Bump version to 1.35.2

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

 Fix Camargo evenness computed on wrong entries (#231)

camargo() never removed zeroes (x[x > 0] was not assigned) but looped
over the first N positions, where N is the number of nonzero taxa. The
result therefore depended on the order of taxa and was wrong for any
sample with a zero before its last observed taxon. The index is now
computed over the observed taxa, as defined by Camargo (1992), using a
sorted-abundance form of the pairwise sum. Empty samples return NA.

Fixes #231

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

 commit new vignette names
 

 Change R version to 4.3.3 and update dependencies

Updated R version in workflow matrix and modified dependency installation. 

 Bump version to 1.11.9 in DESCRIPTION file

Bump after man and citation 

 Merge pull request #60 from snaketron/fix-attach-clonotypes-validation

Fix attach clonotypes validation 

 Add wrapped validation helper to attach_clonotypes and enforce consistent input checks 

 Refactor author field in CITATION file

Updated author field to include multiple authors as person objects. 

 Merge pull request #220 from gdrplatform/GDR-3720

fix: store the package versions instead of the whole sessionInfo in .internal 

 docs: start the changelog entry with a valid verb
 

 fix: store the package versions instead of the whole sessionInfo in .internal
 

 Fix percentvar scale, row/col error msg, and update actions
 

 Rewrap a brs_genes paragraph that ran past 80 columns

BiocCheck flagged two lines of the Alias resolution section; an earlier
edit had joined them. Documentation only: no figure or code changes, so
the session records from f897ffb still stand.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01JtWEbZHJ2RaRo57NBGeKH9
 

 Resolve FLJ23867 to QSOX1 and use all 71 signature genes

FLJ23867 is a cDNA clone name, not a symbol or alias, so org.Hs.eg.db never
returned it and the package dropped it, scoring on 70 genes. Its NCBI Gene
record (200058, 1q25.2) was withdrawn in 2018 and merged into 5768, QSOX1,
whose record lists FLJ23867 among its clone names. brs_genes now maps it to
QSOX1 and the classifier uses all 71 published genes.

In 2014 FLJ23867 was still its own Gene ID, so QSOX1 is the closest current
gene rather than necessarily the same feature; the documentation says so.
QSOX1 behaves like the rest of block 2 (log2 BRAF-RAS 1.41, Spearman 0.705
with the axis of the other genes, block-2 median 0.697), loads with its
block's sign on GSE33630, and is selected in 42.5% of re-derivation
iterations. validate_tcga.R now prints the first two; check_symbols.R
records the merge and checks that 5768 is still QSOX1.

Figures recomputed with the data-raw scripts and updated in README, the
vignette, the man pages, data-raw notes and NEWS. Against the published
classes one tumor changes side, TCGA-ET-A4KN, the closest to zero of 505;
removing any single gene moves concordance by at most one sample. Spearman
0.941 -> 0.940, held-out concordance 96.4% -> 95.5%, CV 99.7% unchanged.
preds_tcga.csv is rewritten. The sessioninfo records are refreshed in the
next commit, run from this one.

Also: na.omit() calls left over from the NA entry removed from examples, the
vignette and tests; Assisted-by headers updated; bump to 0.99.9.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01JtWEbZHJ2RaRo57NBGeKH9
 

 update installation instructions from github
 

 Bump version to 1.23.6 in DESCRIPTION file 

 fix SpectronauttoMSstatsFormat docs (#146) 

 Added data.frame validation for converter inputs (#134)



Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com> 

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

 Update issue templates

Adding bug report and feature request templates 

 Removing Description header, a bit redundant
 

 Updating covr file based on `usethis` pakage
 

 bump version and date
 

 Merge pull request #218 from gdrplatform/GDR-3705

test: compare the combination datasets with their references 

 fix: match the rows of the reference tests on their identifiers
 

 test: compare the combination datasets with their references
 

 chore: regenerate the combination reference datasets
 

 Merge remote-tracking branch 'origin/main' into GDR-3705

# Conflicts:
#	NEWS.md
 

 chore: bump version to 0.99.2
 

 fix: keep all rows when reading BED, GFF and VCF files

Files were read with DuckDB guessing each column's type and silently
dropping rows that did not fit. With chromosome names like 1, 2, ..., X,
MT, the chromosome column was guessed to be a number and every X, Y and
MT row was lost. Columns are now read as text and only positions and
scores are converted, so a malformed value becomes NA instead of
removing its row. UCSC track and browser lines are skipped, and file
paths are quoted safely.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

 Merge pull request #239 from seandavi/docs/news-2.82.0

docs: 2.82.0 release summary in NEWS 

 Merge pull request #236 from seandavi/fix/issue-235

fix: read RNA-seq annotation from FTP mirror (#235) 

 fix: read RNA-seq annotation from FTP mirror (#235, #230)

NCBI reCAPTCHA-gates the shared annotation file on the web download
endpoint; read the copy on ftp.ncbi.nlm.nih.gov/geo/rnaseq_counts/annot/.
Bump to 2.81.35.

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

 Merge pull request #232 from seandavi/fix/ncbi-flaky-build

fix: keep R CMD check off live NCBI and fail clearly on reCAPTCHA pages (#230) 

 fix: keep R CMD check off live NCBI E-utilities calls

The Bioc 3.24 taishan builder failed CHECK twice from one NCBI hiccup:
EInfo returned an HTML error page instead of XML, so both the
searchFieldsGEO() example and the ungated test_search.R test died with
"Opening and ending tag mismatch: br line 196 and p".

- Wrap the searchFieldsGEO() and hasRNASeqQuantifications() examples in
  \donttest{} (hasRNASeqQuantifications scrapes the GEO download page on
  every check too).
- Gate the live searchFieldsGEO() test with skip_if_no_integration(),
  matching the rest of the network suite (#169).
- Add an offline test that mocks rentrez::entrez_db_searchable() and pins
  the reshaping into one row per field.

Version bump to 2.81.34.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

 Merge pull request #228 from seandavi/fix/retry-transport-failures

fix: retry NCBI connection failures, not just retryable statuses 

 fix: retry NCBI connection failures, not just retryable statuses

The shared httr2 request builder set `is_transient` for HTTP status codes
but left `retry_on_failure` at its default of FALSE. A refused TCP
connection produces no response at all, so `is_transient` is never
consulted and the request fails on the first try. NCBI sheds connections
under load, which made the scheduled integration workflow fail weekly with

    Couldn't connect to server [www.ncbi.nlm.nih.gov]:
    Failed to connect to ... port 443 after 68 ms

Set `retry_on_failure = TRUE` in `.geo_request()`, and route the three
hand-rolled request builders through it instead of duplicating the policy:
`getGSEDownloadPageURLs()`, `.fetch_gds_esummary_json()`, and the
supplementary-file fetch in `getGEOSuppFiles()` (which had no retry or
timeout at all).

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

 feat: batched JSON esummary backend for searchGEO() (#223)
 

 feat: resolve GEO accessions to SRA accessions via Entrez (#219)
 

 feat: checksum verification helper for downloaded files (#222)
 

 docs: document how issues, ADRs, NEWS, and PRs link

Expand the CONTRIBUTING ADR section with the cross-linking conventions
(Fixes #NNN, Implements ADR-XXXX, ADR Context links the issue, NEWS cites
the ADR + PR) so external contributors and maintainers follow one chain.

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

 deprecate: GDS2MA() and move limma to Suggests

GDS2MA()'s limma MAList return type is superseded by GDS2eSet()'s
ExpressionSet (coercible to SummarizedExperiment). Deprecate GDS2MA() with
.Deprecated(), guard the limma::MAList construction behind requireNamespace,
and move limma from Imports to Suggests so it is no longer installed with
GEOquery. GDS2eSet() is unchanged. Tests assert the deprecation warning.

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

 refactor: drop rvest and stringr dependencies

Replace rvest with xml2 (already a dependency) for GEO download-page link
parsing, and the few stringr helpers with base R equivalents (grep, sub,
strsplit, startsWith). Extract .extractGeoDownloadLinks() so the previously
network-only parsing is covered by an offline test. No user-facing change.

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

 fix: repair corrupted printHead() so GEODataTable show() previews rows

The internal printHead() helper had a garbled definition (the same line
repeated 18 times, each the body of the previous function(x)), which made
it return a function instead of printing. The show() method for GSM/GPL/GDS
data tables therefore printed a function object instead of the leading rows.
Collapse it to the single intended definition and add an offline regression
test.

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

 docs: adopt jujutsu (jj) for local version control

Colocate jj with git and document the workflow. GitHub/Bioconductor still
see plain git branches; jj only replaces local commit mechanics.

- CLAUDE.md: Version control (jujutsu, colocated) section
- CONTRIBUTING.md: jj/git equivalents in the workflow + optional
  'jj for git users' section, incl. the operation-log undo net
- .claude/skills/jj-flow: on-demand git->jj cheatsheet

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

 require(Biostrings
 

 chore: Switch entityName to entity_name for displayLabelType cytoscapeNetwork (#234) 

 fix(qc): Pass the Plotly canvas width to dataProcessPlots (#233) 

 Bump version from 1.5.4 to 1.5.5 

 Warn on unlabelled weight matrices, drop CWM total IC, fix complexity alphabet

- create_motif() read a matrix with negative values as a PWM and, with
  the default type, silently turned it into a PPM, so contribution
  weights became nearly uniform columns. It now warns and points to
  type = "PWM" or "CWM".
- CWMs reported a total IC computed from their weights, which has no
  meaning. Their icscore is now NA, left out when printing, and computed
  when a CWM is converted to another type; filter_motifs() drops motifs
  without one when filtering on it.
- calc_complexity() scored each string against its own letters, so
  ATATATATAT counted as a two-letter sequence and homopolymers gave NaN.
  It now uses ACGT or ACGU when the strings are DNA or RNA, and otherwise
  the letters of all the strings together.
 

 Fix enrichment bugs found while porting

- motif_coocc() computed odds ratios with integer cells, so the products
  overflowed past 2^31 and gave NA with a warning.
- match_bkg(genome = ...) drew window widths with sample(), which takes
  a single target width n as 1:n.
- motif_peaks() numbered motifs by sort(), which follows the locale's
  collation, so motif.i could differ between machines; it now sorts by
  code point.
- motif_proximity() numbered motifs by their rank among sorted names; it
  now keeps the index from scan_sequences(), or the order in which the
  motifs first appear.
 

 Fix motif comparison bugs found while porting

- compare_motifs_lite() kept whichever tied alignment summed larger in
  the last bit, which depends on the compiler, so P-values and strands
  could differ between machines and score matrices could be asymmetric.
  Ties within 1e-10 now go to the longer overlap and then to the first
  alignment found.
- Its consensus strings used T for RNA and their own 75% rule; they now
  follow the motif consensus rule for the motif's alphabet.
- Scores beyond the reach of the coarse parametric null got P-values of
  exactly 0; they now get the probability of the null's highest score.
- WPCC weights summed to 2, so weighted means were doubled and WPCC with
  a uniform background was not PCC.
- KL and ALLR computed 0 * log(0) as NaN for letters with probability 0
  in both columns.
 

 Fix logo and tree plotting bugs found while porting

- Negative letters were only drawn when one reached 0.03, whatever the
  logo's scale, so CWMs of negative TF-MoDISco patterns came out empty;
  the scaled min.height is now used.
- flip_neg_letters() restacked negative letters without the y.spacer
  gaps used above zero, so the stack also fell short of its values.
- The top break of ICM and PWM axes could round up past the axis and be
  dropped; it is now rounded down.
- CWM axes were padded below by a fixed 0.1 and had unrounded breaks;
  they now get round breaks and a twentieth of the range as padding.
- motif_tree_lite() tip logos failed for motifs sharing a name, as the
  logos kept the original names while the tips were made unique; logos
  are now matched to tips by position.
 

