  size of its response stays. It reaches the heatmaps and the comparison
  plots; the ion images stay uncorrected, because an image should show the
  intensity that was measured. A corrected report says so and gains
  `blocked` in its filename. `blockCentre()` is exported.

* `output: ion_images:` collects the display settings every image in the
  report shares. `percentile:` is the cap -- previously the animation was
  fixed at 95, the dropdown computed its own, and the concentration images
  silently took 99. `scale_within:` gives each block its own colour scale,
  drawn as one column per block with its groups as rows and replicates
  across, each column stating the value it is capped at.

* `stitchAcquisitions(overlap = )` and `parameters: stitch_overlap:` for
  pieces of one tissue that share a strip. `error` stays the default.

* `fData()` carries `collision_eV` and `cone_V`, so the feature table tells
  two transitions apart without a trip to the raw data.

* A sample's group is given by `group:` rather than `label:`, and
  `baseline_label:` by `baseline_group:`. Both old names keep working and
  `validateConfig()` says how many samples still use them.

* `heatmap_style: auto` no longer picks the contribution heatmap when the
  z-score behind it cannot resolve anything: that score is taken within a
  region, so a region of two rows saturates whatever the data says.
 

    

  
    

      Package: dominoSignal

      Commit: 80f2f89695bb4a2849b0fc7b53b8fd140aa2014c

      Author:  kjkrishnan <60410113+kjkrishnan@users.noreply.github.com> 

      Date: 2026-10-15 12:39:30 -0400

      Commit message:


	  
		
 Promote dev to master (v1.7.1)

Bioconductor devel release in preparation for 3.24 

    

  
    

      Package: dominoSignal

      Commit: e2b463afdfba73352d218733f905467dc39a3a88

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-14 13:03:59 -0400

      Commit message:


	  
		
 Logo update with bioconductor template
 

    

  
    

      Package: dominoSignal

      Commit: 2f922f03410a8f7c87ab6d3ebc8524b24df5c9f3

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-14 13:02:23 -0400

      Commit message:


	  
		
 Logo update with bioconductor template
 

    

  
    

      Package: dominoSignal

      Commit: 12b3415417fd26dc0f0dc75ebe919017927aeb01

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-12 22:29:37 -0400

      Commit message:


	  
		
 Address review comments and add associated tests
 

    

  
    

      Package: dominoSignal

      Commit: 609ed42ba3b2b51996caf716859be9d89fcb46f8

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-12 12:00:29 -0400

      Commit message:


	  
		
 Stop tracking inst/pkgdown.yml file
 

    

  
    

      Package: dominoSignal

      Commit: 6e1ae49a310902de361edb18c25593e128f361da

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-12 11:17:04 -0400

      Commit message:


	  
		
 Merge master into dev history for sync (keep dev content, master fixes manually ported to dev already)
 

    

  
    

      Package: dominoSignal

      Commit: 552034101cffbc3badc913a1621b5a78c4cbf43a

      Author:  kjkrishnan <60410113+kjkrishnan@users.noreply.github.com> 

      Date: 2026-10-12 11:01:59 -0400

      Commit message:


	  
		
 Merge pull request #200 from FertigLab/sync/compress_data

Recompress test data 

    

  
    

      Package: dominoSignal

      Commit: 9124cfdb16cff27e89e71d43c09fdbea3245f3c0

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-09 21:55:34 -0400

      Commit message:


	  
		
 Recompress sysdata with xz instead of bzip2
 

    

  
    

      Package: dominoSignal

      Commit: 9caf04fc97a0f82adb8001e455ec346df4285b61

      Author:  kjkrishnan <60410113+kjkrishnan@users.noreply.github.com> 

      Date: 2026-10-09 20:51:44 -0400

      Commit message:


	  
		
 Merge pull request #199 from FertigLab/review/example_data

Regenerate example data with newest version, update vignettes and other documentation 

    

  
    

      Package: dominoSignal

      Commit: f9d340eee262d38e8496a44a0c0e2231a7cf930a

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-09 19:48:49 -0400

      Commit message:


	  
		
 Update roxygen2 version; fix favicons
 

    

  
    

      Package: dominoSignal

      Commit: 5d46a89e8c4bafa37303bf582d6b6e80f01907b9

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-09 19:23:27 -0400

      Commit message:


	  
		
 Update and organize changelog.
 

    

  
    

      Package: dominoSignal

      Commit: 0182c6601e84dcb23a7104f8862e7a2cb476b4ee

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-09 18:00:18 -0400

      Commit message:


	  
		
 Regenerate example data with newest version, update vignettes and documentation for consistent terminology and accuracy, clean up links in vignettes, improve accessibility
 

    

  
    

      Package: dominoSignal

      Commit: f45472fb1850c5ad7304c582ad68e10754f362ae

      Author:  kjkrishnan <60410113+kjkrishnan@users.noreply.github.com> 

      Date: 2026-10-08 20:18:07 -0400

      Commit message:


	  
		
 Merge pull request #198 from FertigLab/review/tweaks

Minor tweaks to documentation, parameters, error handling 

    

  
    

      Package: dominoSignal

      Commit: d2660717d0edbb3743e39f375becce6e5e2dff98

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-08 19:52:11 -0400

      Commit message:


	  
		
 Generate documentation, fix typos, clarify wording.
 

    

  
    

      Package: dominoSignal

      Commit: 61b356687450a1b1289e4b6bfc409c51fa209acb

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-08 19:39:32 -0400

      Commit message:


	  
		
 Update documentation, update function parameters, use log10(x+1) instead of log10(x) in heatmap plots to avoid errors, explicitly handle 0/0 in signaling network, fixed scenic commands + comments in vignette
 

    

  
    

      Package: dominoSignal

      Commit: 4e11808b081450e6ae113a075e56dbfa08a41141

      Author:  kjkrishnan <60410113+kjkrishnan@users.noreply.github.com> 

      Date: 2026-10-08 18:28:41 -0400

      Commit message:


	  
		
 Merge pull request #197 from FertigLab/review/bugfixes

Bug fixes and changes to data validation to avoid silent crashes, along with better handling of different inputs, and clearer warning/error/messages to user. 

    

  
    

      Package: dominoSignal

      Commit: a4720f9eec38f5ccbea74070e18eb622f410a95e

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-08 18:03:00 -0400

      Commit message:


	  
		
 Fix error handling in dom_to_df when complexes miss components (and associated tests).
 

    

  
    

      Package: dominoSignal

      Commit: f32f40755b5e1b79192875a9bff29e5e94708b9b

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-08 15:42:32 -0400

      Commit message:


	  
		
 Fix copilot bugs - error handling in create_domino for missing receptor genes, create_rl_map_cellphonedb gene conversion edge cases, returning appropriate objects even with empty results
 

    

  
    

      Package: dominoSignal

      Commit: 7c5e68b3a6aa83f21012f2b67bd87d8525331c8a

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-07 18:34:34 -0400

      Commit message:


	  
		
 Fix typos, update news, move pull request template and workflow documentation to avoid pkgdown quirk
 

    

  
    

      Package: dominoSignal

      Commit: dc2aeae3a0b716239db37fe916c462e0118c3b77

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-07 17:28:02 -0400

      Commit message:


	  
		
 Bugfixes for dom_to_df: default parameter for exp_type is counts, empty data frame returned if no signaling is found, handles objects with no complexes (and associated tests).
 

    

  
    

      Package: dominoSignal

      Commit: 8133b48b7fede4348113409486fc9f681eb3c6f7

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-07 17:03:22 -0400

      Commit message:


	  
		
 Bugfixes for create_rl_map_cellphonedb: skip interactions when components lack orthologs, handle missing receptor annotations in protein input, update documentation for gene conversion options (and associated tests).
 

    

  
    

      Package: dominoSignal

      Commit: 30b49071fc93bfbe5aede6fdaad511b769773f72

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-07 16:07:20 -0400

      Commit message:


	  
		
 Bugfix for count_linkage: correctly count subjects when name column is a factor (and associated tests)
 

    

  
    

      Package: dominoSignal

      Commit: a6df5f84a800435214177b5803a47541d1d224a9

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-07 15:49:31 -0400

      Commit message:


	  
		
 Bugfixes for linkage summary functions: update ordering/matching for subject names and metadata, improve error handling, add validity checks to linkage summary object, and associated tests.
 

    

  
    

      Package: dominoSignal

      Commit: 031a7deefd14fe69024b6f421a088cfe6fb81331

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-07 15:26:16 -0400

      Commit message:


	  
		
 Bugfixes for build_domino function: update parameter descriptions, fix error messages, add message for no active TFs, adjust handling of complex ligands, and associated tests.
 

    

  
    

      Package: dominoSignal

      Commit: 804c5d426d2f23abc3028cbcef404ecacf033e77

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-07 14:15:36 -0400

      Commit message:


	  
		
 Bug fixes for create_domino function: improve parameter descriptions, add checks/warnings for invalid inputs, refine handling of rl interactions, and associated tests.
 

    

  
    

      Package: dominoSignal

      Commit: f767e33bcea4b54f1ad63c60a19acb345afe1af9

      Author:  kjkrishnan <60410113+kjkrishnan@users.noreply.github.com> 

      Date: 2026-10-06 18:05:54 -0400

      Commit message:


	  
		
 Merge pull request #196 from FertigLab/changes/params

Update parameters (and address bugs, validity checks, and documentation), resulting in some breaking changes. 