 Fix motif object bugs found while porting

- motif_rc() referred to an undefined variable for motifs with
  higher-order matrices and reversed their k-mer rows without
  complementing them; it also dropped gaps.
- trim_motifs() and trim_cwm() kept stale gap positions, and
  trim_motifs() wrote nsites = 100 into motifs without one.
- create_motif() collapsed one-column matrices with row names, ignored
  letters outside a custom alphabet and took any 20-row matrix as AA.
- Validation skipped single gaps and gap sizes, and accepted NaN and
  negative pseudocounts.
- ppm_to_pcm() could give uneven or negative counts; it now uses the
  largest remainders when rounding overshoots by more than one.
- round_motif(), normalize() and convert_type() with a new pseudocount
  left the total IC and consensus stale.
- Relative entropy was NaN for zero probabilities, motif_range() gave NA
  with -Inf scores, and log_string_pval() failed below 1e-308 where long
  double is no wider than double.
 

 fix: read long tables as text when saving them as tsv

read_excel() guesses column types from the first 1000 rows and fread() drops leading zeros, so a column that turns from numbers to text after the first rows lost those values in the copy. Reading everything as text keeps the copy as written and leaves the parsing to the loader.
 

 chore: bump version to 1.11.12 and update NEWS
 

 closes #73
 

 fix: validate bench input next to a .qs2 and loosen two readout heuristics

A .qs2 next to the bench files switched the whole run to MAE validation, so data4 and data5 as shipped (with ref_l.qs2) were never loaded; MAE input is now only chosen when there is no bench input, and the .qs2 is listed as not used. Plates without a cell line or Duration in the manifest are left out of the outlier groups instead of being pooled into one NA group. The Duration check flags control wells only when they read more than 20% lower at a longer Duration, since a small drop is normal at confluence.
 

 chore: bump version to 1.11.11 and update NEWS
 

 feat: note plates read without a barcode in the import record

The EnVision reader takes the barcode from the plate header, then from the Background section, and skips the plate when both are empty. A placeholder like "N/A" is taken as the barcode. None of this was visible after the import. Each such plate is now logged with its file, plate number and the barcode it was imported under, and load_data() keeps them in the import record as plates_without_barcode.
 

 update docs
 

 NEWS: leave release notes to the maintainer

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

 interpret: send every input gene and every fold change of the sent terms' genes

The prompt no longer truncates gene-level input: every input gene is listed (most
up-regulated first when gene_fold_change is supplied; previously the first 20), every
fold change of the sent terms' genes is given (previously the 20 largest), the
leading-edge genes of a gseaResult (core_enrichment) now receive their fold changes,
and an agent cluster without enriched terms lists every input gene (previously 50).
Prompt headers drop "Top". R CMD check OK on the execution node (2026-10-12).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

 interpret: send every significant term, reduced, instead of the top 20

interpret(), interpret_agent() and interpret_hierarchical() passed the 20 (agent: 50) most
significant terms to the model. On a long result those are near-synonyms of a few themes,
so most of the significant biology never reached the prompt.

reduce_redundancy() keeps one representative per group of near-duplicate significant terms:
Wang similarity for GO results (GOSemSim, DAG only, no OrgDb needed), Jaccard overlap of the
reported member genes for KEGG and every other gene-set collection. It handles enrichResult,
gseaResult and compareClusterResult (within each cluster; GO ALL within each ontology), and
on GO lists selects exactly the terms reduce_go_redundancy() selects.

The entry points now default to reduce = TRUE and n_pathways = NULL (every significant term
after reduction). n_pathways = 20, reduce = FALSE restores the earlier behaviour; reduce_go /
go_reduction_threshold are still accepted, with their old 0.7 default.

Also fixed while testing on real objects:
- gseaResult member genes (core_enrichment) were left out of the prompt, so GSEA terms
  reached the model with no genes at all
- the greedy selection never removed the kept term when threshold >= 1 and looped forever
  (also in reduce_go_redundancy(), which now shares the helper)
- all-NA padding rows were sent as terms and made a GO result look non-GO

Seven new tests; R CMD check Status: OK.

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

 interpret: read the object's symbols, and export the grounding check as evidence_status()

Two changes, both found by running the layer on a real annotation task (10k PBMCs, Seurat
clusters, SingleR as the external annotator) rather than on curated marker sets.

1. The marker list handed to the model came from the object's INPUT gene slot, which holds the
   identifiers the enrichment was run on -- ENTREZID in a standard enrichGO pipeline -- while the
   term table it was shown alongside holds symbols. The model was reading numbers where it
   expected gene names, and nothing in the output said so. `get_genes()` now maps those
   identifiers through the object's own `gene2Symbol` table, and `gene_fold_change` is renamed
   with the same table so it still matches; identifiers with no mapping pass through untouched,
   so objects built on symbols behave exactly as before. On the PBMC panel this moved
   `interpret(task = "cell_type")` from 7 of 16 clusters to 12 of 16 against a marker panel
   declared in advance, and the `prior` arm from 10 to 13, while a bare-prompt arm that never
   touches that slot stayed at 14 of 16 -- the control that says the fix acted where it should.

2. `evidence_status()` exports the grounding check itself: given an interpretation and the
   enrichment object it came from, it returns every gene the record names as `observed` or
   `out_of_evidence` by set membership, with no model call. This is the deterministic half of
   what the optional Reviewer agent does in prose, and it exists because the prose half is not
   selective: measured across five models, the audited draft hedges grounded mentions as often
   as ungrounded ones on some of them (0% -> 71% grounded hedged on one). A set-membership test
   cannot hedge a gene that is in the evidence, because it never reads the sentence.
   An explicit stop list for upper-case words that are also symbols (SET, MAX, REST, ...) ships
   with the function rather than being applied after the fact.

man/evidence_status.Rd is written by hand to match the roxygen block; document() still has to be
re-run on the execution node before the upstream PR, together with the split described in
dev/FORK_STATUS.md.

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

 provenance: capture Anthropic cached prompt tokens

Anthropic-format responses report cached prompt tokens outside prompt_tokens, in
cache_read_input_tokens / cache_creation_input_tokens. .prov_record() did not read them, so a
largely cached prompt logged an input count in the single digits: this project's own stamps
show cleaner calls at prompt_tokens = 2 against a synthesizer at 505 in the same run. Any cost
figure derived from those stamps understates the input side by an unknown amount.

Adds cache_read_tokens, cache_creation_tokens and prompt_tokens_effective. Fields are read
from the normalised usage list or the raw response body, and stay NA where the provider emits
nothing -- 0 would assert that no caching occurred, which is a different claim from not knowing
whether it did. prompt_tokens_effective is NA-safe: if no component is reported it stays NA
rather than collapsing to a confident 0. Non-Anthropic providers are unaffected.

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

 interpret: stop the failure handler from destroying the failure

.call_generate_object() names the model in three messages by pasting the `model` argument
into a string. `model` may be an aisdk LanguageModelV1, which is an ENVIRONMENT, so
paste0("Model: ", model) raises

    cannot coerce type 'environment' to vector of type 'character'

Two of the three sites are in the FAILURE branches. So whenever the underlying call fails for
any reason -- a bad endpoint, a timeout, a schema rejection -- the handler throws while
formatting its own diagnostic, the caller is handed a type error that reads like a fault in
their own input object, and the real cause is unrecoverable. interpret_agent() does not use
this function, which is why only interpret() was affected.

One root cause behind three separately-investigated failures in this project: a public-case
interpret() failure, all nine arms of a GO-reduction ablation, and every call of a
prior-correction run. Runtimes of 35-40s fit: the call was made and did fail before the
handler fired.

Fix: resolve a printable id once via .model_identity() (itself fully guarded) and use it in
all three messages; an unrecognisable object degrades to "" rather than
raising. Verified without a model call: the old expression raises the error byte-identical to
the one recorded in the run artifacts, the new one returns the model id.

All three sites are present verbatim in the upstream base of this branch.

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

      Package: clusterProfiler

      Commit: 05241c0897520130c0d07d96a2e9abd344cdddf6

      Author:  treywea <treywea@gmail.com> 

      Date: 2026-09-03 11:13:24 +0800

      Commit message:


	  
		
 interpret: report an unparsed model response instead of returning NULL

generate_object() raises no condition when the transport succeeds and the response body fails
to validate against the schema -- it returns normally with object = NULL and the raw text
intact. All four agents in interpret_agent() returned a bare gen$object, so the NULL
propagated: the downstream is.list()/!is.null() guards skipped silently, and for the
synthesizer the NULL reached .postprocess_network(), where 'class(res) <-' on NULL aborts the
whole run with 'attempt to set an attribute on NULL'. The caller reads that as a fault in
their own input.

.stop_if_unparsed() raises a diagnostic carrying finish_reason and raw-text length at all four
agent sites, so the failure routes to each existing handler and is recorded rather than fatal.
.postprocess_network() gains a NULL guard as defence in depth.

Observed 2026-08-27 on both review = TRUE arms of a public-case ablation. The crashing code is
present in the upstream base of this branch; it is not introduced by the Reviewer feature.

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

      Package: clusterProfiler

      Commit: 169bc1b8714fc8a862ba565ae374c19672b27b8f

      Author:  treywea <treywea@gmail.com> 

      Date: 2026-08-26 23:03:35 +0800

      Commit message:


	  
		
 interpret: add optional Reviewer agent, execution provenance, and GO redundancy reduction

Three additions to the interpret module, all opt-in or additive:

1. Agent 4 "Reviewer" for interpret_agent(review = TRUE, default TRUE).
   Audits the synthesized draft against the evidence actually supplied for
   grounding, experimental-label/contrast fidelity, and overclaiming. Returns
   verdict, grounding_score, issues, evidence_sufficiency, supported_resolution,
   abstain_recommended, adjusted_confidence and reader warnings; when the verdict
   is "revise" the corrected overview replaces `overview` and the original is
   kept as `overview_original`. Set review = FALSE for the previous three-agent
   behaviour.

2. Execution provenance, exposed via provenance(x) and a print method.
   Records the model requested and, where the provider echoes one, the model
   that actually served the response (model_served / model_matches_request),
   the requested decoding parameters, SHA-256 digests of system prompt, user
   prompt, raw response and input evidence, token usage, finish_reason,
   per-call status and package versions. Parameters the response does not echo
   are recorded as NA rather than assumed honoured.

   This also makes a transport-layer failure distinguishable from an empty
   answer: interpret() does not raise on an API error, it returns the error
   string inside `overview`, so callers should check provenance(x)$ok before
   treating an interpretation as data.

3. reduce_go_redundancy() plus interpret(reduce_go=, go_reduction_threshold=).
   Optional semantic-similarity collapsing of redundant GO terms before
   interpretation, cutting input noise and token count. Off by default.
   Built on GOSemSim, already an Imports dependency; `method` defaults to Wang,
   which reads the GO DAG directly and needs no corpus statistics, while the
   information-content measures remain available at a cost. The `rrvgo_*`
   result attributes are kept for backwards compatibility with existing
   ablation outputs and predate the switch away from rrvgo.

digest is reached through requireNamespace() and is declared in Suggests only.

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

      Package: gDRutils

      Commit: 82d08c9e786d13ea4faf5e06554ff6ad90ad3bb5

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

      Date: 2026-10-23 12:36:01 +0200

      Commit message:


	  
		
 Merge pull request #208 from gdrplatform/GDR-3735

fix: keep partial results when a whole row or column has no fit 
    
  
    

      Package: gDRutils

      Commit: 7ff26745d2d0de3bc6d65163379d1952f7d844f6

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

      Date: 2026-10-21 08:01:52 +0200

      Commit message:


	  
		
 chore: bump version to 1.11.20
 
    
  
    

      Package: gDRutils

      Commit: 8f6f6ac7ffc986c5f7a1b2f3d3e4702158a92941

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

      Date: 2026-10-21 08:01:52 +0200

      Commit message:


	  
		
 docs: state that a registered fit profile lasts only for the session
 
    
  
    

      Package: gDRutils

      Commit: aa323d50f7205b9530f7a7a48c2fadcb9ec50c6c

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

      Date: 2026-10-21 08:01:52 +0200

      Commit message:


	  
		
 feat: add convert_dt_to_se to build an SE from a long table
 
    
  
    

      Package: gDRutils

      Commit: 5ade1aa0e84cd6613f80d251267e952643a3e4d2

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

      Date: 2026-10-21 07:49:56 +0200

      Commit message:


	  
		
 fix: keep partial results when a whole row or column has no fit
 
    
  
    

      Package: BANDITS

      Commit: 27f01ddc796362839b9d6a9eff5aac08c3ded10a

      Author:  Simone Tiberi <simone.tiberi@unibo.it> 

      Date: 2026-10-23 11:22:25 +0200

      Commit message:


	  
		
 Update
 
    
  
    

      Package: BANDITS

      Commit: 7ade58a3b6e67f641bf6f094118e2f949c96b943

      Author:  Simone Tiberi <simone.tiberi@unibo.it> 

      Date: 2026-10-23 11:19:44 +0200

      Commit message:


	  
		
 DRIMSeq dependency removed
 
    
  
    

      Package: CAGEr

      Commit: 2f5ca0db9d301d100543469a0b8536794c703252

      Author:  Charles Plessy <charles.plessy@oist.jp> 

      Date: 2026-10-23 17:58:43 +0900

      Commit message:


	  
		
 Release 2.19.1
 
    
  
    

      Package: CAGEr

      Commit: 776a2bebaecdc07005f596ed9273f721226150e8

      Author:  Charles Plessy <charles.plessy@oist.jp> 

      Date: 2026-10-23 17:57:19 +0900

      Commit message:


	  
		
 Roxygen refresh and fixes
 
    
  
    

      Package: CAGEr

      Commit: e8dc27577b035433133343a5f5fb2bde56bfdce0

      Author:  Charles Plessy <charles.plessy@oist.jp> 

      Date: 2026-10-23 15:36:21 +0900

      Commit message:


	  
		
 Add the vectorised approach to the BED12 blocks benchmark.

Benchmark f.vectorised(), the approach now used by exportToTrack(),
against the previous best one, f.mat.direct(), looped on all the
clusters of one sample: the results are identical, and the vectorised
approach is about 700x faster (2 ms instead of 1.2 s for 532 clusters).

The markdown output is re-rendered with the current package and tools,
so the date, the code fences, the 2021 timings and the printed example
clusters change as well.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: CAGEr

      Commit: e57ff2681c88971b394d337705be1a6a4b31ffdd

      Author:  Charles Plessy <charles.plessy@oist.jp> 

      Date: 2026-10-23 15:36:21 +0900

      Commit message:


	  
		
 Speed up exportToTrack() when qLow and qUp are given.

Build the BED12 blocks of all clusters at once: compute the candidate
starts and ends of the up to three blocks of each cluster in matrices
with one column per cluster, create all the blocks with a single call to
IRanges(), and split them by cluster with relist() and
PartitioningByEnd().  This replaces a loop that built and concatenated
IRanges objects cluster by cluster, which took ~2.5 ms per cluster.

On exampleCAGEexp, exporting tag clusters with quantiles is 12-19x
faster and consensus clusters 10x faster, and the results, including
the BED12 files written by rtracklayer, are identical.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: CAGEr

      Commit: 6e19960a52b5ec38c0ba22326bbb323f1f6f98b4

      Author:  Charles Plessy <charles.plessy@oist.jp> 

      Date: 2026-10-23 15:13:42 +0900

      Commit message:


	  
		
 Speed up paraclu() and the summary of clusters.

In .paraclu(), build each cluster as a numeric vector and combine them
with base::rbind() instead of one-row data frames combined with the S4
rbind() generic from BiocGenerics, whose dispatch was most of the cost
of the recursion.

In .ctss_summary_for_clusters(), find the dominant CTSS of all clusters
at once with vectorised list operations on decoded scores, instead of an
sapply() loop on the elements of an RleList.  Cluster scores are still
summed on the RleList, so that they stay bit-identical.  Stop with an
explicit error when a cluster does not overlap any CTSS, which used to
fail with "non-numeric argument to binary operator".

On exampleCAGEexp, paraclu() is 10-13x faster, distclu() ~3.7x and
aggregateTagClusters() ~2x, and their outputs are identical.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: CAGEr

      Commit: b7a950559417b913b015c965c21ace4d3d9c5ae4

      Author:  Charles Plessy <charles.plessy@oist.jp> 

      Date: 2026-10-23 15:07:41 +0900

      Commit message:


	  
		
 Simplify
 
    
  
    

      Package: CAGEr

      Commit: 86c21f89320567ac4882bcc41dfcaf28cb8a9ac2

      Author:  Charles Plessy <charles.plessy@oist.jp> 

      Date: 2026-10-13 19:06:19 +0900

      Commit message:


	  
		
 Bump the version to 2.19.1.

The changes in consensus-cluster expression are backwards-incompatible,
so mark them with a patch-version bump, and update the Date field as was
done for the previous patch releases.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: CAGEr

      Commit: 5f9a14eb5e3b5737e82cf0df2ab30ee38de26ff5

      Author:  Charles Plessy <charles.plessy@oist.jp> 

      Date: 2026-10-13 18:42:40 +0900

      Commit message:


	  
		
 Announce the changes in consensus-cluster expression in NEWS.

Describe in the development-version section that tpmThreshold of
aggregateTagClusters() now only selects the tag clusters that define
consensus-cluster boundaries, that consensus-cluster expression is the
sum of the CTSSs passing filteredCTSSidx() when aggregateTagClusters()
is run, and that the hidden filters removed from aggregateTagClusters()
and CustomConsensusClusters() change expression values, outOfClusters,
and the number of consensus clusters.  Also announce the deprecation of
excludeSignalBelowThreshold.

Explain how that argument behaved: up to CAGEr 1.20 (Bioconductor 3.6),
TRUE summed in each sample the signal of the tag clusters passing
tpmThreshold, as announced in the 1.2.7 entry, whereas from CAGEr 1.22.0
(Bioconductor 3.7) it discarded the individual CTSSs below tpmThreshold
in every sample.  The switch to per-CTSS filtering came with commit
5447ae1 (2017-09-14), whose message does not mention it, and the 1.22.0
NEWS entry did not announce it.

This entry is kept in its own commit because the development-version
section of NEWS.md does not exist on the release branch: a backport of
the code changes needs its own NEWS entry.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: CAGEr

      Commit: 23d5089ee7df81a5a8d789f1e45bb834a9c1bcf7

      Author:  Charles Plessy <charles.plessy@oist.jp> 

      Date: 2026-10-13 18:15:58 +0900

      Commit message:


	  
		
 Describe consensus-cluster expression in the vignette.

Explain that the tpmThreshold of aggregateTagClusters() only serves to
define the consensus clusters, and that their expression in each sample
is the sum of the CTSSs that they contain among those not flagged by
filterLowExpCTSS().

Also correct the column in which consensusClustersGR() returns the
total signal when no sample is given: it is `score`, not `tpm`, which
only exists when a sample is selected.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: CAGEr

      Commit: e9bb6f840b0b3c27087d9218887f1c1caeb229b3

      Author:  Charles Plessy <charles.plessy@oist.jp> 

      Date: 2026-10-13 18:12:54 +0900

      Commit message:


	  
		
 Correct the documentation of flagLowExpCTSS() to match its code.

flagLowExpCTSS() keeps (TRUE) the CTSSs whose signal is strictly above
the threshold in at least nrPassThreshold samples, nrPassThreshold
being capped at the number of samples, and flags (FALSE) the others.
The documentation said instead that CTSSs with a signal below the
threshold are flagged, while a signal equal to the threshold is flagged
too, and that CTSSs are flagged when their signal is below the
threshold in at least nrPassThreshold samples, which describes a
different filter: with the default nrPassThreshold = 1, only the CTSSs
that are at or below the threshold in all samples are flagged.

The behaviour of the function does not change.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: CAGEr

      Commit: 8c909d01d614aa89b7561f7052d27d90c5ec47d8

      Author:  Charles Plessy <charles.plessy@oist.jp> 

      Date: 2026-10-13 18:10:17 +0900

      Commit message:


	  
		
 Remove hidden CTSS filters from consensus-cluster expression.

aggregateTagClusters() used tpmThreshold not only to select the tag
clusters that define the consensus clusters, but also twice more to
filter the CTSSs contributing to their expression: when
excludeSignalBelowThreshold = TRUE (the default), only CTSSs with a
normalised signal above tpmThreshold in at least one sample were
counted, and .CCtoSE() then dropped the CTSSs whose normalised signal
summed over all samples was not above tpmThreshold.  The second filter
made the results depend on the number of samples, and could not be
disabled without also disabling the selection of tag clusters.  These
filters did not change cluster boundaries, but lowered expression
values, removed clusters in which no CTSS survived, and inflated
outOfClusters.  The documentation described excludeSignalBelowThreshold
as acting on tag clusters, not CTSSs.

The expression of a consensus cluster is now the sum of the CTSSs that
it contains among those flagged as passing in filteredCTSSidx() at the
time aggregateTagClusters() is run, a flag normally set by
filterLowExpCTSS() before tag clustering.  The stored score, the
normalized assay, and the nr_ctss and dominant_ctss columns are thus
computed from the same set of CTSSs.

excludeSignalBelowThreshold is deprecated: it is kept in the signature,
its value is ignored, and a warning is emitted when it is supplied.
The examples no longer pass it.

CustomConsensusClusters() also called .CCtoSE(), with its default
threshold of 1, so it silently dropped CTSSs with a summed normalised
signal of 1 or less, on top of its explicit threshold and
nrPassThreshold filter.  Removing the filter from .CCtoSE(), together
with its now unused tpmThreshold parameter, fixes this as well.

The data in exampleCAGEexp are not affected.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: CAGEr

      Commit: 86aac0cdc0db9186d450b8d2626f6260c1205717

      Author:  Charles Plessy <charles.plessy@oist.jp> 

      Date: 2026-10-13 17:43:59 +0900

      Commit message:


	  
		
 Add tests for consensus-cluster expression in aggregateTagClusters().

Add a testthat (edition 3) suite built on a small synthetic CAGEexp
object (three samples, a dozen CTSSs, and a padding CTSS that sets
library sizes so that TPM values are simple multiples of the counts).
Expected values are derived by hand from the definitions of consensus
clusters and written as arithmetic in the comments.

The tests check that a broad cluster made only of low CTSSs is kept,
that cluster expression is the sum of the CTSSs passing
filteredCTSSidx(), that expression in a sample does not depend on the
number of samples in the object, that cluster boundaries follow the
tag clusters with score >= tpmThreshold, that outOfClusters is
consistent with that, that excludeSignalBelowThreshold is deprecated
and ignored, and that CustomConsensusClusters() keeps clusters made of
low CTSSs while its threshold and nrPassThreshold arguments still work.

The CTSS filtering thresholds used in the tests do not fall on a count
or TPM value of the synthetic data, so that the results do not depend
on whether flagLowExpCTSS() compares signal strictly with the
threshold, a point on which its documentation and code disagree.
testthat 3.1.5 is required for expect_no_warning().

Most of these tests fail until the hidden CTSS filters applied after
consensus-cluster construction (the excludeSignalBelowThreshold filter
and the sum-over-samples filter in .CCtoSE()) are removed.  The tests
for cluster boundaries and for the explicit filters of
CustomConsensusClusters() already pass.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: CAGEr

      Commit: cc000abd08f0a0e99c9642005f058334c483cd31

      Author:  Charles Plessy <charles.plessy@oist.jp> 

      Date: 2026-10-13 15:46:01 +0900

      Commit message:


	  
		
 Fix vignette build with recent S4Vectors.

The table() method for Rle objects in S4Vectors does not accept the
useNA argument anymore.  Decode the Rle before tabulating it.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpectraStash

      Commit: 4450091878a74b02d4becbbdbb67383c24172e1c

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

      Date: 2026-10-23 10:09:02 +0200

      Commit message:


	  
		
 Merge pull request #18 from rformassspectrometry/jomain

feat: add support for MsBackendSql backends 
    
  
    

      Package: SpectraStash

      Commit: 060731c907f68820298fb7a110aa70bcfe93f737

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

      Date: 2026-10-23 10:08:33 +0200

      Commit message:


	  
		
 Address Gabriele's comments
 
    
  
    

      Package: SpectraStash

      Commit: f8fe9fecc9f5a5a7c699e695ad1238f760f6abba

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

      Date: 2026-10-23 08:33:53 +0200

      Commit message:


	  
		
 feat: add support for MsBackendSql backends

- Add alabaster and plain text stash format support for `MsBackendSql`
  backends (for certain supported database systems).
 
    
  
    

      Package: prolfqua

      Commit: 0726bc3c1001b999013bee2174ba3a46dd90edb9

      Author:  Christian Panse <cp@fgcz.ethz.ch> 

      Date: 2026-10-23 10:07:47 +0200

      Commit message:


	  
		
 version bump 0.99.3
 
    
  
    

      Package: exploreSE

      Commit: 9a4efa3f7afb15bdb6bf5ace5c8a2d45393118b8

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

      Date: 2026-10-23 09:43:44 +0200

      Commit message:


	  
		
 example contexts, readme and vignette updates
 
    
  
    

      Package: exploreSE

      Commit: 39a87c37ef012ac7ae76369c51f02715a26a6f6a

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

      Date: 2026-10-23 09:21:58 +0200

      Commit message:


	  
		
 adapted screenshots
 
    
  
    

      Package: gDR

      Commit: 6f7cbd639f5698196a4025f685f291c95faf67e5

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

      Date: 2026-10-23 01:58:11 +0200

      Commit message:


	  
		
 Merge pull request #71 from gdrplatform/GDR-3739

fix: keep the rendered report when only the publication step fails 
    
  
    

      Package: gDR

      Commit: b61c337e04a54c4f949837ab86f48edb9cc879b1

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

      Date: 2026-10-23 00:09:31 +0200

      Commit message:


	  
		
 Merge remote-tracking branch 'origin/main' into GDR-3739

# Conflicts:
#	DESCRIPTION
#	NEWS.md
 
    
  
    

      Package: gDR

      Commit: 2c458cee5c7c06f38e662f0747e9ef64a9314988

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

      Date: 2026-10-21 12:19:46 +0200

      Commit message:


	  
		
 chore: reword the NEWS entry with a known verb
 
    
  
    

      Package: gDR

      Commit: a2792fcb894a7813327d0f9bad2b9674287f3440

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

      Date: 2026-10-20 22:19:41 +0200

      Commit message:


	  
		
 chore: bump version to 1.11.13
 
    
  
    

      Package: gDR

      Commit: 253da393b8c56fac4221527849171243f194c8c8

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

      Date: 2026-10-20 22:19:41 +0200

      Commit message:


	  
		
 test: cover the clean-up after a failed publication step
 
    
  
    

      Package: gDR

      Commit: c6786945884c58d1aae944ab2401e96cba33a480

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

      Date: 2026-10-20 22:19:41 +0200

      Commit message:


	  
		
 fix: keep the rendered report when only the publication step fails
 
    
  
    

      Package: AnnotatedBCGEData

      Commit: 3f5c4dff869df3e210ecae89a24e1e25b81857d7

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

      Date: 2026-10-22 15:58:40 -0600

      Commit message:


	  
		
 added author
 
    
  
    

      Package: gDR

      Commit: 982e514283a6df5395a41563032193b2151b959c

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

      Date: 2026-10-22 23:25:39 +0200

      Commit message:


	  
		
 Merge pull request #69 from gdrplatform/GDR-3703

feat: show how the numbers were produced in the processing reports 
    
  
    

      Package: gDR

      Commit: aa48d398fff08b54a1b575c41e2489a9d5d09b52

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

      Date: 2026-10-21 12:21:37 +0200

      Commit message:


	  
		
 Merge remote-tracking branch 'origin/main' into GDR-3703

# Conflicts:
#	DESCRIPTION
#	NEWS.md
 
    
  
    

      Package: gDR

      Commit: 6bd55b9887912fd562ac62a7ed88a1effdd6a214

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

      Date: 2026-10-15 12:14:39 +0200

      Commit message:


	  
		
 chore: bump version to 1.11.12 and update NEWS
 
    
  
    

      Package: gDR

      Commit: eb793f233bdb0bfdc3cdfbb4f4b08b2a0f3fd546

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

      Date: 2026-10-15 12:14:39 +0200

      Commit message:


	  
		
 feat: show the recorded fits and processing steps in the processing reports
 
    
  
    

      Package: betterChromVAR

      Commit: d64e3b5d0f52fa449c248be5e59010c8055da9ec

      Author:  Pierre-Luc <pl.germain@gmail.com> 

      Date: 2026-10-19 11:23:34 +0200

      Commit message:


	  
		
 Merge pull request #5 from plger/fpc

Merge FPC into main/devel 
    
  
    

      Package: betterChromVAR

      Commit: ffb24e2c6885a75c2ae2e90d5e3fd42cf8c7ed2f

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

      Date: 2026-10-18 18:28:21 +0200

      Commit message:


	  
		
 adjusted news
 
    
  
    

      Package: betterChromVAR

      Commit: 1e91f22c10776254154d64fbfca7a6dd6e812394

      Author:  Pierre-Luc <pl.germain@gmail.com> 

      Date: 2026-10-18 18:27:10 +0200

      Commit message:


	  
		
 Merge pull request #4 from koefoeden/fix-background-variance

Simplified, faster variance computation; shrinkage now affects only the expectation, not its variance 
    
  
    

      Package: betterChromVAR

      Commit: 9e8be3d366a91c940c8d6617e1ea7c6a9f881dc2

      Author:  koefoeden <koefoeden@gmail.com> 

      Date: 2026-10-16 16:13:29 +0200

      Commit message:


	  
		
 Subtract the squared background means in place to save memory
 
    
  
    

      Package: betterChromVAR

      Commit: 69d0b53e478b198b4421407e56014e6b96489665

      Author:  koefoeden <koefoeden@gmail.com> 

      Date: 2026-10-16 13:38:03 +0200

      Commit message:


	  
		
 Compute background variance over each bin's background peaks
 
    
  
    

      Package: betterChromVAR

      Commit: b10738ea8c88c9bcf6b0c17c6a8b66933a06cb8e

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

      Date: 2026-10-08 14:32:50 +0200

      Commit message:


	  
		
 updated doc
 
    
  
    

      Package: betterChromVAR

      Commit: 0ef3a0cf4a54816895566356d32f7df610dd6198

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

      Date: 2026-10-08 14:28:50 +0200

      Commit message:


	  
		
 claude-generated unit tests...
 
    
  
    

      Package: betterChromVAR

      Commit: a81a7b226fbd42a93aca6166d4b66baca386c77e

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

      Date: 2026-10-08 14:27:49 +0200

      Commit message:


	  
		
 motif reliability and variability
 
    
  
    

      Package: betterChromVAR

      Commit: b526a0be9c6c5ccb6a98f202fd416cacd25a622e

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

      Date: 2026-10-08 14:26:39 +0200

      Commit message:


	  
		
 updated vignette
 
    
  
    

      Package: betterChromVAR

      Commit: 9ef5978346cd7a663428254015278875308a6fea

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

      Date: 2026-10-08 12:43:28 +0200

      Commit message:


	  
		
 added kNN smoothing
 
    
  
    

      Package: betterChromVAR

      Commit: e3093403fdfa6f034bc84e01989d395f6af59b4f

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

      Date: 2026-10-08 12:42:37 +0200

      Commit message:


	  
		
 added motif reliability and empirical noise estimate
 
    
  
    

      Package: betterChromVAR

      Commit: 5d0969361be9174c71bfc4306eae1caa57dcca9b

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

      Date: 2026-10-08 12:41:58 +0200

      Commit message:


	  
		
 added fpc
 
    
  
    

      Package: betterChromVAR

      Commit: f48405e2769237a3e31f52a9a42c271595a92956

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

      Date: 2026-10-08 12:41:30 +0200

      Commit message:


	  
		
 Neff in normalization doc
 
    
  
    

      Package: betterChromVAR

      Commit: 2d75dba32ffb4f3b22ebab21dbb83f7130308c1d

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

      Date: 2026-10-08 12:37:50 +0200

      Commit message:


	  
		
 fixed variance
 
    
  
    

      Package: betterChromVAR

      Commit: 4f2a5090d2e68d73f41675d01a6c8802acc92d1f

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

      Date: 2026-10-08 12:27:39 +0200

      Commit message:


	  
		
 fixed analytical variance and added finite-pop correction
 
    
  
    

      Package: GSVA

      Commit: 9db994d166da271490ac5214b9935625c51e18e5

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

      Date: 2026-10-22 19:55:18 +0200

      Commit message:


	  
		
 Fix glued variable in error message when annotation package is not installed
 
    
  
    

      Package: exploreSE

      Commit: 6b04053c642f66f229cb0026c8f6761140c7dcf0

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

      Date: 2026-10-22 16:55:39 +0200

      Commit message:


	  
		
 adjusted defaults and organisation of options
 
    
  
    

      Package: exploreSE

      Commit: 4023b9758d84dec13b94a0b54f872fc2dd1a02e5

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

      Date: 2026-10-22 16:27:42 +0200

      Commit message:


	  
		
 added example contexts
 
    
  
    

      Package: exploreSE

      Commit: 4fc30ce8bda93cc195080407ce2e653ba9292b44

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

      Date: 2026-10-22 15:59:58 +0200

      Commit message:


	  
		
 added a get genes button
 
    
  
    

      Package: exploreSE

      Commit: 61adfcafcad21dfa38e2b7165076acd26e4f025e

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

      Date: 2026-10-22 15:37:19 +0200

      Commit message:


	  
		
 replaced adjusted P value with FDR
 
    
  
    

      Package: exploreSE

      Commit: 7c1a98d39ce390413775fd484e117e682f42b232

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

      Date: 2026-10-22 15:28:35 +0200

      Commit message:


	  
		
 add the line annotation and remove upscaling for the points
 
    
  
    

      Package: scCertify

      Commit: aa7bc12e6aaeccc3fbd2b052d68f72549bdfea0b

      Author:  Jaya-Surya-dev <jayasuryadoddetipalli@gmail.com> 

      Date: 2026-10-22 19:03:00 +0530

      Commit message:


	  
		
 Bump package version to 0.99.8
 
    
  
    

      Package: scCertify

      Commit: 633e20ee2599521f1f0c2581cb5e7dd578f84a04

      Author:  Jaya Surya Doddetipalli <jayasuryadoddetipalli@gmail.com> 

      Date: 2026-10-22 18:52:42 +0530

      Commit message:


	  
		
 Merge pull request #1 from Jaya-Surya-dev/discovery-aware-development

Add discovery-aware annotation features 
    
  
    

      Package: scCertify

      Commit: 819932e320fcc2de200dd312f7eae151f0d2932b

      Author:  Jaya-Surya-dev <jayasuryadoddetipalli@gmail.com> 

      Date: 2026-09-13 13:21:59 +0530

      Commit message:


	  
		
 Address reviewer feedback for discovery-aware analysis
 
    
  
    

      Package: scCertify

      Commit: e653c67436acde2b4a5c1ffb68f1b62ac4161d59

      Author:  Jaya-Surya-dev <jayasuryadoddetipalli@gmail.com> 

      Date: 2026-09-13 12:46:08 +0530

      Commit message:


	  
		
 Add discovery-aware annotation features
 
    
  
    

      Package: MsBackendMetabolomicsWorkbench

      Commit: aa52e90eda7a5d6c9249c5fa02fb71f521c74d48

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

      Date: 2026-10-22 15:51:49 +0200

      Commit message:


	  
		
 Merge pull request #13 from rformassspectrometry/gabri

fix: metadata download after changes in JSON parsing 
    
  
    

      Package: MsBackendMetabolomicsWorkbench

      Commit: ea254590972d581b3816ebc2ee7f4f872e795eec

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

      Date: 2026-10-22 15:26:05 +0200

      Commit message:


	  
		
 address Johannes comments
 
    
  
    

      Package: MsBackendMetabolomicsWorkbench

      Commit: e07b5fce01023a76716c6f6960776db7b36485b4

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

      Date: 2026-10-22 09:43:44 +0200

      Commit message:


	  
		
 fix: metadata download after changes in JSON parsing
 
    
  
    

      Package: MsBackendMetabolomicsWorkbench

      Commit: 09587bca2b827f76ea4dee8163b17319b1320637

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

      Date: 2026-10-02 15:36:29 +0200

      Commit message:


	  
		
 Merge pull request #12 from rformassspectrometry/gabri

fix: parsing filename with "+" and same filename in subfolders 
    
  
    

      Package: MsBackendMetabolomicsWorkbench

      Commit: 1104974c81dcab8b3f038c7b7ca7ab79d85e3a6d

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

      Date: 2026-10-02 10:05:42 +0200

      Commit message:


	  
		
 fix: issue Check if issues from MsBackendMetaboLights are also a problem here
Fixes #11 . Fix bug in parsing file name with "+"
 
    
  
    

      Package: powerTCR

      Commit: 8972e9287e8691ef62340fed5af9347e9e0d57f3

      Author:  Hillary Koch <hbk5086@psu.edu> 

      Date: 2026-10-22 09:28:50 -0400

      Commit message:


	  
		
 update structure check for model fit
 
    
  
    

      Package: mia

      Commit: b3ac981d010626e3566bb85845fcae19a0f384eb

      Author:  Muluh <127390183+0xMuluh@users.noreply.github.com> 

      Date: 2026-10-22 10:14:37 +0300

      Commit message:


	  
		
 Add Allen's phylogenetic entropy and Rao's quadratic entropy to addAlpha (#845) (#847)

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

      Package: mia

      Commit: d4884e76c3ff4890aa5a73cc1b593afd41926cf6

      Author:  Rasmus Hindström <56149499+raivo-otus@users.noreply.github.com> 

      Date: 2026-10-20 10:57:16 +0300

      Commit message:


	  
		
 Fix/optimize multiple alpha index rarefaction (#857)

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

      Package: mia

      Commit: 5e65c510856f8eeaf0266ca237c36b5b6dc1939b

      Author:  Rasmus Hindström <56149499+raivo-otus@users.noreply.github.com> 

      Date: 2026-10-19 10:06:02 +0300

      Commit message:


	  
		
 Fix/alpha rarefaction bug (#854)

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

      Package: miaTime

      Commit: 534c76d28cf77ba29781b4e58c86f94ed28f38fa

      Author:  Muluh <127390183+0xMuluh@users.noreply.github.com> 

      Date: 2026-10-22 16:27:03 +0300

      Commit message:


	  
		
 add getSurvival (#112)

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

      Package: miaTime

      Commit: de5b9a9dbc6617c18d7cb0f640babd1c43cd4791

      Author:  Muluh <127390183+0xMuluh@users.noreply.github.com> 

      Date: 2026-10-22 10:46:44 +0300

      Commit message:


	  
		
 Add reference sections to pkgdown site (#128) 
    
  
    

      Package: periodicDNA

      Commit: 73d785f756bdbf0ffe9d56e6c6ad10a4494cbe48

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-10-22 14:48:00 +0200

      Commit message:


	  
		
 bump to 1.23.1
 
    
  
    

      Package: periodicDNA

      Commit: 9c79080090460308b5c985418e81118f18095452

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-10-22 14:47:49 +0200

      Commit message:


	  
		
 fix: use importFrom syntax for magrittr
 
    
  
    

      Package: periodicDNA

      Commit: b35a6ce9601be6a80401f337d45b3c88fbee6d1a

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-10-22 14:47:34 +0200

      Commit message:


	  
		
 fix: update ggplot2 language
 
    
  
    

      Package: SpatialFeatureExperiment

      Commit: 82fed2166a4472d50a1ef9fa1ce52fb2809b6487

      Author:  Lambda Moses <lambda.calc29@gmail.com> 

      Date: 2026-10-22 19:47:17 +0800

      Commit message:


	  
		
 Deprecated split z and split by cell components in transcript spots and dealt with failed unit tests
 
    
  
    

      Package: SpectraStash

      Commit: 0fe6b50d40df294b7e7ef2d5531ca782a2b7bb88

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

      Date: 2026-10-22 13:42:11 +0200

      Commit message:


	  
		
 Merge pull request #17 from rformassspectrometry/jomain

feat: add alabaster stash for MsBackendOfflineSql 
    
  
    

      Package: SpectraStash

      Commit: 0069be8f5bf2262a65495a65d5360ab9138b0af4

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

      Date: 2026-10-22 07:24:01 +0200

      Commit message:


	  
		
 feat: add alabaster stash for MsBackendOfflineSql

- Add alabaster stash format for `MsBackendOfflineSql` with all related unit
  tests and documentation.