    

  
    

      Package: dominoSignal

      Commit: 5ec98d9e9d206cd65f080333cc9972145b8d69ee

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-06 15:35:32 -0400

      Commit message:


	  
		
 Bugfixes:
- create_vars stored in domino object in addition to build_vars
- cluster networks built in build_domino for all tf selection methods
- validity check for object handles empty matrices and unnamed clusters
- fix max_tf_pval argument name
- Update/add appropriate tests
 

    

  
    

      Package: dominoSignal

      Commit: 8bf62febc1914d18df29da05907b7ca4ecb3dba7

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-05 19:16:06 -0400

      Commit message:


	  
		
 Update metadata and readme/index
 

    

  
    

      Package: dominoSignal

      Commit: aa844568d1668788333198abe9b31e9682ae5e15

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-05 18:36:07 -0400

      Commit message:


	  
		
 Vignette tweaks
 

    

  
    

      Package: dominoSignal

      Commit: f60d6ebac3f27d4b82d412748bb9947f73c7a399

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-05 16:43:07 -0400

      Commit message:


	  
		
 Regenerate example data with updated package to fix bugs
 

    

  
    

      Package: dominoSignal

      Commit: ada1f94fc4c4b1d11aec60493b972ab9dd1bb109

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-05 16:12:44 -0400

      Commit message:


	  
		
 Bugfix: align cell inputs by name in create_domino and require matching cell order in domino validity check
 

    

  
    

      Package: dominoSignal

      Commit: 5e6062ee548f654ab2422f169466e477d020cdc2

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-05 15:32:44 -0400

      Commit message:


	  
		
 Report package version in print/show and access function
 

    

  
    

      Package: dominoSignal

      Commit: f2fc5a937579c732e96336575be99b24a1fc82c5

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-05 14:33:44 -0400

      Commit message:


	  
		
 Add create/build version to domino object and check object validity
 

    

  
    

      Package: dominoSignal

      Commit: 41c23409f8d992de952298c0481a4b7593ce4420

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-10-05 14:17:23 -0400

      Commit message:


	  
		
 Update default parameters in create_domino
 

    

  
    

      Package: dominoSignal

      Commit: dedead4fbe65904efd979c1bd42629163f75a287

      Author:  kjkrishnan <60410113+kjkrishnan@users.noreply.github.com> 

      Date: 2026-09-25 15:37:24 -0400

      Commit message:


	  
		
 Merge pull request #195 from FertigLab/documentation/differential_workflow

Document differential domino workflow 

    

  
    

      Package: dominoSignal

      Commit: 00f36ffa5677b2b05a20d587a08171748a2d4ae3

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-25 14:54:50 -0400

      Commit message:


	  
		
 Update documentation
 

    

  
    

      Package: dominoSignal

      Commit: a79eda4dd2e3a7dfcaa5fb29b471bd080c016b5a

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-25 14:52:02 -0400

      Commit message:


	  
		
 Spell check, linting, address copilot review notes
 

    

  
    

      Package: dominoSignal

      Commit: a6b65f65e17036c4cf61bb9bf28c02a56a6c79bf

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-24 18:45:49 -0400

      Commit message:


	  
		
 Merge origin dev into documentation/differential_workflow
 

    

  
    

      Package: dominoSignal

      Commit: b97735c4d8b04ecf068bcef1a7a8037df1fc37e7

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-24 18:42:43 -0400

      Commit message:


	  
		
 Add example runs to dominoSignal and differential workflow vignettes
 

    

  
    

      Package: dominoSignal

      Commit: bd8a53a84e4b60e36a95e3ec74aedea7c37e3fd8

      Author:  kjkrishnan <60410113+kjkrishnan@users.noreply.github.com> 

      Date: 2026-09-24 18:19:13 -0400

      Commit message:


	  
		
 Merge pull request #193 from FertigLab/bugfix/differential_functions

Bug fixes for differential workflow 

    

  
    

      Package: dominoSignal

      Commit: f3dc18aae9ebddca9e9f0927bd9b4f869c672f52

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-24 13:43:41 -0400

      Commit message:


	  
		
 Update show-linkage_summary method
 

    

  
    

      Package: dominoSignal

      Commit: abcd2e9b346566a7de617c406406684047f59e71

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-24 13:42:50 -0400

      Commit message:


	  
		
 Add linkage_summary object validation, update show/print methods, add tests
 

    

  
    

      Package: dominoSignal

      Commit: 1377c9ac779e499d7644e711504128767f1f140c

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-24 11:16:23 -0400

      Commit message:


	  
		
 Address linkage_summary subset comments
 

    

  
    

      Package: dominoSignal

      Commit: 9073df4cc5d3afaec1e22cf009b1e070e2e27c76

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-24 10:49:34 -0400

      Commit message:


	  
		
 Update link_summary argument in data-raw/ scripts for test/tiny data; remove test_name
 

    

  
    

      Package: dominoSignal

      Commit: 84b2bc99f014fdc35ae114023de7a3e9be41953e

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-24 10:41:27 -0400

      Commit message:


	  
		
 Update plot_differential_linkages function:
- Gradient argument
- Allow plotting odds.ratio (check for NA values)
- Improved checks for statistic range
- Added tests
 

    

  
    

      Package: dominoSignal

      Commit: 1a085bab618be5ecaa10660478c56813d32b75c8

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-24 10:36:54 -0400

      Commit message:


	  
		
 Add vignette for differential signaling workflow
 

    

  
    

      Package: dominoSignal

      Commit: be50b353a7c330d2fa12bdf9ca463df0385e0617

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-22 18:09:27 -0400

      Commit message:


	  
		
 update bioc gha with libomp for mac
 

    

  
    

      Package: dominoSignal

      Commit: 3bed14c4da52a0160deef908a7f609dec8e0d5ed

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-22 18:07:37 -0400

      Commit message:


	  
		
 Merge branch 'bugfix/differential_functions' of https://github.com/FertigLab/dominoSignal into bugfix/differential_functions
 

    

  
    

      Package: dominoSignal

      Commit: 2a71b172374998c03dcd022c9b32b6db480e9606

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-22 12:41:10 -0400

      Commit message:


	  
		
 Make libomp available in R scripts for bioccheck gha
 

    

  
    

      Package: dominoSignal

      Commit: 16629df797abc74e599fd2b20115c628ad1671b6

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-22 17:50:11 -0400

      Commit message:


	  
		
 Make libomp available in R scripts for bioccheck gha
 

    

  
    

      Package: dominoSignal

      Commit: 23edef2a607b6ec2b0d98f9de1e92ea3b800c579

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-22 13:00:53 -0400

      Commit message:


	  
		
 Install libomp in bioc GHA /nocache
 

    

  
    

      Package: dominoSignal

      Commit: f6fdefd42a5d16da8b514051241c19ea66a295ad

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-22 12:41:10 -0400

      Commit message:


	  
		
 Update bioc GHA /nocache
 

    

  
    

      Package: dominoSignal

      Commit: 2ac6425d170f338ba569aa9dc511244049f8cd95

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-21 17:39:34 -0400

      Commit message:


	  
		
 Update summarize_linkages example documentation
 

    

  
    

      Package: dominoSignal

      Commit: 10b9db3e804a5b092ab48d75ff851778d0f16010

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-21 16:43:52 -0400

      Commit message:


	  
		
 Add BrE alternative spellings for relevant function names
 

    

  
    

      Package: dominoSignal

      Commit: d96f63add18b07315e1ab8dd947cc2c788a30a81

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-21 16:26:34 -0400

      Commit message:


	  
		
 Bug fix: empty linkages in summarise_linkage function no longer return spurious NA <- NA results
 

    

  
    

      Package: dominoSignal

      Commit: 47a0f1d9e06615ceec68f1feefd1373d6f9431d1

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-21 15:46:13 -0400

      Commit message:


	  
		
 Bug fix: implement filtering by subject_names in count_linkage and test_differential_linkages
 

    

  
    

      Package: dominoSignal

      Commit: ee2f20f79b7e47ec61d48068f68316e0412dd29c

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-18 18:56:33 -0400

      Commit message:


	  
		
 Merge branch 'dev' of https://github.com/FertigLab/dominoSignal into bugfix/differential_functions
 

    

  
    

      Package: dominoSignal

      Commit: cde785e6f0ac78a66c380b542a6111eba88991a3

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-18 18:56:16 -0400

      Commit message:


	  
		
 Add subset method for linkage_summary class (and associated tests)
 

    

  
    

      Package: dominoSignal

      Commit: 39c5781ec4d2b0645880c24ac66219f5cc8cc60d

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-18 17:41:55 -0400

      Commit message:


	  
		
 Fix odds.ratio assignment in test_differential_linkages for more than 2 groups and add test.
 

    

  
    

      Package: dominoSignal

      Commit: 5e4cda58af4037a41202364a61180a14da521aa2

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-18 17:27:59 -0400

      Commit message:


	  
		
 Update count_linkage() argument
 

    

  
    

      Package: dominoSignal

      Commit: c5beca896a4e93dab116caf38df06674bfa9ff2d

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-18 17:09:58 -0400

      Commit message:


	  
		
 Update test_differential_linkages arguments
 

    

  
    

      Package: dominoSignal

      Commit: 597cb42a643cb6b4a8a225934c561b2bf346fda0

      Author:  kjkrishnan <60410113+kjkrishnan@users.noreply.github.com> 

      Date: 2026-09-18 16:36:49 -0400

      Commit message:


	  
		
 Merge pull request #192

Bug fixes (issue #191, silent failures for single ligand/receptor for a cluster) 

    

  
    

      Package: dominoSignal

      Commit: 1f7e91636da0a8097ea5bb7bf465e6340f52fab2

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-18 14:44:49 -0400

      Commit message:


	  
		
 expect_identical -> expect_equal for object comparison in create_domino test
 

    

  
    

      Package: dominoSignal

      Commit: 1e53b5f2411d392028fb02ec3286c7cb9eac19f7

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-17 15:32:08 -0400

      Commit message:


	  
		
 Bug fixes:
- Fix create_domino to work with custom rl_map without name columns
- Fix build_domino silent exclusions for single ligand or receptor
 

    

  
    

      Package: dominoSignal

      Commit: 35e84fd1b6cce862d44d6f88ae33af62a6ce78ac

      Author:  kjkrishnan <60410113+kjkrishnan@users.noreply.github.com> 

      Date: 2026-09-17 11:08:29 -0400

      Commit message:


	  
		
 Update GHAs

Update GHAs for documentation, docker build, BiocCheck 

    

  
    

      Package: dominoSignal

      Commit: b257e8bcfb461fe643fa5261498075bc25e83dd5

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-16 15:05:37 -0400

      Commit message:


	  
		
 Include testthat in Bioc Check
 

    

  
    

      Package: dominoSignal

      Commit: 4036292ceabe96e656d826ae0fff53dc6a34652d

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-16 14:50:21 -0400

      Commit message:


	  
		
 Update roxygen2 version and documentation
 

    

  
    

      Package: dominoSignal

      Commit: 74abd9ae022bbfed130d54f3951bdf4c2fb69ad7

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-16 14:10:02 -0400

      Commit message:


	  
		
 Remove docs files; fix pkgdown references; update documentation workflow
 

    

  
    

      Package: dominoSignal

      Commit: e68ddc4e462f840cd4112dcc897ee21f55cf5c18

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-09-16 11:57:03 -0400

      Commit message:


	  
		
 Address copilot reviews
 

    

  
    

      Package: dominoSignal

      Commit: bb01efb10484bcb33142b41e50b7e4871e8d0275

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-06-04 12:52:06 -0400

      Commit message:


	  
		
 Update GHAs and admin:
- Consolidate .gitignore files
- Update Dockerfile
- Add bioccheck GHA
- Add PR templates and GHA for master branch PR checklist
- Change documentation GHA from commit to check
- Update page deployment workflow version for pkgdown deployment
- Add concurrency checks to avoid duplicate actions simultaneously
 

    

  
    

      Package: dominoSignal

      Commit: f72df40c4d8d5828fb71d70fdccb9e9e9e4e38af

      Author:  kjkrishnan <60410113+kjkrishnan@users.noreply.github.com> 

      Date: 2026-05-26 13:43:19 -0400

      Commit message:


	  
		
 Merge pull request #189 from FertigLab/sync/pull_master-dev

reconcile master-only changes into dev after bioconductor release 

    

  
    