Note that we are still not importing from the *MsBackendSql* package, but only
listing this package in *Suggests* to keep the dependency tree of *SpectraStash*
somewhat manageable.
 
    
  
    

      Package: PasillaTranscriptExpr

      Commit: a8c00fa51878fb8fad18205ff176f06d505c64ce

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

      Date: 2026-10-22 07:41:22 -0400

      Commit message:


	  
		
 User requested deprecation
 
    
  
    

      Package: BgeeDB

      Commit: ca3e6af3cadbeca5421734382e71885b1d06a83e

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

      Date: 2026-10-22 11:36:18 +0200

      Commit message:


	  
		
 bump version
 
    
  
    

      Package: BgeeDB

      Commit: e0334b8951ef62d2bb3f3a7d2b5efb8386dfb2e0

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

      Date: 2026-10-22 11:35:47 +0200

      Commit message:


	  
		
 update example to work with new fast fisher approach not using topGo for propagation
 
    
  
    

      Package: GSVA

      Commit: 926e1e53a60bb190fbf6ff212750983ff56e1bf6

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

      Date: 2026-10-22 10:42:46 +0200

      Commit message:


	  
		
 Replace BiocParallel::bpiterate(), which is not supported by the
DoparParam back-end, by calls to bplapply() in rounds of one block per
worker, when socket or foreach workers receive blocks of an in-memory
input from the main process. The main process frees the blocks of each
round before taking the next ones, and the copies it holds are now
included in the memory budget given by 'maxmem' and in the memory
estimated before the calculations start. Added doParallel and foreach to
Suggests, for a new unit test on the DoparParam back-end.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: limma

      Commit: d6e69a137f5f27020f6c33ebb711aeeadb13f451

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

      Date: 2026-10-22 19:41:57 +1100

      Commit message:


	  
		
 limma 3.99.3

- New argument 'fixed' and code speed-up for strplit2().
 
    
  
    

      Package: AHMassBank

      Commit: 420bc31e455be8104e2b8b688ef65bba5a84003b

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

      Date: 2026-10-22 10:34:14 +0200

      Commit message:


	  
		
 Add additional resources, retrievable from GitHub
 
    
  
    

      Package: Chromatograms

      Commit: 32220289a83d21fd461907b3223ef72df12cbdee

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-10-22 09:36:04 +0200

      Commit message:


	  
		
 fix: CITATION duplicated URL and missing issue number
 
    
  
    

      Package: Chromatograms

      Commit: 68d9ae670b65416f1cae641e73c24f3f0c8eba28

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-10-22 09:31:19 +0200

      Commit message:


	  
		
 Merge Bioconductor devel into main
 
    
  
    

      Package: Chromatograms

      Commit: 83d904c5a9292237bfe65a8a0a0ec9ab24d886cb

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

      Date: 2026-10-16 12:44:50 +0200

      Commit message:


	  
		
 Merge pull request #66 from rformassspectrometry/gabri

feat: functions to generate ggplot2 figures 
    
  
    

      Package: Chromatograms

      Commit: bc8f21f04651e3b1b342d0304f5308095a478f48

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

      Date: 2026-10-16 11:31:31 +0200

      Commit message:


	  
		
 tests: add unit test for as.data.frame.Chromatograms
 
    
  
    

      Package: Chromatograms

      Commit: 382ed75689e6485314fb078b6a6cdc5da6e1645c

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

      Date: 2026-10-16 09:14:18 +0200

      Commit message:


	  
		
 fix: address Phili comments
 
    
  
    

      Package: Chromatograms

      Commit: a007394a21f3878be80e0eec83737f745fb0597e

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

      Date: 2026-10-15 15:46:19 +0200

      Commit message:


	  
		
 fix: update wrong variable
 
    
  
    

      Package: Chromatograms

      Commit: 6c2c99508713685f4fc214318b9b29a34939edf5

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

      Date: 2026-10-15 15:41:32 +0200

      Commit message:


	  
		
 Address Phili comments
 
    
  
    

      Package: Chromatograms

      Commit: a91df7f65337a6347247c7762efdd0351275d4fa

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

      Date: 2026-10-12 13:38:52 +0200

      Commit message:


	  
		
 address Johannes comments
 
    
  
    

      Package: Chromatograms

      Commit: 29ded92b295280d22bed15e7c98b611b07952017

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

      Date: 2026-10-09 10:34:09 +0200

      Commit message:


	  
		
 fix: citation
 
    
  
    

      Package: Chromatograms

      Commit: 3a1991c1e9abeb22a4376c7d7c0f5b17952aaf00

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

      Date: 2026-10-09 09:52:36 +0200

      Commit message:


	  
		
 Merge branch 'main' into gabri
 
    
  
    

      Package: Chromatograms

      Commit: 340d0ef025d0019789603f5adaf90d75f30bb336

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

      Date: 2026-10-08 17:49:37 +0200

      Commit message:


	  
		
 update as.data.frame.chromatogram following Johannes comments
 
    
  
    

      Package: Chromatograms

      Commit: 45d3cfe867d8bdb7a0cdd408d2c8ce305ce5b326

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

      Date: 2026-10-07 11:51:12 +0200

      Commit message:


	  
		
 refactor: function from chromatograms to data.frame
 
    
  
    

      Package: Chromatograms

      Commit: 19e4f8f5431f2acf75a7b4c50133b2a43ae4a541

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-10-06 11:33:40 +0200

      Commit message:


	  
		
 Version 1.3.4
 
    
  
    

      Package: Chromatograms

      Commit: 230a44e619e584b7141fad7ae5bb911ef102488e

      Author:  Philippine Louail <philippine.louail@outlook.com> 

      Date: 2026-10-05 13:54:35 +0200

      Commit message:


	  
		
 Merge pull request #69 from rformassspectrometry/jomain

Add citation 
    
  
    

      Package: Chromatograms

      Commit: 344f0175df65c57ba8cefd6f0481046c45c9d505

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

      Date: 2026-10-05 13:38:57 +0200

      Commit message:


	  
		
 Add citation
 
    
  
    

      Package: Chromatograms

      Commit: 7fccade0dcea0dbfb00e497a62003f28f964e8e8

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

      Date: 2026-09-28 09:45:09 +0200

      Commit message:


	  
		
 refactor: move ggiraph to Suggests to decrease dependencies
 
    
  
    

      Package: Chromatograms

      Commit: 83c779f784a323f01cd479f4e9ff09f7d93e1cb7

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

      Date: 2026-09-08 07:24:19 +0200

      Commit message:


	  
		
 Merge pull request #67 from rformassspectrometry/jomain

Add logo 
    
  
    

      Package: Chromatograms

      Commit: fab04d8fe796f21af8bf9737159c3bce9740d7a7

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

      Date: 2026-09-07 16:52:23 +0200

      Commit message:


	  
		
 Add logo
 
    
  
    

      Package: Chromatograms

      Commit: 32ab92123d1c0952599c1c5c11ba8a5f52c68b9b

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

      Date: 2026-09-03 14:42:11 +0200

      Commit message:


	  
		
 docs: update documentation
 
    
  
    

      Package: Chromatograms

      Commit: c48d955b586c8af0cb99af0d928aa83448021ac6

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

      Date: 2026-09-03 09:48:36 +0200

      Commit message:


	  
		
 refactor: change ggplot function for color
 
    
  
    

      Package: Chromatograms

      Commit: f731e8056fc23bc21067df620625b10a3d82e568

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

      Date: 2026-08-27 14:17:48 +0200

      Commit message:


	  
		
 add unit test for ggplot figures
 
    
  
    

      Package: Chromatograms

      Commit: 58099c5c57ff3f55d9228aa92c74989d054c8ab3

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-08-18 13:55:10 +0200

      Commit message:


	  
		
 Merge branch 'main' into phili
 
    
  
    

      Package: Chromatograms

      Commit: 44f00b2285a79db039a9c534fc44ee7f83626b1c

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-08-18 12:47:36 +0200

      Commit message:


	  
		
 Update Supplementary_Material_3_interoperability_chromExtract.pdf
 
    
  
    

      Package: Chromatograms

      Commit: 57a7e7ac7041278336c6714f44acba5794b03332

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

      Date: 2026-08-07 14:09:41 +0200

      Commit message:


	  
		
 feat: add parameter to hide axis to ggplot
 
    
  
    

      Package: Chromatograms

      Commit: 7a5ef8a04a535ab58b4d8401f8e20d1661c49fd0

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

      Date: 2026-08-06 15:49:30 +0200

      Commit message:


	  
		
 separate plot and ggplot. Add interactivity
 
    
  
    

      Package: Chromatograms

      Commit: f1b9327d4356cae14dbf990a322f3a11febb3639

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

      Date: 2026-08-06 11:26:53 +0200

      Commit message:


	  
		
 Merge branch 'main' into gabri
 
    
  
    

      Package: Chromatograms

      Commit: 09ac528a75a51357720cab3c2de4950febd57ac5

      Author:  Philippine Louail <philippine.louail@outlook.com> 

      Date: 2026-08-05 13:59:10 +0200

      Commit message:


	  
		
 Merge pull request #63 from rformassspectrometry/paper-revision

Paper revision (benchmarks) 
    
  
    

      Package: Chromatograms

      Commit: 6392ec65746c9a4dfbfbee0f322d2344bfe0a4a5

      Author:  Philippine Louail <philippine.louail@outlook.com> 

      Date: 2026-08-05 13:52:31 +0200

      Commit message:


	  
		
 Merge pull request #64 from rformassspectrometry/paper-revision-jo

Update Supp 3 
    
  
    

      Package: Chromatograms

      Commit: 958759e3e74ea70728326cb3675bd696f7052d1d

      Author:  Philippine Louail <philippine.louail@outlook.com> 

      Date: 2026-08-05 13:40:57 +0200

      Commit message:


	  
		
 Merge pull request #65 from rformassspectrometry/jomain

Update and restructure README 
    
  
    

      Package: Chromatograms

      Commit: ec485abb447f09d10ac167b0064327924211cf65

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

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

      Commit message:


	  
		
 Update and restructure README
 
    
  
    

      Package: Chromatograms

      Commit: efb61f134b865612b1f22b89e342047cf0ba3c99

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

      Date: 2026-08-05 12:33:42 +0200

      Commit message:


	  
		
 Update Supp 3
 
    
  
    

      Package: Chromatograms

      Commit: db39064e08e7e0bb6740604e225a722c32e8d600

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-08-04 19:16:52 +0200

      Commit message:


	  
		
 Update Supplementary_Material_3_interoperability_chromExtract.qmd
 
    
  
    

      Package: Chromatograms

      Commit: 953c82fbcbdca052d3286dac79834cbbe2da7d74

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-08-04 13:07:50 +0200

      Commit message:


	  
		
 refactor: benchmark display xcms integration and chromExtract on large scale data
 
    
  
    

      Package: Chromatograms

      Commit: c5a9b7185769a68438d8071a932714159c6ae003

      Author:  Philippine Louail <philippine.louail@outlook.com> 

      Date: 2026-08-04 12:53:52 +0200

      Commit message:


	  
		
 Merge pull request #61 from rformassspectrometry/paper-revision-jo

refactor: adapt to the large-scale data 
    
  
    

      Package: Chromatograms

      Commit: cd50475a8f3a6e912a40344027fd44d4fbae2cd7

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

      Date: 2026-08-04 11:04:56 +0200

      Commit message:


	  
		
 Update Supp 3
 
    
  
    

      Package: Chromatograms

      Commit: d832ada0cdec43fc0a57a606225187f557f80ad1

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

      Date: 2026-08-03 15:54:31 +0200

      Commit message:


	  
		
 feat: update from plot to ggplot
 
    
  
    

      Package: Chromatograms

      Commit: 0a711bd777ca48253913a0203cd1d150aa8b84cb

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

      Date: 2026-08-03 11:26:31 +0200

      Commit message:


	  
		
 Add Supplementary file 2 qmd
 
    
  
    

      Package: Chromatograms

      Commit: f90f190da4ec0f4e302d964592d7cf27be9de586

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

      Date: 2026-08-03 11:10:02 +0200

      Commit message:


	  
		
 Merge remote-tracking branch 'origin/main' into paper-revision-jo
 
    
  
    

      Package: Chromatograms

      Commit: 2f0d6182a77da888907d212c739f64533d119e0b

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

      Date: 2026-07-31 11:58:34 +0200

      Commit message:


	  
		
 small fix
 
    
  
    

      Package: Chromatograms

      Commit: 0cb4ce4a3d9c04f0282fe5c15306c121c2d25d14

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

      Date: 2026-07-31 11:57:22 +0200

      Commit message:


	  
		
 Update/fix format of supplements
 
    
  
    

      Package: Chromatograms

      Commit: 8696f4d906acfb602ad2d6beb7d7e1e90022a4f6

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

      Date: 2026-07-31 11:19:23 +0200

      Commit message:


	  
		
 Update Supplementary Material 3
 
    
  
    

      Package: Chromatograms

      Commit: ef7e39cea24b6c9b26884a4298ea342ada66258b

      Author:  Philippine Louail <philippine.louail@outlook.com> 

      Date: 2026-07-31 10:36:13 +0200

      Commit message:


	  
		
 Merge pull request #60 from rformassspectrometry/chrom-extract-ref

perf(chromExtract): avoid re-validating backend when matching chromData 
    
  
    

      Package: Chromatograms

      Commit: fabd81c2ea703e1d70584f534b111e5c19d79a16

      Author:  Philippine Louail <philippine.louail@outlook.com> 

      Date: 2026-07-31 10:35:21 +0200

      Commit message:


	  
		
 Merge pull request #62 from rformassspectrometry/jomain

Additional performance improvements for ChromBackendSpectra 
    
  
    

      Package: Chromatograms

      Commit: 4bf3a95b1d8ddfedab40e6a7945430cffa4665f6

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

      Date: 2026-07-31 08:47:23 +0200

      Commit message:


	  
		
 Update title
 
    
  
    

      Package: Chromatograms

      Commit: 78d9c8e42783b5ac194dc386973c6e1be682cb4b

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

      Date: 2026-07-31 08:31:46 +0200

      Commit message:


	  
		
 refactor: further performance improvements for ChromBackendSpectra

- Avoid repeated calls to extract data from a `Spectra` object.
- Use `rbindlist()` instead of `rbindFill()` to combine `data.frame`s.
 
    
  
    

      Package: Chromatograms

      Commit: 26b20aa6a6debc04455aa6c611abb6659e0d781b

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

      Date: 2026-07-31 08:16:02 +0200

      Commit message:


	  
		
 Small update
 
    
  
    

      Package: Chromatograms

      Commit: 33584466fb0181b1f9c8124f18f64ba5b7ad3188

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

      Date: 2026-07-31 07:44:28 +0200

      Commit message:


	  
		
 refactor: small update
 
    
  
    

      Package: Chromatograms

      Commit: dcc19a2a0dce2b53089c6f2b3ce0867c1cdebf91

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

      Date: 2026-07-31 07:25:09 +0200

      Commit message:


	  
		
 rename supp material 3
 
    
  
    

      Package: Chromatograms

      Commit: 55065ef650847319ab3c5503625ebb60abb10191

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

      Date: 2026-07-31 07:17:33 +0200

      Commit message:


	  
		
 Update Supplementatry Material 1: include large scale data
 
    
  
    

      Package: Chromatograms

      Commit: 5ac3a360be16831885efaba11f677a22e8b720d5

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-07-30 17:48:02 +0200

      Commit message:


	  
		
 perf(ChromBackendSpectra): avoid re-validating Spectra when setting chromSpectraIndex
 
    
  
    

      Package: Chromatograms

      Commit: fe493e24e0f565b97969dda5d13b73ce3a965fbe

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

      Date: 2026-07-30 07:56:42 +0200

      Commit message:


	  
		
 refactor: adapt to the large-scale data
 
    
  
    

      Package: Chromatograms

      Commit: c302f3cb82735fc2dd30c4f8e93e0310c1323762

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-07-29 17:18:34 +0200

      Commit message:


	  
		
 Update helpers.R
 
    
  
    

      Package: Chromatograms

      Commit: a0fa6ac7b2ff34a717b53fdaa122a17a86a249d7

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-07-29 17:13:50 +0200

      Commit message:


	  
		
 perf(chromExtract): avoid re-validating backend when matching chromData
 
    
  
    

      Package: Chromatograms

      Commit: 00c00b70a513b68fe2fa1b203d67ca4ec7b1ca59

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-07-28 15:34:05 +0200

      Commit message:


	  
		
 prototype-qmd
 
    
  
    

      Package: Chromatograms

      Commit: 386f2fbca870eadeccf867859dc6564a823d0de3

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-07-23 11:32:41 +0200

      Commit message:


	  
		
 Merge branch 'main' into phili
 
    
  
    

      Package: Chromatograms

      Commit: 054d2b9b6b400290cffc07b20c962627595c2deb

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-07-22 18:09:08 +0200

      Commit message:


	  
		
 Remove stale tests
 
    
  
    

      Package: Chromatograms

      Commit: b2aec72c0186f67161c28f7a3dc777555e15a7df

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-07-22 17:42:03 +0200

      Commit message:


	  
		
 refactor: peaksData() improvments for overlapping RT windows
 
    
  
    

      Package: Chromatograms

      Commit: 275c951aacf3b7a23401917fc875395d806547fb

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-07-22 14:04:44 +0200

      Commit message:


	  
		
 refactor: peakBoundary for efficiency
 
    
  
    

      Package: anndataR

      Commit: 339176dfe3c961c5aa329d700af59d398a19f3ab

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-10-22 08:47:15 +0200

      Commit message:


	  
		
 Fix setting obsm/varm to NULL on backed objects (#536)

* Test that setting obsm/varm to NULL writes a null element

* Accept extra arguments in the null writers 
    
  
    

      Package: anndataR

      Commit: 24f52ce320b3dad9d15bad7c11c6803efd93a285

      Author:  Max Frank <max.frank@czbiohub.org> 

      Date: 2026-10-21 11:31:00 -0700

      Commit message:


	  
		
 Write obs_names/var_names as the index of obsm/varm data frames (#501)

* Write obs_names/var_names as the index of obsm/varm data frames
* Cover data frames in the obsm/varm roundtrip tests
* Check the index of R generated obsm/varm data frames with h5diff
* Test obsm/varm data frames with missing values

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

      Package: anndataR

      Commit: 322eabe3bcd7c3f9b858f442854bcceccb502623

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-10-21 17:31:17 +0200

      Commit message:


	  
		
 Use Python 3.14 in benchmark and pkgdown workflows (#534) 
    
  
    

      Package: anndataR

      Commit: 824b775de59d33cb1fc867134d314d8292d0e8fe

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-10-21 16:41:59 +0200

      Commit message:


	  
		
 Error instead of skip when Python tests are required (#533)

* route python skip helpers through one helper

* add test for strict python test mode

* error instead of skip when python tests are required

* document strict python test mode

* fix lint

* update news

* bump version 
    
  
    

      Package: anndataR

      Commit: f9d753429d122f80d9fb07fc5af2e8459cbf4774

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

      Date: 2026-10-21 13:38:43 +0200

      Commit message:


	  
		
 Bump bencherdev/bencher from 0.6.11 to 0.6.13 (#528)

Bumps [bencherdev/bencher](https://github.com/bencherdev/bencher) from 0.6.11 to 0.6.13.
- [Release notes](https://github.com/bencherdev/bencher/releases)
- [Commits](https://github.com/bencherdev/bencher/compare/v0.6.11...v0.6.13)

---
updated-dependencies:
- dependency-name: bencherdev/bencher
  dependency-version: 0.6.13
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

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

      Package: anndataR

      Commit: 1db33d1536b034800821a75cb80080837680b086

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

      Date: 2026-10-21 12:03:22 +0200

      Commit message:


	  
		
 Bump dawidd6/action-download-artifact from 21 to 27 (#529)

Bumps [dawidd6/action-download-artifact](https://github.com/dawidd6/action-download-artifact) from 21 to 27.
- [Release notes](https://github.com/dawidd6/action-download-artifact/releases)
- [Commits](https://github.com/dawidd6/action-download-artifact/compare/v21...v27)

---
updated-dependencies:
- dependency-name: dawidd6/action-download-artifact
  dependency-version: '27'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

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

      Package: anndataR

      Commit: 581123a9e2f55cb9042ac8b64d0af75c3755981e

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-10-21 09:16:58 +0200

      Commit message:


	  
		
 Add 1.2.1 and 1.2.2 entries to NEWS (#530) 
    
  
    

      Package: Statial

      Commit: d2cb1f8ba252505264f4f8a67ac20ea95c0ad94c

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

      Date: 2026-10-22 17:13:30 +1100

      Commit message:


	  
		
 pkgdown workflow: run on devel, build against Bioconductor devel (3.24) with spicyR from its GitHub devel branch, as lisaClust's

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 
    
  
    

      Package: Spectra

      Commit: 7f8fc2fee96dc3e20c3994e90b390d9a1343dcf9

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

      Date: 2026-10-22 07:55:29 +0200

      Commit message:


	  
		
 docs: update citation info and add additional backend links
 
    
  
    

      Package: spicyR

      Commit: fc1719c1c463f96090e82a905a67dfb5f61fa7c3

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

      Date: 2026-10-22 16:40:24 +1100

      Commit message:


	  
		
 1.99.39: pkgdown reference sections from roxygen @concept tags (has_concept), not a hand-kept list

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 
    
  
    

      Package: lisaClust

      Commit: 26cbfdd44915a975528460f32b273e3d35f5cade

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

      Date: 2026-10-22 16:21:13 +1100

      Commit message:


	  
		
 pkgdown workflow: build against Bioconductor devel (3.24), as spicyR's does, so the devel spicyR and spatialdataR resolve

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 
    
  
    

      Package: spicyR

      Commit: 03ed13ef694a2aee8e0fe836ead76280429e6c68

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

      Date: 2026-10-22 15:59:26 +1100

      Commit message:


	  
		
 pkgdown: calibrationCheck in the reference index

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 
    
  
    

      Package: lisaClust

      Commit: 1268f99f67d0e6a1ba679acec24b9d3ba215f8a3

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

      Date: 2026-10-22 15:59:20 +1100

      Commit message:


	  
		
 pkgdown workflow: spicyR from its GitHub devel branch (lisaClust 1.21.11 needs spicyR 1.99.38, not yet built by Bioconductor)

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 
    
  
    

      Package: Statial

      Commit: 1a656cb96082668c30c1d87f7b910c72d8f25e24

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

      Date: 2026-10-22 15:41:03 +1100

      Commit message:


	  
		
 1.15.6: simpler vignette (defaults no longer passed, one-step survival vector, colTest() matching by name, coord_cartesian zoom, bcells fix)

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 
    
  
    

      Package: lisaClust

      Commit: 029e4dcaa5b3078fdad5acfdfefc860b586ee5ef

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

      Date: 2026-10-22 15:40:56 +1100

      Commit message:


	  
		
 1.21.11: regionBoxPlot(subject =); regionMap() labels upright with many regions; simpler vignette (named examples, medians from colTest(), subject)

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 
    
  
    

      Package: spicyR

      Commit: 5f9ace461f9f5fba2ad01d68f0f3a6d01ef86e6a

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

      Date: 2026-10-22 15:19:46 +1100

      Commit message:


	  
		
 1.99.38: colTest() takes subject, reports group medians with the Wilcoxon test, and matches rows to a named condition

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 
    
  
    

      Package: spicyR

      Commit: 738dfd8a580032bbdf69b4656020198c1def7060

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

      Date: 2026-10-22 13:10:34 +1100

      Commit message:


	  
		
 1.99.37: calibrationCheck() (the shuffle check the vignette recommends); simpler vignette: imageID/cellType set once, ER.Status as it is, cores named, whole data set in the store section

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 
    
  
    

      Package: VISTA

      Commit: 283ac73bb057141e28cc973d969f9556a269a60c

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-10-22 12:21:28 +1100

      Commit message:


	  
		
 Bump to 1.1.7: make the gene-order test invariant to eigenvector sign

R-CMD-check failed on Linux CI for 1.1.6 in test-label-value-integrity.R:
shuffling the genes passed to get_pca_plot() returned both PCA axes negated
-- the same embedding, mirrored -- and the permutation-invariance test read
that as an order dependence. The test shuffles with sample() and no seed, so
it was a coin flip on that BLAS build; 1.1.5 passed by chance and nothing in
1.1.6 caused it. It is the failure c22fd55 fixed for the snapshots, in a test
that fix did not reach.

Orient the PCA (PC1/PC2) and MDS (Dim1/Dim2) axes with canon_axis() before
comparing, as the snapshots already do. canon_axis() moves to helper-data.R
so both files share one definition. A new test pins the property: negating
an axis passes, moving a point still fails, and without orientation the flip
fails as it did on CI.