      Package: dominoSignal

      Commit: 70540f6c803a6d4927782fe247c61ed7024e5402

      Author:  kjkrishnan <kjkrishnan@users.noreply.github.com> 

      Date: 2026-05-18 21:37:56 +0000

      Commit message:


	  
		
 Update documentation
 

    

  
    

      Package: dominoSignal

      Commit: f39358333dadcf8a672c64fdcafd1058c2c661ba

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-05-18 17:36:13 -0400

      Commit message:


	  
		
 documentation fixes
 

    

  
    

      Package: dominoSignal

      Commit: f8c24040640da5cbdcdd26903898fb0b49882288

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-05-18 17:22:22 -0400

      Commit message:


	  
		
 Add zero protection to link subsetting in gene_network function
 

    

  
    

      Package: dominoSignal

      Commit: 6f6834f319fa50ec114b3cb4582310fe7a0c968c

      Author:  kjkrishnan <kjkrishnan@users.noreply.github.com> 

      Date: 2026-05-11 17:43:11 +0000

      Commit message:


	  
		
 Update documentation
 

    

  
    

      Package: dominoSignal

      Commit: 2f933cb75096d62a65866af0f4947a12da5e2184

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-05-08 15:55:55 -0400

      Commit message:


	  
		
 Update vignettes to fix URLs
 

    

  
    

      Package: dominoSignal

      Commit: aa6ae2e70600d8ac8da5b6c0bf431d0e6c84d8e9

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-05-06 17:42:38 -0400

      Commit message:


	  
		
 Fixes to gene_network() function
(see commits b3e8b65 and 0c864dd)
 

    

  
    

      Package: dominoSignal

      Commit: 688746d3d75d2f6c3905dc3b15d7c916c2d5f320

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-05-06 17:07:20 -0400

      Commit message:


	  
		
 Documentation and pkgdown updates
- Fix _pkgdown.yml to include accessible colors for dev site version
- Update citation in CITATION, README.md, and DESCRIPTION
- Change installation information to reflect Bioconductor
- Update URLs for links
- Update NEWS.md to match stable release versioning
- Add workflow notes for bioconductor and github sync
- Remove out of date GHAs

(pulled from commit 86b9188; syncs changes from commits 069cd9, d5c2e57, 3780907, 9c3c131)
 

    

  
    

      Package: dominoSignal

      Commit: 9e7da9df315e389078523907af42891131930934

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-05-06 15:16:41 -0400

      Commit message:


	  
		
 Documentation updates
- Add @family and @seealso to function documentation
- Clarified parameters
(see commits 0c55514 and b46572c)
 

    

  
    

      Package: dominoSignal

      Commit: 86b9188b10ac19d264e3329178eeb0521a6a3d2c

      Author:  kjkrishnan <60410113+kjkrishnan@users.noreply.github.com> 

      Date: 2026-05-05 14:24:44 -0400

      Commit message:


	  
		
 Merge pull request #185 from FertigLab/bioconductor/devel-3.23

Set master branch of repository to mirror devel branch of Bioconductor 3.23 release. 

    

  
    

      Package: dominoSignal

      Commit: 7f49e0c8465d95a8778ce65fbcd65d91560d5d42

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-04-17 18:25:51 -0400

      Commit message:


	  
		
 Swapped to native R pipe instead of magrittr; added .log for BiocCheck outputs to .gitignore
 

    

  
    

      Package: dominoSignal

      Commit: 86ff8e95c34949c201cb849d7a8c3e7f0402705f

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-04-17 18:24:58 -0400

      Commit message:


	  
		
 Bug fix for dom_to_df
- Fixed bug resulting from rowname assignment in get_ligand_expression helper function
- Added message for duplicate clusters
- Added filtering for ligand/receptor expression if using counts, tf_auc for both counts and z_scores to be greater than 0
- Implemented tests for duplicated ligand/receptor/complex names
- Implemented tests for filtering
- Updated existing tests based on changes to intermediate data structures
- Added helper functions for to modify domino objects in testing

Hopefully resolves #183
 

    

  
    

      Package: dominoSignal

      Commit: 0c9462b9de1408e9f25ef381b6355b56ffc8daf6

      Author:  kjkrishnan <60410113+kjkrishnan@users.noreply.github.com> 

      Date: 2026-03-17 17:20:34 -0400

      Commit message:


	  
		
 Merge pull request #140 from branch for issue #138

add test if build_domino fails w/o tf p-values < thd

resolves #138: build_domino fails when no TFs have a p-value below the threshold for one or more clusters. 

    

  
    

      Package: dominoSignal

      Commit: 00bc7a59b0ff8132ce0ad5454f26c728c835c456

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-17 16:46:56 -0400

      Commit message:


	  
		
 update test parameters for new argument checks
 

    

  
    

      Package: dominoSignal

      Commit: dd82ff206ec796430bf0177bb79f12794534fa9c

      Author:  kjkrishnan <60410113+kjkrishnan@users.noreply.github.com> 

      Date: 2026-03-17 16:00:52 -0400

      Commit message:


	  
		
 Merge branch 'dev' into 138-build_domino-fails-when-no-tfs-have-a-p-value-below-the-threshold-for-one-or-more-clusters 

    

  
    

      Package: dominoSignal

      Commit: 14472cd5596bbb2c5f1cb7f5972b799d2a7b57d7

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-17 15:58:54 -0400

      Commit message:


	  
		
 move new build_domino test to correct file for merge to dev
 

    

  
    

      Package: dominoSignal

      Commit: 45ecac27378a52bc49feaac8028b6cd60f158db2

      Author:  dimalvovs <dlvovs1@jh.edu> 

      Date: 2026-03-17 13:27:36 -0400

      Commit message:


	  
		
 Update tests/testthat/test-processing_fxns.R

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> 

    

  
    

      Package: dominoSignal

      Commit: 245efc64fb104cebad9009e9b49a233633d2e4aa

      Author:  kjkrishnan <60410113+kjkrishnan@users.noreply.github.com> 

      Date: 2026-03-16 17:38:20 -0400

      Commit message:


	  
		
 Merge pull request #175 from FertigLab/feature/dom_to_df

Add dom_to_df function, along with helper functions and associated tests. 

    

  
    

      Package: dominoSignal

      Commit: 2b815fc8007f339a43128ffcf8df7042b5c7465d

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-16 16:37:03 -0400

      Commit message:


	  
		
 copilot fixes
avoid direct modification of test fixtures
remove NAs when subsetting ligands
 

    

  
    

      Package: dominoSignal

      Commit: 000b8e6c4e1ac426a0e1e995bb07165ccf3b8409

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-13 14:16:13 -0400

      Commit message:


	  
		
 Refine tests, fix typos
 

    

  
    

      Package: dominoSignal

      Commit: 5161a252a0cf02d18f2a678c491487237bde4260

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-12 19:30:52 -0400

      Commit message:


	  
		
 Simplified if statements in get_signaling_info function
 

    

  
    

      Package: dominoSignal

      Commit: 2f0bf6ec45ca06e2b14ad0b53ea85bbcacedc74f

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-12 19:07:19 -0400

      Commit message:


	  
		
 Added tests for dom_to_df and related helper functions.
 

    

  
    

      Package: dominoSignal

      Commit: 9061258c96bc0a8d72f1ef6b40e719c46b937e4c

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-11 19:01:17 -0400

      Commit message:


	  
		
 Add dom_to_df function and helper functions
 

    

  
    

      Package: dominoSignal

      Commit: 80085faffd17d36a32d1bc4108b29af212548f56

      Author:  kjkrishnan <60410113+kjkrishnan@users.noreply.github.com> 

      Date: 2026-03-11 14:25:54 -0400

      Commit message:


	  
		
 Merge fix/plotting bugs

Address bugs in gene_network and signaling_network functions.
Update testing suite to use testthat v3 (with related testing adjustments). 

    

  
    

      Package: dominoSignal

      Commit: ba17c0c403db4fa75889709409b9e9e624f0ed9a

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-11 13:00:14 -0400

      Commit message:


	  
		
 address applicable copilot comments
 

    

  
    

      Package: dominoSignal

      Commit: 6848271ff73685d51db303e5572ec0be61c1e5f2

      Author:  kjkrishnan <kjkrishnan@users.noreply.github.com> 

      Date: 2026-03-10 19:18:36 +0000

      Commit message:


	  
		
 Update documentation
 

    

  
    

      Package: dominoSignal

      Commit: 2c03c708691f8931db435743fd140216e9b89107

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-10 15:17:05 -0400

      Commit message:


	  
		
 Fix bug in signaling_plot
Addresses NA values created by scaling in signaling_plot
Changed warning to error if no signaling is found with parameters entered
May help to resolve #155 (if the NAs were causing that issue, which is not totally clear)
 

    

  
    

      Package: dominoSignal

      Commit: 466f9fa6eeadb33721e31b432e330eee71c499dd

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-09 17:51:58 -0400

      Commit message:


	  
		
 Pull changes made to dev into branch before any other conflicts arise
 

    

  
    

      Package: dominoSignal

      Commit: b2ebea5b0a37102f25975973a7ebe4bef4863043

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-09 17:15:14 -0400

      Commit message:


	  
		
 Bugs in gene_network function:
Moved cluster naming outside of loop to prevent repeated prefixing.
Should resolve issues #166, #157, #156
(also updated testthat to v3 and modified a few tests to address changes)
 

    

  
    

      Package: dominoSignal

      Commit: 60e3582eefb4049e38f97869a52645f36f2b4563

      Author:  kjkrishnan <60410113+kjkrishnan@users.noreply.github.com> 

      Date: 2026-03-09 17:10:36 -0400

      Commit message:


	  
		
 Merge from refactor/testing_data to dev

Create more comprehensive example and testing data 

    

  
    

      Package: dominoSignal

      Commit: f5f96e82606da47d34ba08ac445ed0f1f639016c

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-09 16:27:00 -0400

      Commit message:


	  
		
 address relevant copilot comments
 

    

  
    

      Package: dominoSignal

      Commit: 32f01bd92fc9ad08076a6601def62b799500225d

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-09 15:35:04 -0400

      Commit message:


	  
		
 Set up testing:
- Testing file for each file for easier use
- Bare minimum test for every function (function runs)
- All tests use internal testing data
 

    

  
    

      Package: dominoSignal

      Commit: d2a20c0ecf49bb4fb8e05cb603f374472ef3750f

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-09 14:07:37 -0400

      Commit message:


	  
		
 documentation fixes
 

    

  
    

      Package: dominoSignal

      Commit: d9b53b7e5ffec48e0bd51f18428bba928a5934f4

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-09 13:02:53 -0400

      Commit message:


	  
		
 add test data for linkage functions
 

    

  
    

      Package: dominoSignal

      Commit: b7420f566c319a94db85fac8dd2e17504a2b05f5

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-06 18:17:42 -0500

      Commit message:


	  
		
 clean up extra code now that tests/examples are simpler
 

    

  
    

      Package: dominoSignal

      Commit: 641bbaae6a488c40a53a96a161f627a7601d9300

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-06 17:58:14 -0500

      Commit message:


	  
		
 examples now use toy data instead of relying on other function examples
 

    

  
    

      Package: dominoSignal

      Commit: 16c0e9bd1027016dae8a8b167f96380976f4b7f3

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-06 17:32:28 -0500

      Commit message:


	  
		
 simplify tests by reducing internal function calls
 

    

  
    

      Package: dominoSignal

      Commit: cdc8124a4ef5bdae0d358b3e47bfd99f23e27b66

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-06 16:53:27 -0500

      Commit message:


	  
		
 run scripts and save outputs for exported and internal data. update names of data exports where necessary.
 

    

  
    

      Package: dominoSignal

      Commit: 9aa125addac64e560975f3b1e80d348558d794be

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-06 16:01:40 -0500

      Commit message:


	  
		
 separate creation of exported and internal data
 

    

  
    

      Package: dominoSignal

      Commit: be3a612f122b1ab24789bd7548e6b6541e4e25d7

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-06 15:08:40 -0500

      Commit message:


	  
		
 Create multiple domino objects for testing
 

    

  
    

      Package: dominoSignal

      Commit: 67e2d4661ae90e0a3bfe34fc3d8880ed01d818a3

      Author:  kjkrishnan <60410113+kjkrishnan@users.noreply.github.com> 

      Date: 2026-03-05 19:41:33 -0500

      Commit message:


	  
		
 Merge pull request #170 from FertigLab/refactor/check_inputs

Add input validation to exported functions 

    

  
    

      Package: dominoSignal

      Commit: 0cc61260448a3c105df406b37786f23a8ae5841d

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-05 19:29:57 -0500

      Commit message:


	  
		
 address copilot review comments
 

    

  
    

      Package: dominoSignal

      Commit: b624ba609388545e610f99a4047312007cb3d8c1

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-05 18:30:48 -0500

      Commit message:


	  
		
 more precise input checks
 

    

  
    

      Package: dominoSignal

      Commit: 46f6671b482f8f70c90c66ff18c409b1b5e282ad

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-05 18:09:31 -0500

      Commit message:


	  
		
 check inputs for linkage functions
 

    

  
    

      Package: dominoSignal

      Commit: 42c67683e5217918372c32fff40c6e2bf4fe8163

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-05 17:59:28 -0500

      Commit message:


	  
		
 check inputs for count_linkages, plots
 

    

  
    

      Package: dominoSignal

      Commit: 155533f8df708c893835a1df8ce6fbab7bc55f00

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-05 17:18:47 -0500

      Commit message:


	  
		
 check inputs for gene conversion, object modification, circos plots, differential linkage plots
 

    

  
    

      Package: dominoSignal

      Commit: aa4fd2719fa94b06a8a618ee9add223527b69a84

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-04 17:42:40 -0500

      Commit message:


	  
		
 More input validation:
- cor_scatter
- count_linkage
- create_regulon_list_scenic
- create_rl_map_cellphonedb
- expression functions
 

    

  
    

      Package: dominoSignal

      Commit: c31349913bb42bac8f25dd5722898a4f8db28d2e

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-04 16:55:51 -0500

      Commit message:


	  
		
 recompress rda file (as recommended in check note)
 

    

  
    

      Package: dominoSignal

      Commit: 6342444afcb0c9a6e63898adcb6d32215374db26

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-04 16:52:25 -0500

      Commit message:


	  
		
 check arguments for build_domino
 

    

  
    

      Package: dominoSignal

      Commit: 5964fe5def07ec7fce0aca6cd6d4533f52e2ff5e

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-04 16:40:21 -0500

      Commit message:


	  
		
 add domino object input check to access functions
 

    

  
    

      Package: dominoSignal

      Commit: d046f380264412bfc03bef76b3de4115f2c15904

      Author:  kjkrishnan <60410113+kjkrishnan@users.noreply.github.com> 

      Date: 2026-03-04 16:20:31 -0500

      Commit message:


	  
		
 Merge refactor/syntax to dev

Code changes for clarity, consistency, robustness, based on R best practices. Should not change functionality (except for hopefully handling some edge cases more gracefully). 

    

  
    

      Package: dominoSignal

      Commit: 9f7246b6a4462aa0a773516307732e135d52b24f

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-04 16:03:45 -0500

      Commit message:


	  
		
 Pull automatically updated documentation.
 

    

  
    

      Package: dominoSignal

      Commit: 6350b115c3ec5ab28c65c0a1c15d1194c456a1c0

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-04 16:02:36 -0500

      Commit message:


	  
		
 bug in rl_map gene name assignment; update show/print for linkage_summary
 

    

  
    

      Package: dominoSignal

      Commit: 9f55e3f281c71d4fc60dab8803efa98ef990d64b

      Author:  kjkrishnan <kjkrishnan@users.noreply.github.com> 

      Date: 2026-03-04 19:14:13 +0000

      Commit message:


	  
		
 Update documentation
 

    

  
    

      Package: dominoSignal

      Commit: 3e93257bd4011bebdff570e53f250d80c9b564f1

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-04 14:12:35 -0500

      Commit message:


	  
		
 fix typos, small tweaks from copilot review
 

    

  
    

      Package: dominoSignal

      Commit: d04d8ac7886a3133e9d6476d4d124d3ca7dc0fdc

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-04 13:42:25 -0500

      Commit message:


	  
		
 add create rl_map with gene conversion (ensembl and table options)
 

    

  
    

      Package: dominoSignal

      Commit: 4d542b06df7db28cde3ed53015cd224b36d4f0f7

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-04 13:06:32 -0500

      Commit message:


	  
		
 Merge branch 'dev' of https://github.com/FertigLab/dominoSignal into refactor/syntax
 

    

  
    

      Package: dominoSignal

      Commit: fbe636e3a2edf533ac055ce515b430fc36fa87e8

      Author:  kjkrishnan <60410113+kjkrishnan@users.noreply.github.com> 

      Date: 2026-03-04 12:00:49 -0500

      Commit message:


	  
		
 Merge pull request #163 from FertigLab/refactor/function_to_file

Refactor R source files to split into smaller, more focused files (and updating documentation accordingly). Should cause no functional changes. 

    

  
    

      Package: dominoSignal

      Commit: 3c93e07a7e222e5920e0dc77334b0b31f1e69af0

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-03 16:28:00 -0500

      Commit message:


	  
		
 Merge branch 'refactor/function_to_file' to refactor/syntax after changes to function_to_file based on copilot review
 

    

  
    

      Package: dominoSignal

      Commit: cd1fc7e7b5c1eef81a5a185cd94a4bd1a49378e2

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-03 15:27:12 -0500

      Commit message:


	  
		
 small fixes from copilot code review
 

    

  
    

      Package: dominoSignal

      Commit: 8fa54f7cacdd797e3c82738e7f61d649f47f3d23

      Author:  kjkrishnan <kjkrishnan@users.noreply.github.com> 

      Date: 2026-03-03 19:44:01 +0000

      Commit message:


	  
		
 Update documentation
 

    

  
    

      Package: dominoSignal

      Commit: 81a6cefaf840be6331575ae0f4cb0a79bf6e2505

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-03 14:40:49 -0500

      Commit message:


	  
		
 Linkage functions:
- simplify logical tests
- remove unnecessary paste inside warnings
- change c() to NULL or types
 

    

  
    

      Package: dominoSignal

      Commit: 26aca2937f062f6cfbffce26c33f6a3c16c58912

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-03 14:12:51 -0500

      Commit message:


	  
		
 Plotting functions:
- replace nested if/else statements with switch
- make sure variables don't overwrite anything
- use isTRUE and isFALSE to handle arguments that can be boolean or string
- replace c() with NULL or types
- &/| -> &&/||
- tried to simplify extra loops
 

    

  
    

      Package: dominoSignal

      Commit: 658e90d57fa389f0f9d218d90b39bb3234d042cf

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-02 17:24:33 -0500

      Commit message:


	  
		
 Pull automatic documentation updates
 

    

  
    

      Package: dominoSignal

      Commit: b670fa17f40b4b4745b089f06f95135a66fa7e1f

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-02 17:23:44 -0500

      Commit message:


	  
		
 Classes and utility functions:
- removed unneeded c()
- avoid variable names overwriting things
- use inherits for class checks
- tried to simplify nested if statements/unnecessary ifelse
 

    

  
    

      Package: dominoSignal

      Commit: 2c7b3e34b880d00aeee076343a613bf4776d5a06

      Author:  kjkrishnan <kjkrishnan@users.noreply.github.com> 

      Date: 2026-03-02 21:02:09 +0000

      Commit message:


	  
		
 Update documentation
 

    

  
    

      Package: dominoSignal

      Commit: 50f241f077690428f451d03e279d7ab9753f6117

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-02 16:00:27 -0500

      Commit message:


	  
		
 Pull automatic update of documentation and merge into feature branch.
 

    

  
    

      Package: dominoSignal

      Commit: 9c4e9a8c5ed44c0b7a92ee2dce5938f36c35a429

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-02 15:56:10 -0500

      Commit message:


	  
		
 generics for show/print for linkage_summary class
 

    

  
    

      Package: dominoSignal

      Commit: f70e2b6799a2949108205778f8058f3384619f21

      Author:  kjkrishnan <kjkrishnan@users.noreply.github.com> 

      Date: 2026-03-02 20:38:23 +0000

      Commit message:


	  
		
 Update documentation
 

    

  
    

      Package: dominoSignal

      Commit: d525c018e1f40bd7b29482b787be7044010d3c28

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-02 15:36:27 -0500

      Commit message:


	  
		
 Syntax fixes
- domino_class: cat -> message, use of nlevels
- expression_functions: seq_len(length) -> seq_along, linting
- gene_conversion: import biomart, implement check_arg, update documentation
 

    

  
    

      Package: dominoSignal

      Commit: cd8ffebb0f85bdfbbc534dba55db81b9bde9d7d7

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-02 13:51:42 -0500

      Commit message:


	  
		
 Regulons/RL Map
- create_regulon_list: fixed patterns for string splits, linting
- create_rl_map: remove extra c(), && in if, fixed patterns, nzchar for empty strings, linting
 

    

  
    

      Package: dominoSignal

      Commit: a1542fd3e00959cb19f31b4e7fa59809c2bc2950

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-03-02 13:08:29 -0500

      Commit message:


	  
		
 Syntax and linting
- cor_scatter: linting
- count_linkage: ensure variable names aren't overwriting anything, linting
- create_domino: update for fixed grep patterns, ensure variable names aren't overwriting things, simplify if statements, linting
 

    

  
    

      Package: dominoSignal

      Commit: 1e37ab8d1f230778f25a6614b339230277578fce

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-02-27 17:42:13 -0500

      Commit message:


	  
		
 Build domino:
- Added fixed = TRUE to grepl for efficiency
- Replaced sapply with vapply with type
- Made sure variables don't overwrite anything
- Seed empty vectors with types
- Linting for legibility
 

    

  
    

      Package: dominoSignal

      Commit: 671d37197274bf76dc1e55da8888399793e24bb0

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-02-27 16:55:01 -0500

      Commit message:


	  
		
 Access functions:
- Use switch instead of nested if statements
- Switch from & to && in if statements
- Make sure variables don't overwrite anything
- Linting for legibility
 

    

  
    

      Package: dominoSignal

      Commit: 5db80780c62dcdf09d8a3b34de6d5f8d587eb1e2

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-02-26 16:16:33 -0500

      Commit message:


	  
		
 Moved functions into separate files
 

    

  
    

      Package: dominoSignal

      Commit: 5f1821daa9e0e025300fef65c2d8cd626cecb0ff

      Author:  kjkrishnan <60410113+kjkrishnan@users.noreply.github.com> 

      Date: 2026-02-26 13:06:52 -0500

      Commit message:


	  
		
 Merge pull request #162 from FertigLab/fix/pkgdown_build

Update documentation and accessibility for pkgdown site. 