Test-only change; no user-visible behaviour changes.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: spicyR

      Commit: abc77723e4235a9e9e7f8869eaadfb6ffdcffcda

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

      Date: 2026-10-22 12:17:41 +1100

      Commit message:


	  
		
 1.99.36: comments link each SpatialData-writer workaround to its upstream issue (Rarr #260, #261; spatialdataR #115, #287)

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 
    
  
    

      Package: spicyR

      Commit: f00e9780befaa9710afb1cafbafa44b16685cf38

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

      Date: 2026-10-22 10:49:40 +1100

      Commit message:


	  
		
 1.99.35: writeCellStore() writes the cells of each image as a points element, so the table annotates elements of the store

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 
    
  
    

      Package: spicyR

      Commit: 348ffacfbc112f380f5bfc408e8a02d1968ea827

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

      Date: 2026-10-22 10:49:40 +1100

      Commit message:


	  
		
 1.99.34: writeCellStore() writes a whole SpatialExperiment (assays, rowData, reducedDims, images); writer in spatialdataR's idiom on Rarr

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 
    
  
    

      Package: spicyR

      Commit: 022ed2c40e8b5f7371225014f4bd92c13dc76ec3

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

      Date: 2026-10-22 10:49:34 +1100

      Commit message:


	  
		
 1.99.33: writeCellStore() takes a SpatialExperiment; plotImage() without a pair shows every cell type; vignette store section on the SpatialExperiment

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 
    
  
    

      Package: SpaNorm

      Commit: 6f7ffeb2297bb157ef9845aecdd3b8c42995dde4

      Author:  Dharmesh D Bhuva <30132854+bhuvad@users.noreply.github.com> 

      Date: 2026-10-21 11:08:42 +1000

      Commit message:


	  
		
 Fix plotSpatial()/plotCovariate() for genes with non-syntactic names (e.g. HLA-B)

as.character() on the aesthetic expressions wrapped such names in backticks,
so no feature matched. Take the names with a shared aesColnames() helper.

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 8e854a1bb99a199b9e868f71a307ed2766b46100

      Author:  Dharmesh D Bhuva <30132854+bhuvad@users.noreply.github.com> 

      Date: 2026-10-20 18:25:23 +1000

      Commit message:


	  
		
 site: remove the gap between the navbar and the home page hero

Quarto's main.content has a 1em top margin that the negative hero margin only
partly cancelled (a ~14px light strip showed under the navbar).

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_012hFT9QMAZMopnJeA2VW41B
 
    
  
    

      Package: SpaNorm

      Commit: 24b316bbc8d3fb4bcaf499279cbfb7ee5309ebc6

      Author:  Dharmesh D Bhuva <30132854+bhuvad@users.noreply.github.com> 

      Date: 2026-10-20 16:44:09 +1000

      Commit message:


	  
		
 site: forest-green redesign, landing page and footer

Palette from the hex logo, system fonts, dark navbar with gold active
indicator, title banners, styled code/tables/tabsets, landing page with
hero, feature cards, install, cite and project cards, page footer. Home
page has no table of contents or empty References heading.

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_012hFT9QMAZMopnJeA2VW41B
 
    
  
    

      Package: SpaNorm

      Commit: d4dccdfe8695c88bbacb3a957335bd0c3ec41b1c

      Author:  Dharmesh D Bhuva <30132854+bhuvad@users.noreply.github.com> 

      Date: 2026-10-20 16:38:35 +1000

      Commit message:


	  
		
 site: remove the redundant Articles section

Fold the unique content (polishing options table and held-out genes,
SVG/GPU calls, polish memory budget, static GPU benchmark with caveats,
polishNB pointer) into Get started and delete site/articles and
scripts/article-setup.R along with the navbar and home links.

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_012hFT9QMAZMopnJeA2VW41B
 
    
  
    

      Package: SpaNorm

      Commit: 43b2a57418a93102d749696adb63d642d01a2f69

      Author:  Dharmesh D Bhuva <30132854+bhuvad@users.noreply.github.com> 

      Date: 2026-10-20 17:08:23 +1000

      Commit message:


	  
		
 ci: skip R-CMD-check for website-only changes [skip ci]

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_012hFT9QMAZMopnJeA2VW41B
 
    
  
    

      Package: SpaNorm

      Commit: b3baf9e4df88fbff97301fc470f326efe1b436ce

      Author:  Dharmesh D Bhuva <30132854+bhuvad@users.noreply.github.com> 

      Date: 2026-10-20 14:03:09 +1000

      Commit message:


	  
		
 docs(site): show total Bioconductor downloads (computed at build time) instead of the rank badge; weekly rebuild

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_012hFT9QMAZMopnJeA2VW41B
 
    
  
    

      Package: SpaNorm

      Commit: 9f48be012240d1e504e9b56d09cb3226ad6ad908

      Author:  Dharmesh D Bhuva <30132854+bhuvad@users.noreply.github.com> 

      Date: 2026-10-20 13:10:17 +1000

      Commit message:


	  
		
 ci(site): do not cache the basilisk env (restored venv has dangling interpreter symlinks)

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_012hFT9QMAZMopnJeA2VW41B
 
    
  
    

      Package: SpaNorm

      Commit: 06821c8715969f9253dfcb3befb2f49813b48d34

      Author:  Dharmesh D Bhuva <30132854+bhuvad@users.noreply.github.com> 

      Date: 2026-10-20 13:03:14 +1000

      Commit message:


	  
		
 docs(site): home page with logo, authors, download stats and CI status; add SpaNorm logo

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_012hFT9QMAZMopnJeA2VW41B
 
    
  
    

      Package: SpaNorm

      Commit: 2b95feee27b2474a9831744761e965d2113f95e6

      Author:  Dharmesh D Bhuva <30132854+bhuvad@users.noreply.github.com> 

      Date: 2026-10-20 13:03:14 +1000

      Commit message:


	  
		
 docs: cite the Genome Biology paper instead of the bioRxiv preprint

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_012hFT9QMAZMopnJeA2VW41B
 
    
  
    

      Package: SpaNorm

      Commit: 157be3ec1533eb12e30d729029e476262907b5ec

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun157.hpc.net.uq.edu.au> 

      Date: 2026-10-20 11:56:08 +1000

      Commit message:


	  
		
 site: make every read-only logging-handler stream property assignable (torch's _StderrHandler)

reticulate's output capture failed on torch._logging._internal._StderrHandler, a
different class from logging._StderrHandler that the previous shim patched. Patch all
Handler subclasses with a read-only stream property, including ones defined later
(torch is imported after the shim runs).

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_012hFT9QMAZMopnJeA2VW41B
 
    
  
    

      Package: SpaNorm

      Commit: 4db11b37d3cb331f4ac016b1aef16ed63733c152

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun157.hpc.net.uq.edu.au> 

      Date: 2026-10-20 10:58:58 +1000

      Commit message:


	  
		
 ci(site): latest R + Bioc devel, drop reticulate/R pins; shim logging._StderrHandler.stream for reticulate capture

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_012hFT9QMAZMopnJeA2VW41B
 
    
  
    

      Package: SpaNorm

      Commit: d8d49e14d1ab28001b4b6fa65b8d904972f949d5

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun157.hpc.net.uq.edu.au> 

      Date: 2026-10-20 10:23:01 +1000

      Commit message:


	  
		
 ci(site): build on R 4.5 so the pinned reticulate 1.44.1 compiles

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_012hFT9QMAZMopnJeA2VW41B
 
    
  
    

      Package: SpaNorm

      Commit: afe34866d2410b16068e43bb2bf09ea656e94684

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun157.hpc.net.uq.edu.au> 

      Date: 2026-10-20 10:06:17 +1000

      Commit message:


	  
		
 ci: pin reticulate 1.44.1 (1.47.0 py_capture_output breaks on logging._StderrHandler); print py_config

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_012hFT9QMAZMopnJeA2VW41B
 
    
  
    

      Package: SpaNorm

      Commit: f233b7be4b11399bb5ae8eca2b2da43bb75b679e

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun157.hpc.net.uq.edu.au> 

      Date: 2026-10-20 09:01:26 +1000

      Commit message:


	  
		
 fix: compute the dispersion winsorisation cap on finite log-dispersions only

A single NaN psi made psi.max NaN and turned every gene's logPAC/Pearson/
median-bio output into NaN; psi = 0 (log -Inf) dragged the median to -Inf.
Shared internal helper .psiMax() used by winsorisePsi() and subsetFitGenes().
Bump to 1.7.16.

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 953ee6fcb314f7b0593a9d6d0bc5e45456fca731

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun157.hpc.net.uq.edu.au> 

      Date: 2026-10-20 08:51:38 +1000

      Commit message:


	  
		
 ci(site): use the runner's Quarto when present, require >= 1.8

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: ec6dd518f77f8e170e782d0f7695df352985ca01

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun157.hpc.net.uq.edu.au> 

      Date: 2026-10-19 21:14:14 +1000

      Commit message:


	  
		
 docs: combined R/Python Quarto website, built and deployed by GitHub Actions

Replaces pkgdown with a single Quarto site serving SpaNorm (R) and spanormpy
(Python): tabbed R|Python Get started, articles, R and Python reference, and an
R vs Python page. Only site sources are committed (site/ is in .Rbuildignore);
.github/workflows/quarto-site.yaml renders and deploys to gh-pages.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: RAMEN

      Commit: 3cdc9cab1a4ca5d07d965619ace4c7dac7dcb4a7

      Author:  Erick Navarro <ericknadel98@ciencias.unam.mx> 

      Date: 2026-10-21 14:31:00 -0700

      Commit message:


	  
		
 Fix bug due to nested internal functions in parallel workers
 
    
  
    

      Package: lisaClust

      Commit: 318165b1c29f4bdeafd9572b607cdfd18408007c

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

      Date: 2026-10-22 08:07:54 +1100

      Commit message:


	  
		
 1.21.10: parallel test passes with a single-threaded BLAS (Bioconductor build machines)

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 
    
  
    

      Package: RAMEN

      Commit: f7ff222cf97e16e14d9e090f84c80017574bcc32

      Author:  Erick Navarro <ericknadel98@ciencias.unam.mx> 

      Date: 2026-10-21 13:42:31 -0700

      Commit message:


	  
		
 Bump R version
 
    
  
    

      Package: RAMEN

      Commit: 7e47a44cb0f360633803fe1f06aaf6888f3bba0c

      Author:  Erick Navarro <ericknadel98@ciencias.unam.mx> 

      Date: 2026-10-21 13:37:40 -0700

      Commit message:


	  
		
 Export internal functions to workers, so they are available when using PSOCK
 
    
  
    

      Package: RAMEN

      Commit: ca2b90a00440b588210cf3981250eafebb1943e5

      Author:  Erick Navarro <ericknadel98@ciencias.unam.mx> 

      Date: 2026-10-21 12:56:46 -0700

      Commit message:


	  
		
 Add peer review issue links
 
    
  
    

      Package: RAMEN

      Commit: 8a2ed6e69affadb8c6156fe47fa4bb178a719684

      Author:  Erick Navarro <ericknadel98@ciencias.unam.mx> 

      Date: 2026-10-21 12:52:38 -0700

      Commit message:


	  
		
 Bump patch version
 
    
  
    

      Package: RAMEN

      Commit: b21015840b2452a17eef3f531e2a98335b222df6

      Author:  Erick Navarro <ericknadel98@ciencias.unam.mx> 

      Date: 2026-10-21 12:51:53 -0700

      Commit message:


	  
		
 Add github installation instructions as alternative
 
    
  
    

      Package: RAMEN

      Commit: 854e8ea75ba030c5dc48fd01bad7629405a42994

      Author:  Erick Navarro <ericknadel98@ciencias.unam.mx> 

      Date: 2026-10-21 12:50:22 -0700

      Commit message:


	  
		
 Update version to upcoming release
 
    
  
    

      Package: eiR

      Commit: 428c2a8a5574f523c8f8a575eb3a0a8b31ed9575

      Author:  khoran <khoran@cs.ucr.edu> 

      Date: 2026-10-21 11:15:30 -0700

      Commit message:


	  
		
 fix unit test to be more robust against random initial conditions
 
    
  
    

      Package: sesame

      Commit: df2946fc60f17f00eaa4a6dfc9d24c77193d6679

      Author:  Wanding Zhou <zhouw3@email.chop.edu> 

      Date: 2026-10-21 12:27:59 -0400

      Commit message:


	  
		
 1.31.8: CITATION reads without a declared encoding

inst/CITATION spelled one author name with a literal non-ASCII character
(Szabó, the MM285 paper). utils::readCitationFile() without a declared
encoding refuses non-ASCII input, so BiocCheck warned "Unable to read
CITATION file" (bioc R-universe, 1.31.7). The name is now the escape
"Szabó": the file is pure ASCII and renders the same.
 
    
  
    

      Package: MACSr

      Commit: a05551948a56776664fc9ef861996e52f452b3fd

      Author:  qhu <huqmail@gmail.com> 

      Date: 2026-10-21 12:18:20 -0400

      Commit message:


	  
		
 Upgrade to MACS 3.1.0, add threads argument, version bump 1.21.4

- Use Python 3.12 and macs3 3.1.0 in the basilisk environment.
- hmmratac: add remove_dup and em_jump, deprecate keepduplicates,
  and default decoding_steps to 5000 as in MACS 3.1.0.
- Add threads (default 1) to callpeak, predictd, pileup, filterdup,
  randsample, refinepeak, hmmratac and callvar. callvar: deprecate np.
- pileup: detect the input format in R when format = "AUTO", since
  MACS3 pileup rejects AUTO. Add a test for it.
- Add inst/CITATION for the MACS3 paper.
 
    
  
    

      Package: BiocDuckDB

      Commit: d0fbd4601dda6a4709c728fd51d78989c59ceaf0

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

      Date: 2026-10-21 09:13:30 -0700

      Commit message:


	  
		
 fix: add missing sf-signature spatialMatch/spatialJoin methods (0.99.28)

spatialMatch/spatialJoin had no method for a plain sf object. An sf is a
base S3 class (c("sf", "data.frame")), not an S4Vectors::DataFrame, so
the existing DataFrame-signature methods never matched it -- calling
either with a real sf object errored with "unable to find an inherited
method" rather than falling through to anything.