    

  
    

      Package: dominoSignal

      Commit: d27177732e7218bf481a059436bf5c99bcf861ae

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-02-25 17:24:57 -0500

      Commit message:


	  
		
 r-cmd-check badge removed
 

    

  
    

      Package: dominoSignal

      Commit: 85475a3cf1f31aae20c767d882823277759e4d9d

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-02-25 16:28:03 -0500

      Commit message:


	  
		
 Added alt text to vignette plots
 

    

  
    

      Package: dominoSignal

      Commit: 5911e126fc1750a6307b4c1b2a1eb17226b38c85

      Author:  kjkrishnan <kkrishnan@som.umaryland.edu> 

      Date: 2026-02-25 14:56:26 -0500

      Commit message:


	  
		
 Update pkgdown documentation
- Use keyword internal for circos functions used inside plotting function
- Fix logo file path in index.rmd
- Update URL in description
- Rebuild favicons
 

    

  
    

      Package: dominoSignal

      Commit: 83c35d3737d282b825c7e1d413f53817c1266265

      Author:  dimalvovs <dmitrijs.lvovs@gmail.com> 

      Date: 2024-11-13 10:10:52 -0600

      Commit message:


	  
		
 add test if build_domino fails w/o tf p-values < thd
 

    

  
    

      Package: Rarr

      Commit: a48e22c20c857bd7539e15d88a67547047f5f9a2

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-15 15:19:09 +0200

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: Rarr

      Commit: 3201f76088f828523d734b7f9aed785b80efa7ff

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-15 15:18:51 +0200

      Commit message:


	  
		
 Document update_zarr_array() skipping writes
 

    

  
    

      Package: Rarr

      Commit: deb7c785674c130247c0920d293423448189673e

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-15 15:17:30 +0200

      Commit message:


	  
		
 Add test for empty chunks in update_chunk()
 

    

  
    

      Package: Rarr

      Commit: 73a21eaa473957a2973974a4a820a6b42b778afd

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-15 15:14:49 +0200

      Commit message:


	  
		
 Avoid writing or rewriting in update_chunk()
 

    

  
    

      Package: Rarr

      Commit: 46097aa003176dbcbf927cbf79002fa0f37183e9

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-15 15:13:49 +0200

      Commit message:


	  
		
 Reimplement is_all_fill in C
 

    

  
    

      Package: Rarr

      Commit: 8fea57d1ae388898957e0c1c0497fddbf88d6779

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-15 13:57:13 +0200

      Commit message:


	  
		
 Implement is_all_fill() helper
 

    

  
    

      Package: Rarr

      Commit: 6aa29f1034d24b986e54e229793a82ae30a772db

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-14 19:09:41 +0200

      Commit message:


	  
		
 Add has_zstd() shortcut for R 4.5
 

    

  
    

      Package: spicyR

      Commit: c369940dac7ebe8dc3cd69d6b403dcb08dee9f5c

      Author:  EllisPatrick <ellis.patrick@sydney.edu.au> 

      Date: 2026-10-16 01:20:56 +1100

      Commit message:


	  
		
 1.99.21: the cell method's image-by-image loop in the shared C++ core; imageInfo and tableKey; writeCellStore() and a store example in the vignette

- src/core/src/stream.cpp, spicyglm/stream.hpp (new, shared with spicyr): batch_totals(), rows_totals() and
  stream_totals() run each image in a Dataset of its own, the images handed out to threads in turn; scan_codes(),
  constant_within(), rows_differing(), rows_of_images() and first_appearance_codes() are the passes over the codes.
  src/glm_bindings.cpp keeps thin wrappers (cell_block_scan replaces cell_layout). Results identical: 222/236
  test expectations, memref 8 of 8 identical(), the 100M store identical() to the data.frame run (1 and 8 cores),
  100M and 1B results identical() to 1.99.20.
- spicy(): `table` is renamed `tableKey`; new `imageInfo` (data.frame or the name of a table of the store or
  SpatialData object) for condition, subject, covariates or a Surv outcome missing from the cell table, for
  data.frames and stores (survival from a store now works). Errors for missing and unknown images.
- writeCellStore() (exported) writes cells as a SpatialData store with anndataR; spatialdataR and anndataR in
  Suggests. Vignette: "Very large data sets: SpatialData stores".

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
 

    

  
    

      Package: spicyR

      Commit: 1bfe9a915dd06cea72c9f2f5628c1638e70930de

      Author:  EllisPatrick <ellis.patrick@sydney.edu.au> 

      Date: 2026-10-15 21:47:58 +1100

      Commit message:


	  
		
 1.99.20: NEWS with the timings from stores of 10M, 100M and 1B cells; spicy.Rd

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
 

    

  
    

      Package: spicyR

      Commit: 85d1bdc13cf8808da848e0b3d4b14663e85bb393

      Author:  EllisPatrick <ellis.patrick@sydney.edu.au> 

      Date: 2026-10-15 20:51:50 +1100

      Commit message:


	  
		
 1.99.20: spicy() takes a SpatialData object (spatialdataR): read from its store, or from its table in memory

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
 

    

  
    

      Package: spicyR

      Commit: 22bdadf2022c3b719391670b399c19d4831132a1

      Author:  EllisPatrick <ellis.patrick@sydney.edu.au> 

      Date: 2026-10-15 20:48:11 +1100

      Commit message:


	  
		
 1.99.20: each image in a Dataset of its own, images handed to threads in turn; batch coordinates read a block of rows at a time

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
 

    

  
    

      Package: spicyR

      Commit: 966e64d96e1cb04720cdffe6ce5ace03b417bf39

      Author:  EllisPatrick <ellis.patrick@sydney.edu.au> 

      Date: 2026-10-15 20:31:57 +1100

      Commit message:


	  
		
 1.99.20: one C++ pass per block of rows; coordinates read once per batch and passed as the matrix; batches capped at 2^26 cells

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
 

    

  
    

      Package: spicyR

      Commit: 023a91919f93fe3a93793dbb3f800eea24dd5592

      Author:  EllisPatrick <ellis.patrick@sydney.edu.au> 

      Date: 2026-10-15 20:10:30 +1100

      Commit message:


	  
		
 1.99.20: spicy() cell method reads a SpatialData / AnnData Zarr store block by block and image batch by image batch (identical results)

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
 

    

  
    

      Package: spicyR

      Commit: df798054af2705b9f4d0e77eba46af161a86b6c9

      Author:  EllisPatrick <ellis.patrick@sydney.edu.au> 

      Date: 2026-10-15 19:02:07 +1100

      Commit message:


	  
		
 1.99.19: spicy() cell method reads the cells image by image (identical results; ~1 GB instead of ~17 GB above the data at 100M cells)

- cell_stream_totals (R bindings only; src/core untouched): gathers a batch of whole images (about 2^21 cells per
  thread) from the unsorted columns into its own Dataset and calls the same Dataset functions, so every image's
  sums are bit-identical to the whole-data Dataset's.
- .cell_context: no sorted copies; one C++ pass (cell_layout) gives cells and first row per (image, type);
  constancy of condition/subject checked in C++ with an exact as.character() fallback; whole-data Dataset only with
  dataset = TRUE (Kontextual, label-clustering factor, tests).
- .format_data(sort = FALSE) for spicy(); character imageID/cellType become factors in one pass when ASCII
  (first_appearance_factor), else factor() as before.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
 

    

  
    

      Package: spicyR

      Commit: 1cb0cafabb73b75ff33ee97e0c76e1a6c98c8b14

      Author:  EllisPatrick <ellis.patrick@sydney.edu.au> 

      Date: 2026-10-15 17:51:17 +1100

      Commit message:


	  
		
 1.99.18: spicy() cell method uses far less memory and time on large data (identical results)

- .format_data(ids = FALSE) for the cell method: no cellID / imageCellID string per cell (unused there).
- .cell_context keeps one row per image (ctx$pheno) instead of a reordered copy of the whole cell table, and the
  cells per image and type (nCells) from its counts instead of tabulating every cell again.
10 million cells: peak 4.3 -> 1.35 GB above the data, 78 -> 24 s. 100 million: about 28 -> 17 GB.
All spicy() outputs identical() to 1.99.17 on 8 configurations (fraction, count, kNN, 3 radii, Davies over 10,
subject, covariate, diabetesData); 199 tests pass.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
 

    

  
    

      Package: exploreSE

      Commit: 6a224d7af43c1ef158a7d3416049828b0d81ee67

      Author:  Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com> 

      Date: 2026-10-15 15:38:17 +0200

      Commit message:


	  
		
 toggles for various plots, expression, enrichment
 

    

  
    

      Package: mitology

      Commit: be6407d63d13b2a01d5c8c6d601a687f9f90376d

      Author:  Stefania Pirrotta <s.pirrotta.sp@gmail.com> 

      Date: 2026-10-15 14:45:29 +0200

      Commit message:


	  
		
 Update NEWS
 

    

  
    

      Package: mitology

      Commit: 2db59cc1eef28b4f399b1b6349707d48bf01c628

      Author:  Stefania Pirrotta <s.pirrotta.sp@gmail.com> 

      Date: 2026-10-15 14:45:05 +0200

      Commit message:


	  
		
 Update MitoGenesDB object
 

    

  
    

      Package: mitology

      Commit: 526512090bcd6e9d430101d901b9266268835d84

      Author:  Stefania Pirrotta <s.pirrotta.sp@gmail.com> 

      Date: 2026-10-15 14:44:33 +0200

      Commit message:


	  
		
 update gseaMito function
 

    

  
    

      Package: OMA

      Commit: 61c23de087f3b21162722e7f87215abefee0b530

      Author:  Muluh <127390183+0xMuluh@users.noreply.github.com> 

      Date: 2026-10-15 10:11:40 +0300

      Commit message:


	  
		
 Update link to clustering information in community_similarity.qmd (#843)

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

    

  
    

      Package: OMA

      Commit: 4142bdb338375413ccbb8eb895859e515bfa1ab3

      Author:  Muluh <127390183+0xMuluh@users.noreply.github.com> 

      Date: 2026-10-15 10:07:29 +0300

      Commit message:


	  
		
 Add HuMMANet resource reference (#888)

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

    

  
    

      Package: OMA

      Commit: bbf4728ec28022b6a791eba2ff6f634367a5f1cd

      Author:  Muluh <127390183+0xMuluh@users.noreply.github.com> 

      Date: 2026-10-15 09:51:58 +0300

      Commit message:


	  
		
 Remove deprecated workflow telemetry action (#880)

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

    

  
    

      Package: OMA

      Commit: 4db61b951d548484d3c12d6b3f0433724797a075

      Author:  Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

      Date: 2026-10-15 09:47:11 +0300

      Commit message:


	  
		
 Fix build (#901) 

    

  
    

      Package: OMA

      Commit: 729ef8438e47a1eb899519a79994d0b93e45c426

      Author:  Muluh <127390183+0xMuluh@users.noreply.github.com> 

      Date: 2026-10-15 09:40:58 +0300

      Commit message:


	  
		
 Document swapping alternative experiments (#884) 

    

  
    

      Package: OMA

      Commit: bcc80a289dd91acf16c9876be40b110005108057

      Author:  Muluh <127390183+0xMuluh@users.noreply.github.com> 

      Date: 2026-10-15 09:16:36 +0300

      Commit message:


	  
		
 [Urgent] Repository-wide whitespace and styling cleanup (#897) (#898)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

    

  
    

      Package: OMA

      Commit: 25867ad77383fa2764001dc7839ad8a98f68efc9

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

      Date: 2026-10-15 09:04:33 +0300

      Commit message:


	  
		
 Bump docker/login-action from 2 to 4 (#893)

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Muluh <127390183+0xMuluh@users.noreply.github.com>
Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

    

  
    

      Package: OMA

      Commit: 7a87c1e8df4cce3b8abe1de850f189883e5dba30

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

      Date: 2026-10-15 08:56:15 +0300

      Commit message:


	  
		
 Bump JamesIves/github-pages-deploy-action from 4.4.3 to 4.9.0 (#891)

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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Muluh <127390183+0xMuluh@users.noreply.github.com>
Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

    

  
    

      Package: OMA

      Commit: fa69edce1a81abbb13dd822fd2bdb3bd3ab59c32

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

      Date: 2026-10-15 08:50:35 +0300

      Commit message:


	  
		
 Bump actions/checkout from 2 to 7 (#892)

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Muluh <127390183+0xMuluh@users.noreply.github.com>
Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

    

  
    

      Package: OMA

      Commit: eca67ae00c93643e15009013233f60c0a47598e7

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

      Date: 2026-10-15 08:45:51 +0300

      Commit message:


	  
		
 Bump actions/cache from 3 to 6 (#890)

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Muluh <127390183+0xMuluh@users.noreply.github.com> 

    

  
    

      Package: Rsubread

      Commit: b289baf7a283685ded7152086b0bacd0a8946e50

      Author:  Ubuntu <ubuntu@crispr-screening-webservice.novalocal> 

      Date: 2026-10-15 04:13:17 +0000

      Commit message:


	  
		
 removed warnings from makevar and LR mismatch
 

    

  
    

      Package: Rsubread

      Commit: 182d84341c0dde9d924175d21877f3bf1a21f5ef

      Author:  Ubuntu <ubuntu@crispr-screening-webservice.novalocal> 

      Date: 2026-10-15 03:50:37 +0000

      Commit message:


	  
		
 Fixed warnings then bumped version number
 

    

  
    

      Package: carnation

      Commit: f3fb020ede7244bb12ddff1c39a20e90f0cab548

      Author:  Apratim Mitra <16709900+mitraak@users.noreply.github.com> 

      Date: 2026-10-14 15:24:06 -0400

      Commit message:


	  
		
 Merge pull request #46 from NICHD-BSPC/updt_actions

Updt actions

- turn off `sync-devel` action
- set `bioccheck` and `conda` actions to run on devel
- remove reference to `r4.3` branch from README 

    

  
    

      Package: carnation

      Commit: 5d6ecc78aa78446f3dd984f0107ab2c093241173

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-14 15:22:03 -0400

      Commit message:


	  
		
 rm ref to r4.3
 

    

  
    

      Package: carnation

      Commit: 4a7f9809586bd220a52b8f69a585ad0a692b12ac

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-14 15:20:27 -0400

      Commit message:


	  
		
 turn off sync-devel, set bioccheck/conda actions to run on devel
 

    

  
    

      Package: carnation

      Commit: 2c1f20bcefdcd6ff0b8eec25a959d02cedd6d2c1

      Author:  Apratim Mitra <16709900+mitraak@users.noreply.github.com> 

      Date: 2026-10-14 15:14:13 -0400

      Commit message:


	  
		
 Merge pull request #39 from NICHD-BSPC/v1.2.0rc

- volcano plot module (@DaleMcCauley)
- various plot updates
  - MA plot
    - added aspect ratio  and alpha controls
    - new 'refresh' button for reduced reactivity
  - Gene plot
    - add option to show unnormalized counts. This is helpful when the data in the `dds` element is pre-normalized, e.g. in proteomics
  - scatter plot
    - raw p-values added as a plotting option
    - plot/table selection panels now open upon selection
  - aspect ratio control for PCA & scatter plots
- analysis table
  - updated to show all available datasets
  - obtain file info (size, mtime) and show in the table
  - improved selection behavior
    
- misc fixes
  - correctly reset gene scratchpad when loading data so previously added genes don't show up again.
  - the gene plot function now sets the 'text' aesthetic to `factor()` to stop warnings about statistical transformation
  - `fromList.with.names` now uses base R column indexing instead of `dplyr::relocate`. 

    

  
    

      Package: carnation

      Commit: 66fcc7c13fddaf59a8a7c90e692a3474cdad00a7

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-14 14:55:37 -0400

      Commit message:


	  
		
 updt NEWS
 

    

  
    

      Package: carnation

      Commit: 716855b50562b64656f9bb8f8cc97a373167bd62

      Author:  Apratim Mitra <16709900+mitraak@users.noreply.github.com> 

      Date: 2026-10-14 14:48:42 -0400

      Commit message:


	  
		
 Merge pull request #45 from NICHD-BSPC/analysis_tbl

version bump 

    

  
    

      Package: carnation

      Commit: 8e3f0f437fc979427bfdd77b08893d5c1a8d50b6

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-14 14:03:59 -0400

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: carnation

      Commit: e63104db785e62609462971dc6259697373b310e

      Author:  Apratim Mitra <16709900+mitraak@users.noreply.github.com> 

      Date: 2026-10-01 13:39:12 -0400

      Commit message:


	  
		
 Merge pull request #44 from NICHD-BSPC/analysis_tbl

- analysis table
  - updated to show all available datasets
  - obtain file info (size, mtime) and show in the table
  - improved selection behavior
- added aspect ratio control to PCA & scatter plots
- scatter plot
  - raw p-values added as a plotting option
  - plot/table selection panels now open upon selection 

    

  
    

      Package: carnation

      Commit: f3c8cd845cfffa463fa89526f408102a430d8c8d

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-01 13:25:53 -0400

      Commit message:


	  
		
 fix arg in formatStyle call
 

    

  
    

      Package: carnation

      Commit: 3e50d6f63c0b1a6f3e96fed678d9a1230fb61330

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-01 13:13:24 -0400

      Commit message:


	  
		
 add aspect ratio input to pca test
 

    

  
    

      Package: carnation

      Commit: 44da44e929798b49b81946fe41f517917bb19520

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-01 13:13:12 -0400

      Commit message:


	  
		
 clean up comment
 

    

  
    

      Package: carnation

      Commit: 6edfc35c12d079a14665e4509071a37c6fe615df

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-01 13:12:58 -0400

      Commit message:


	  
		
 rm non-existent input frm test
 

    

  
    

      Package: carnation

      Commit: dac91507627488d9fd18df7e554bf6cd84ca0bd3

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-01 12:15:11 -0400

      Commit message:


	  
		
 open plt/tbl sel collapse only after selections & reset on load
 

    

  
    

      Package: carnation

      Commit: ad10455f0a720b81666447cd225ea134cc160f97

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-01 12:14:50 -0400

      Commit message:


	  
		
 rename log2FoldChange to LFC
 

    

  
    

      Package: carnation

      Commit: 20552affc897d127548b4174f746d4315c295ab3

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-01 12:13:24 -0400

      Commit message:


	  
		
 clean up commented lines
 

    

  
    

      Package: carnation

      Commit: abfa31467e6e606b104f5c641531c15105d58f9f

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-01 10:54:52 -0400

      Commit message:


	  
		
 fmt all columns with numeric vals in scatter tbl
 

    

  
    

      Package: carnation

      Commit: eceabf7eee8665738531000f7e307cd94c1880f3

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-01 10:54:19 -0400

      Commit message:


	  
		
 add raw pval option to scatter plt
 

    

  
    

      Package: carnation

      Commit: 31b1e4196713bdd96ca263ac7045499cd78833cc

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-01 10:53:31 -0400

      Commit message:


	  
		
 center scatter plt to handle narrow aspect
 

    

  
    

      Package: carnation

      Commit: 65914561ae2b7ea768ca0bc8aef685b1bb840e14

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-01 10:52:34 -0400

      Commit message:


	  
		
 add aspect ratio ctrl to scatter plt
 

    

  
    

      Package: carnation

      Commit: 3d40cdd6172ab4c254da7afc859f8bd503579df6

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-01 10:28:34 -0400

      Commit message:


	  
		
 simplify grid lines settings for scatter
 

    

  
    

      Package: carnation

      Commit: ecd4ec236084a7cc00fbd388f99299e7161c80cf

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-01 10:12:27 -0400

      Commit message:


	  
		
 clean up commented lines
 

    

  
    

      Package: carnation

      Commit: b83e54f1dceb928bc69beeee314f6a285d2194b4

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-01 10:09:48 -0400

      Commit message:


	  
		
 rm wellPanel, repl w strong plot settings heading
 

    

  
    

      Package: carnation

      Commit: c619dd7dbf28dd133dda18eef3227535aded1d86

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-01 10:03:52 -0400

      Commit message:


	  
		
 mv plt settings out of collapse, deindent
 

    

  
    

      Package: carnation

      Commit: 36a69cfd74c97bde810500d0ce3245132341f133

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-01 10:02:19 -0400

      Commit message:


	  
		
 updt ma plt docs
 

    

  
    

      Package: carnation

      Commit: e8ddfafb96bab2226b08212eadc24690e9d37442

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-01 10:02:03 -0400

      Commit message:


	  
		
 add aspect ratio ctrls to pca plot
 

    

  
    

      Package: carnation

      Commit: 77b48dab72da43a046de047e3a9e95fc6f494ecb

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-01 09:18:01 -0400

      Commit message:


	  
		
 add docs about volcano dashed line
 

    

  
    

      Package: carnation

      Commit: f55bdce23dc1f923e18b6185c29b344206a5cf22

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-30 17:32:07 -0400

      Commit message:


	  
		
 only updt assay input if different
 

    

  
    

      Package: carnation

      Commit: c2e07ce802c55db2507aad27e4bd60338c6137f4

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-30 17:31:52 -0400

      Commit message:


	  
		
 updt analysis tbl based on analysis input
 

    

  
    

      Package: carnation

      Commit: e903fd39334235dade7d466b2953f2f35b3b5654

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-30 17:31:19 -0400

      Commit message:


	  
		
 get analysis frm tbl selection
 

    

  
    

      Package: carnation

      Commit: 4454cd9f0dda59e8950057a0c614e45e7cfb1650

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-30 17:30:38 -0400

      Commit message:


	  
		
 don't wrap size field
 

    

  
    

      Package: carnation

      Commit: 397c87006c86cad3385cbd57e89abadbf588e490

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-30 17:30:30 -0400

      Commit message:


	  
		
 cache analysis desc df
 

    

  
    

      Package: carnation

      Commit: f064b76b256d87bbab551e2c7bff84936a880f7d

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-30 17:29:26 -0400

      Commit message:


	  
		
 show all analysis, handle mult fields in desc
 

    

  
    

      Package: carnation

      Commit: 4657ca92492660888df3c03b9e61a047097ea49d

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-30 17:27:04 -0400

      Commit message:


	  
		
 reorder assay list
 

    

  
    

      Package: carnation

      Commit: 5f7960c406dd733de23805be4f33660aa6078978

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-30 17:25:31 -0400

      Commit message:


	  
		
 get and cache analysis info
 

    

  
    

      Package: carnation

      Commit: 4e1d37a4965460a861ceeaefe88b97f5d8b5e0ce

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-30 17:24:41 -0400

      Commit message:


	  
		
 adj proj/analysis tbl rel widths
 

    

  
    

      Package: carnation

      Commit: e7be5d98114809cbe0a4584c88a435a995274661

      Author:  Apratim Mitra <16709900+mitraak@users.noreply.github.com> 

      Date: 2026-09-30 15:32:57 -0400

      Commit message:


	  
		
 Merge pull request #43 from NICHD-BSPC/volcano_fixes

Volcano fixes

- Makes the default y-axis for the volcano plots based on raw p-value, as opposed to  adjusted p-value. Also, the ability to switch between them. 
- Addresses bugs found related to autoscaling. 
- Addresses bug in coloring of points that are the only one off the plot in a certain direction. 
- Reduced unnecessary branching for displaying clamped points in the interactive plotting function.  

    

  
    

      Package: carnation

      Commit: 851b7217b5531f37441091ee53cb86b0a37bcc7b

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-30 15:15:37 -0400

      Commit message:


	  
		
 adjust modal help
 

    

  
    

      Package: carnation

      Commit: 432dd4bf5e35af1e850fd77b606087312858e2a4

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-30 15:15:17 -0400

      Commit message:


	  
		
 check res cols fr carnation obj
 

    

  
    

      Package: carnation

      Commit: 3753aaa1c22773f38a82c82f2c5584215108cbcf

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-30 15:14:54 -0400

      Commit message:


	  
		
 add validates fr missing cols
 

    

  
    

      Package: carnation

      Commit: 370fdf990f344d2b5d95670c04d5056713007e58

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-30 15:14:00 -0400

      Commit message:


	  
		
 don't use withSpinner to avoid plot snapping to left & back to center
 

    

  
    

      Package: carnation

      Commit: 2fa7ba1df42d168dc5ed5dc4d75e02f508107003

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-30 15:13:34 -0400

      Commit message:


	  
		
 tweak menu and select shown names
 

    

  
    

      Package: carnation

      Commit: e277fb7a31f99c6e65971ea4959e933d82882ca1

      Author:  Dale McCauley <dale.mccauley@nih.gov> 

      Date: 2026-09-29 16:48:11 -0400

      Commit message:


	  
		
 Updated and added test coverage for volcano plot
 

    

  
    

      Package: carnation

      Commit: 737cc7687b0037759cbcb719e09dfce4324cbc80

      Author:  Dale McCauley <dale.mccauley@nih.gov> 

      Date: 2026-09-29 14:56:15 -0400

      Commit message:


	  
		
 Reduced unecessary branching in interactive volcano plotting function, and other smaller cleanups
 

    

  
    

      Package: carnation

      Commit: dd6a48de4803d2ec2bc9e11790ffd903a5134d4c

      Author:  Dale McCauley <dale.mccauley@nih.gov> 

      Date: 2026-09-29 11:47:18 -0400

      Commit message:


	  
		
 Added guards and notification related to having no points on the graph and autoscaling, including if all points have the same y value. Also fixed bug where when a single point was off the top of the plot and clamped to the edge, it would show an incorrect color.
 

    

  
    

      Package: carnation

      Commit: 1e64f0d91fb58e8634a29692d82d0092588ad350

      Author:  Dale McCauley <dale.mccauley@nih.gov> 

      Date: 2026-09-28 16:25:21 -0400

      Commit message:


	  
		
 Made capitilization of colors for the volcano plot more consistent. ggplot expects lowercase and plotly expects upper so it is stored as upper and passed to ggplot with tolower()
 

    

  
    

      Package: carnation

      Commit: 6f299555e00a8b0e6c4eaabd583d1547ca6c1a2c

      Author:  Dale McCauley <dale.mccauley@nih.gov> 

      Date: 2026-09-28 15:33:38 -0400

      Commit message:


	  
		
 Added correct raw p-value fdr significance line for static volcano plot and added generated docs
 

    

  
    

      Package: carnation

      Commit: 5c0b6ccf7da708e4a8b8331c26274cef507a89ba

      Author:  Dale McCauley <dale.mccauley@nih.gov> 

      Date: 2026-09-28 14:37:24 -0400

      Commit message:


	  
		
 Added raw p-value and adjusted p-value modes for plotting
 

    

  
    

      Package: carnation

      Commit: d9c4852e8ccbb2558fa150e0a760db21444acfe3

      Author:  Apratim Mitra <16709900+mitraak@users.noreply.github.com> 

      Date: 2026-09-24 14:52:50 -0400

      Commit message:


	  
		
 Merge pull request #42 from NICHD-BSPC/geneplt_fixes_v2

Geneplt fixes v2

- revert gene plot to using `nrow` not `ncol` control. A couple of reasons for this:

  - Fixing `ncol` in `facet_wrap` was making `ggplotly` behave strangely. Some facets were showing up with no data, facets were being labeled wrong - although the static downloaded plot seemed fine.
  - The solution was to go back to the way this was being handled before and removing the column number control that was implemented.

- misc edits:

  - the gene plot function now sets the 'text' aesthetic to `factor()` to stop warnings about statistical transformation
  - `fromList.with.names` now uses base R column indexing instead of `dplyr::relocate`. 

    

  
    

      Package: carnation

      Commit: fedcccba8677881ef5baa3cdce82ba2475409df5

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-24 14:29:43 -0400

      Commit message:


	  
		
 set aes to factor to stop warnings, repl relocate w base indexing
 

    

  
    

      Package: carnation

      Commit: 6a7f7201197b4eb32466af2781850aadec2a82ef

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-24 14:29:24 -0400

      Commit message:


	  
		
 revert to using nrow fr gene plt, rm ncol cntrl
 

    

  
    

      Package: carnation

      Commit: c0e73b123b6a4455714500da60c7b91957e14fbc

      Author:  Apratim Mitra <16709900+mitraak@users.noreply.github.com> 

      Date: 2026-09-24 12:00:54 -0400

      Commit message:


	  
		
 Merge pull request #41 from NICHD-BSPC/geneplt_fixes

various plot updates:

- MA plot
  - added aspect ratio  and alpha controls
  - new 'refresh' button for reduced reactivity
- Gene plot
  - allow users to fix number of columns in faceted plot
  - add option to show unnormalized counts. This is helpful when the data in the `dds` element is pre-normalized, e.g. in proteomics
- misc fixes
  - correctly reset gene scratchpad when loading data so previously added genes don't show up again.  

    

  
    

      Package: carnation

      Commit: a9de2f2706512fa2cb1c1e370e003640d01b9314

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-24 11:46:50 -0400

      Commit message:


	  
		
 updt README to point to release bioc
 

    

  
    

      Package: carnation

      Commit: 9ef0d82aca0c430dacd04563fe7e2f25e9b87b2e

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-24 11:46:40 -0400

      Commit message:


	  
		
 updt plotMA.label docs
 

    

  
    

      Package: carnation

      Commit: 9579f85b89d3c0e8b0812aebd35ee73d85ad1b24

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-23 13:19:29 -0400

      Commit message:


	  
		
 add opt to show raw counts in gene plt
 

    

  
    

      Package: carnation

      Commit: b611d2c234c1427c037f674dcf5bb773cc2a9920

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-23 13:19:07 -0400

      Commit message:


	  
		
 add reactiveVal for data load
 

    

  
    

      Package: carnation

      Commit: 9aa3cb222740dcd88ec5bea04a19d68e00ed05dc

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-22 19:35:12 -0400

      Commit message:


	  
		
 fix indents, ws
 

    

  
    

      Package: carnation

      Commit: e8eccee411879fcb692c1f6c25622ad7dd128cff

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-22 19:30:58 -0400

      Commit message:


	  
		
 rm withspinner frm uiOutput wrapper
 

    

  
    

      Package: carnation

      Commit: 16281e4b0792fae712e327a56426108e382e8784

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-22 19:30:41 -0400

      Commit message:


	  
		
 convert ma plot padding to proportion
 

    

  
    

      Package: carnation

      Commit: 18c52ddde28b83c9b526bcafe911a1765e53c91a

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-22 19:30:16 -0400

      Commit message:


	  
		
 add refresh btn to ma plot to reduce reactivity
 

    

  
    

      Package: carnation

      Commit: 6cdb2c04f6e2a970e7ea2cb6eaf94bfdf06c1f5c

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-22 19:29:41 -0400

      Commit message:


	  
		
 add aspect ratio ctrl to ma plot
 

    

  
    

      Package: carnation

      Commit: ca5fe77582b249aaafab30c20b15ae4e41da36b8

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-22 19:29:09 -0400

      Commit message:


	  
		
 add plot settings input group
 

    

  
    

      Package: carnation

      Commit: 1d1938c9ce4d4166ce11847e414ebe170c63582a

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-22 19:27:35 -0400

      Commit message:


	  
		
 add alpha controls to ma plot module
 

    

  
    

      Package: carnation

      Commit: 139ab0ad5e0c8f485f9f196599f97cc2020d050d

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-22 19:25:54 -0400

      Commit message:


	  
		
 add alpha args to plotma funcs
 

    

  
    

      Package: carnation

      Commit: 436458cfe900991a51f8cdd77faa97b80c4c8dcb

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-21 16:41:19 -0400

      Commit message:


	  
		
 Merge branch 'v1.2.0rc' into geneplt_fixes
 

    

  
    

      Package: carnation

      Commit: 9846fde276794f962f9f31e8d77017c225228677

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-21 16:39:12 -0400

      Commit message:


	  
		
 reset gene scratchpad when loading new data
 

    

  
    

      Package: carnation

      Commit: bc42ee102c7bb4721f1a94313b2d674901ccc598

      Author:  Apratim Mitra <16709900+mitraak@users.noreply.github.com> 

      Date: 2026-09-21 16:11:02 -0400

      Commit message:


	  
		
 Merge pull request #40 from NICHD-BSPC/volcano-addition

- This PR adds a new volcano plot module. Modeled after the MA plot module, this provides both static and interactive versions and allows the plot to be colored by either significance or `baseMean` (average expression). 

    

  
    

      Package: carnation

      Commit: 065626a63f11dcdf7e59c91999dfef93bb0f5e5c

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-21 15:47:47 -0400

      Commit message:


	  
		
 rm R Depends version
 

    

  
    

      Package: carnation

      Commit: 89a6ffdab9628be79b313a898741d45929f3100e

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-21 15:47:28 -0400

      Commit message:


	  
		
 tweak author order
 

    

  
    

      Package: carnation

      Commit: 14f5eb45078f107a667f72409a48d64e4d24d3cd

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-21 15:47:01 -0400

      Commit message:


	  
		
 updt volcano plt ctrls help
 

    

  
    

      Package: carnation

      Commit: 69f33bb0487d3bbbc7227fe16a6e4c42579309be

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-21 15:45:32 -0400

      Commit message:


	  
		
 use refresh btn to reduce some reactivity
 

    

  
    

      Package: carnation

      Commit: f2a07c3f6815c5b517a285cd97f03c05e76a4ec4

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-21 15:36:42 -0400

      Commit message:


	  
		
 separate colorscale frm fdr/fc thres, save to reactiveVal
 

    

  
    

      Package: carnation

      Commit: 4bef3a540e7ab02ea8236dd62805a90547510c2c

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-21 15:36:09 -0400

      Commit message:


	  
		
 mv axes reset to func
 

    

  
    

      Package: carnation

      Commit: dd92ab9d3ab8dde435627e3423c8a89b91f4e712

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-21 15:33:42 -0400

      Commit message:


	  
		
 add aspect ratio control
 

    

  
    

      Package: carnation

      Commit: a3bd19fc62e86673f83594d7e4db875485a0c5d2

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-21 15:32:19 -0400

      Commit message:


	  
		
 add visual grouping fr plot settings
 

    

  
    

      Package: carnation

      Commit: 97b6882e21b63ccc21ded28a648fd7ad688029b8

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-21 15:31:35 -0400

      Commit message:


	  
		
 convert axis padding to proportions
 

    

  
    

      Package: carnation

      Commit: 13998566b3da5d2ab66f271695cbfd9efc626c0c

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-21 15:31:20 -0400

      Commit message:


	  
		
 add legend title to match MA plot
 

    

  
    

      Package: carnation

      Commit: 04bd20ca337beaecb3a299000a66f488c5e72811

      Author:  Dale McCauley <dale.mccauley@nih.gov> 

      Date: 2026-09-14 17:00:18 -0400

      Commit message:


	  
		
 Attached generated docs from previous commit
 

    

  
    

      Package: carnation

      Commit: 9113146ca4fcee27b336e4fa33166244fb519fe6

      Author:  Dale McCauley <dale.mccauley@nih.gov> 

      Date: 2026-09-14 16:42:13 -0400

      Commit message:


	  
		
 Fixed global variable warning, added name to authors list
 

    

  
    

      Package: carnation

      Commit: a5beca7ab96c39f09e63e0ad57beaf3a8212dcc4

      Author:  Dale McCauley <dale.mccauley@nih.gov> 

      Date: 2026-09-14 14:52:51 -0400

      Commit message:


	  
		
 Simplified axis scaling, improved organization, and added module level documentation and examples to volcano-plot.md
 

    

  
    

      Package: carnation

      Commit: 901f5e13b28c62d7e0d150719430a6351e066ff0

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-09-02 17:29:07 -0400

      Commit message:


	  
		
 mv ui elements fr volcano
 

    

  
    

      Package: carnation

      Commit: f1797c81a72ef043f254e895636c2923eea7b7c7

      Author:  Dale McCauley <dale.mccauley@nih.gov> 

      Date: 2026-08-31 15:48:53 -0400

      Commit message:


	  
		
 Improved scaling system to use reactiveVals and have on contrast change rescaling of ymax, improved alpha slider.
 

    

  
    

      Package: carnation

      Commit: c9bf1fc6a59521b2829f47aa0eccfdf5dae66315

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-08-29 00:03:10 -0400

      Commit message:


	  
		
 updt gene plt test-funcs
 

    

  
    

      Package: carnation

      Commit: 8ca2da9047a0efa40b8e6c193143b45bfba468be

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-08-29 00:02:57 -0400

      Commit message:


	  
		
 updt count plt docs
 

    

  
    

      Package: carnation

      Commit: 2d6199e04f50edf3f770ea073e441ca17a564d74

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-08-29 00:02:44 -0400

      Commit message:


	  
		
 add default ncol fr gene plt
 

    

  
    

      Package: carnation

      Commit: fe66fddda96f0ddc1a41999915ec818095e4f99d

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-08-29 00:02:28 -0400

      Commit message:


	  
		
 add column ctrl fr gene plt
 

    

  
    

      Package: carnation

      Commit: 4241dce0b7763bb8b6ff0c939fc65bf5063e53d2

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-08-29 00:00:43 -0400

      Commit message:


	  
		
 explicitly set group var
 

    

  
    

      Package: carnation

      Commit: ff59d806ae2839ac469f9cf6d3628a1a7ee46303

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-08-29 00:00:14 -0400

      Commit message:


	  
		
 switch count plt arg to ncol from nrow
 

    

  
    

      Package: carnation

      Commit: 6830e97f93ce9a07168e4cb801eb90d98cf68ddf

      Author:  Dale McCauley <dale.mccauley@nih.gov> 

      Date: 2026-08-25 09:57:20 -0400

      Commit message:


	  
		
 Add tests and bug fix
 

    

  
    

      Package: carnation

      Commit: 88f0a702ffe5a62329472f8ef8582b95358ec8bd

      Author:  Dale McCauley <dale.mccauley@nih.gov> 

      Date: 2026-08-24 10:04:06 -0400

      Commit message:


	  
		
 Removed outdated comment
 

    

  
    

      Package: carnation

      Commit: 463542d2ddd893932c19905d0059758ae738b0fe

      Author:  Apratim Mitra <16709900+mitraak@users.noreply.github.com> 

      Date: 2026-08-21 14:20:20 -0400

      Commit message:


	  
		
 Merge pull request #38 from NICHD-BSPC/devel

merge devel into v1.2.0rc 

    

  
    

      Package: carnation

      Commit: 790591a771c14d9b56ae7302977e826e285206d1

      Author:  Dale McCauley <dale.mccauley@nih.gov> 

      Date: 2026-08-21 13:20:58 -0400

      Commit message:


	  
		
 Adding help files for volcanoplot to git
 

    

  
    

      Package: carnation

      Commit: fa460c32d896a0354d5a93693e5b45ec4399f26c

      Author:  Dale McCauley <dale.mccauley@nih.gov> 

      Date: 2026-08-21 12:35:43 -0400

      Commit message:


	  
		
 Wired up an alpha slider for the volcano plots
 

    

  
    

      Package: carnation

      Commit: 07f4a2a84f1a2a7a0b29ceca47cc1e0fcf7b432f

      Author:  Dale McCauley <dale.mccauley@nih.gov> 

      Date: 2026-08-21 12:08:45 -0400

      Commit message:


	  
		
 Fixed a bug in the new trace scheme where scatter wasn't being detected
 

    

  
    

      Package: carnation

      Commit: 9dce4452d61f41d41ece247abb4969b63ec26192

      Author:  Dale McCauley <dale.mccauley@nih.gov> 

      Date: 2026-08-21 11:41:30 -0400

      Commit message:


	  
		
 Made the significance traces work
 

    

  
    

      Package: carnation

      Commit: 90293b5f8a28c053d0b61cbec14b5ad61d4a3c46

      Author:  Dale McCauley <dale.mccauley@nih.gov> 

      Date: 2026-08-21 11:23:35 -0400

      Commit message:


	  
		
 Checkpoint before changing significance traces
 

    

  
    

      Package: GSVA

      Commit: 428c367041833e51d72911ddbd9fdf98619b9562

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

      Date: 2026-10-14 21:11:33 +0200

      Commit message:


	  
		
 Minor fixes to clean some BiocCheck warnings and one error
 

    

  
    

      Package: MSstatsBioNet

      Commit: bdd0d8042c0eaee5b385f49556e3a04369fed1ca

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2026-10-14 14:56:42 -0400

      Commit message:


	  
		
 fix(ptm): Fix PTM filtering and add function to add global profiling results to network (#134) 

    

  
    

      Package: crisprDesign

      Commit: f54cde5da8ddf05e40ec36b96032a847b80d347c

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2026-10-14 11:11:11 -0700

      Commit message:


	  
		
 Added 2026 cfd score
 

    

  
    

      Package: crisprScore

      Commit: 66868bcf3d4ec95f7e9013d8e4918d02242ff708

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2026-10-14 10:41:48 -0700

      Commit message:


	  
		
 Added cfd 2026
 

    

  
    

      Package: crisprScore

      Commit: f4de01c84e2229265e48f673173fa103cfc6db7c

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2026-10-14 10:41:16 -0700

      Commit message:


	  
		
 Modified CasRx
 

    

  
    

      Package: crisprScore

      Commit: 7d9940bd7517e21de19e0fb652459cbb7bf0fc10

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2026-10-14 10:36:13 -0700

      Commit message:


	  
		
 2026 cfd score
 

    

  
    

      Package: Rarr

      Commit: c64dae1ec9d5562f071cd6900d27c9e46447bb79

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-14 14:35:09 +0200

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: Rarr

      Commit: 86b83a0068624b2e255feddb8788313115504f4c

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-14 15:07:05 +0200

      Commit message:


	  
		
 Add backport version for has_zstd
 

    

  
    

      Package: Rarr

      Commit: 0113c9b95835e7f51cc280968532b015f36f6c89

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-14 14:34:48 +0200

      Commit message:


	  
		
 Add a class to the zstd warning
 

    

  
  


</div>

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