This is purely a missing signature, not an S3/S4 dispatch limitation:
setMethod(generic, c(..., "sf"), ...) dispatches on the class vector
directly, no setOldClass() bridging needed. Fixed by adding
c("DuckDBDataFrame", "sf") for spatialMatch, and both
c("DuckDBDataFrame", "sf")/c("sf", "DuckDBDataFrame") for spatialJoin,
delegating to the same existing DuckDBSpatial calls (which already
handle sf input correctly as of DuckDBSpatial 0.99.8).

Added regression tests for all three new signatures. Full test suite:
0 failures.
 
    
  
    

      Package: DuckDBSpatial

      Commit: cbe969f207fa3888c910f9c0b6e91896d80a28f4

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

      Date: 2026-10-21 09:05:51 -0700

      Commit message:


	  
		
 feat: accept WKT-text geometry columns in st_join/st_join_table (0.99.9)

.as_duckdb_table() (the in-memory materializer backing st_join/
st_join_table's sf/data.frame support, added in 0.99.8) only accepted
sfc or raw WKB geometry columns. MultiAssaySpatialExperiment's own
idiomatic DataFrame shape stores geometry as WKT text instead, the same
single-geometry shape .geom_to_sql() already parses, just never
generalized to a whole column.

Added a character-column branch that parses via sf::st_as_sfc(), same
idiom, scaled up. Along the way, found that st_as_sfc() errors outright
on NA ("missing value where TRUE/FALSE needed") rather than tolerating
it the way the sfg/WKB paths do -- any WKT column with a missing
geometry would have crashed. Fixed by substituting
"GEOMETRYCOLLECTION EMPTY" for NA entries first, matching the same
never-matches-anything semantics already used for the NULL-handling in
the WKB-list case.

Added regression tests for a working WKT column, a column with an NA
entry, and genuinely unparseable WKT text. Full test suite: 0 failures.
 
    
  
    

      Package: BiocDuckDB

      Commit: a20e4a2e1059183ef7b31c51eec67a149905a7bb

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

      Date: 2026-10-21 08:34:55 -0700

      Commit message:


	  
		
 fix: add missing spatialJoin mixed-dispatch methods (0.99.28)

spatialJoin was missing the mixed-type method pair
(c("DuckDBDataFrame", "DataFrame")/c("DataFrame", "DuckDBDataFrame")) that
spatialMatch already has. A call with one out-of-core DuckDBDataFrame
side and one in-memory DataFrame side (in either order) therefore had no
applicable method more specific than MultiAssaySpatialExperiment's own
c("DataFrame", "DataFrame") fallback, which materializes both sides'
geometries fully into memory via st_as_sfc() -- silently defeating the
out-of-core path for exactly the mixed case a caller joining a lazy layer
against a small in-memory one would hit.

Found via user feedback flagging that geometries were still loading into
memory. Fixed by adding the missing method pair, delegating to
DuckDBSpatial::st_join_table()/sf::st_join() the same way the existing
c("DuckDBDataFrame", "DuckDBDataFrame") method does (both already accept
a mixed lazy/in-memory pair as of DuckDBSpatial 0.99.8).

Added a regression test covering both argument orders in
test-spatial-dispatch.R. Full test suite: 0 failures.
 
    
  
    

      Package: powerTCR

      Commit: c7ebcf8ea7a30f9fc9ba467119cb1a9376cfe389

      Author:  Hillary Koch <hbk5086@psu.edu> 

      Date: 2026-10-21 10:50:50 -0400

      Commit message:


	  
		
 update .Rbuildignore
 
    
  
    

      Package: powerTCR

      Commit: 5b58d3992d9db6e5357fcb9a4c62a0845357cd1d

      Author:  Hillary Koch <hbk5086@psu.edu> 

      Date: 2026-10-21 10:47:14 -0400

      Commit message:


	  
		
 remove NOTE caused by LICENSE file
 
    
  
    

      Package: powerTCR

      Commit: 5ae7861e39b7608e64d534de277f67858fe552e0

      Author:  Hillary Koch <hbk5086@psu.edu> 

      Date: 2026-10-21 10:40:12 -0400

      Commit message:


	  
		
 switch from evmix to mev
 
    
  
    

      Package: BgeeDB

      Commit: b7baee0c68117ed352bc1587ad4547c7874c1a19

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

      Date: 2026-10-21 16:39:54 +0200

      Commit message:


	  
		
 bump version
 
    
  
    

      Package: BgeeDB

      Commit: 1c98a8e994cd9d8fe12c47b735fbc8ce37b439d8

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

      Date: 2026-10-21 16:36:57 +0200

      Commit message:


	  
		
 restrict the gene list of topAnat to a background, the protein coding genes by default from Bgee 16, and accept the genes of interest alone
 
    
  
    

      Package: BgeeDB

      Commit: 8fdebd1cc7617a50aa2537e37f4c7824927a0a64

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

      Date: 2026-10-21 16:36:51 +0200

      Commit message:


	  
		
 compute the classic Fisher test of the propagated calls without topGO, with the same results, and move the topAnat classes and their methods to their own files
 
    
  
    

      Package: MsBackendMsp

      Commit: 32d130465c28afe482902436212bd2db3db53443

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

      Date: 2026-10-21 16:18:05 +0200

      Commit message:


	  
		
 Merge pull request #22 from rformassspectrometry/jomain

Improve import speed and add new MspSpectra helper function 
    
  
    

      Package: MsBackendMsp

      Commit: b728cd6488158c98d5fd9ae73b5ba64db5c6ce51

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

      Date: 2026-10-21 16:17:27 +0200

      Commit message:


	  
		
 small fix
 
    
  
    

      Package: MsBackendMsp

      Commit: 2fa519082ceb0ae93b3c93d2764e3f5f86eec6d5

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

      Date: 2026-10-21 15:49:39 +0200

      Commit message:


	  
		
 feat: add MspSpectra function
 
    
  
    

      Package: MsBackendMsp

      Commit: c8effe7405cfba087ee5c15924f17d2045f7ec74

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

      Date: 2026-10-21 15:34:52 +0200

      Commit message:


	  
		
 ci: update
 
    
  
    

      Package: MsBackendMsp

      Commit: 32753aa725c11106d7ee19ea930efead68e4e600

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

      Date: 2026-10-21 15:34:10 +0200

      Commit message:


	  
		
 refactor: improve import speed
 
    
  
    

      Package: destiny

      Commit: 60d1159385a31e839f471f2d02d24aca1e6eb282

      Author:  Philipp A. <flying-sheep@web.de> 

      Date: 2026-10-21 16:14:41 +0200

      Commit message:


	  
		
 all NOTEs
 
    
  
    

      Package: destiny

      Commit: 2eddbb18096e5a0c16309532d49ee80c34c76b41

      Author:  Philipp A. <flying-sheep@web.de> 

      Date: 2026-10-21 16:05:04 +0200

      Commit message:


	  
		
 fix tests with irlba 2.4+
 
    
  
    

      Package: destiny

      Commit: 01df106eb1f9566a27abdc92c67f3647b24de879

      Author:  Philipp A. <flying-sheep@web.de> 

      Date: 2026-09-20 15:38:57 +0200

      Commit message:


	  
		
 chore: full pixi support (#74) 
    
  
    

      Package: multipointR

      Commit: 6d94ef19f3a7cd5be7060324b1d33edc79d4057e

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2026-10-21 16:01:46 +0200

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: multipointR

      Commit: e4ac389b777dced1675a4008209a55b05dc27f74

      Author:  Martin Emons <55688661+mjemons@users.noreply.github.com> 

      Date: 2026-10-21 14:00:18 +0200

      Commit message:


	  
		
 Memory footprint (#5)

* fast covariance calculation

* fixed dependencies

* fixed bugs

* added test 
    
  
    

      Package: RegEnrich

      Commit: c0cdec286abb4cce46391da89ba8c9bbe1ca6d69

      Author:  Weiyang Tao <weiyangtao1513@gmail.com> 

      Date: 2026-10-21 18:04:19 +0800

      Commit message:


	  
		
 version bump 1.23.3
 
    
  
    

      Package: RegEnrich

      Commit: c2f4b1be73828e5a9a653d0674c9375b778bc849

      Author:  Weiyang Tao <weiyangtao1513@gmail.com> 

      Date: 2026-10-21 17:58:26 +0800

      Commit message:


	  
		
 set eval=FALSE to avoid errors because of unstable internet
 
    
  
    

      Package: BreastSubtypeR

      Commit: 0e2e4c3735360d31230d510c59c9da4ac3078edf

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-20 19:04:15 +0200

      Commit message:


	  
		
 Merge pull request #179 from JohanHartmanGroupBioteam/fix/178-mapping-max-singleton-na

Preserve singleton gene rows in Mapping(method = "max") 
    
  
    

      Package: BreastSubtypeR

      Commit: 9220afa23ec692d9997d369a8284296b5af40b33

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

      Date: 2026-10-20 18:31:02 +0200

      Commit message:


	  
		
 chore: advance development version to 1.5.9

Official devel remains 1.5.8 and release remains 1.4.1 with no RELEASE_3_24 branch. Apply the author-approved next unused development version; no Bioconductor synchronization.

Prepared with Codex assistance.
 
    
  
    

      Package: BreastSubtypeR

      Commit: b20e62c5895f8404c6baef4f9ceb4233ad5ad686

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

      Date: 2026-10-20 18:30:50 +0200

      Commit message:


	  
		
 docs(mapping): clarify max singleton preservation

Document preservation of remaining NA and NaN measurements in singleton max groups and record issue #178 in development NEWS. Historical 1.5.8 notes remain unchanged.

Prepared with Codex assistance.
 
    
  
    

      Package: BreastSubtypeR

      Commit: 3a44af75d2a0e16615b0cabac0cfa0a7c5f5ef73

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

      Date: 2026-10-20 18:30:42 +0200

      Commit message:


	  
		
 fix(mapping): preserve singleton rows for max selection

Keep singleton measurements unchanged while retaining the existing max calculation for groups with multiple probes. Add focused regression and preservation tests for issue #178.

Prepared with Codex assistance under the author-approved singleton-preservation scope.
 
    
  
    

      Package: BreastSubtypeR

      Commit: 0251efd3310b04315718f426034b0eb2c7c3c2d8

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

      Date: 2026-10-20 11:14:37 +0200

      Commit message:


	  
		
 Merge pull request #175 from JohanHartmanGroupBioteam/docs/readme-build-badges-20261020

Clean up Bioconductor build badges in README 
    
  
    

      Package: BreastSubtypeR

      Commit: a2e2d3a2f0c8cc0070a119c2225d312d5ecd5050

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-20 10:52:36 +0200

      Commit message:


	  
		
 docs(readme): remove external Bioconductor badge labels 
    
  
    

      Package: igblastr

      Commit: 9074537345da2f0160f6487f3dafc95ad3e9c4a9

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

      Date: 2026-10-20 22:56:12 -0700

      Commit message:


	  
		
 igblastr 1.3.24

o install_OGRDB_germline_db() now supports new OGRDB organism Peromyscus
  leucopus (White-footed mouse).

o Complete install_OGRDB_germline_db() man page.

o Add extract_alleles_from_ogrdb_json() utility.

o Add extensive tests for download_OGRDB_germline_sequences().
 
    
  
    

      Package: VISTA

      Commit: 0804d80863ff4a7a327afe374480f26ecdd93b5d

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-10-21 15:42:12 +1100

      Commit message:


	  
		
 Bump to 1.1.6: independent equivalence check, edgeR QL option, tximport fixes

Verification
- benchmark_vista_equivalence() now compares VISTA with reference
  DESeq2/edgeR/limma pipelines that share none of VISTA's code, matched by
  identifier; a test enforces the separation, and injected defects in
  VISTA's own helpers must be reported.

edgeR
- New edger_test = c("LRT", "QL") in create_vista(), run_edger_analysis(),
  benchmark_vista_equivalence() and validate_vista_deep(). LRT stays the
  default; calls that rely on it get a notice that QL becomes the default
  in VISTA 1.4.0 (see ?VISTA-deprecated). The test used is recorded in
  cutoffs(v)$edger_test and in the report.

Bug fixes
- Untested genes were stored with pvalue = 1; they keep the engine's NA.
- Filtering a consensus table on padj returned the union in intersection
  mode.
- DEG-count plots dropped comparisons with no DEGs.
- limma MA plots used log10(log2-CPM + 1) on the x axis.
- An explicit intercept in design_formula survived for edgeR and limma.
- tximport abundance/length could be imported as counts; unscaled tximport
  counts are now converted to lengthScaledTPM (matching tximport), with
  tx2gene summarised as summarizeToGene() does.
- DESeq2 now accepts estimated counts, rounded after a shared filter.
- Negative values are refused; exact TPM/CPM or log-scale input warns.
- RSEM TPM/FPKM columns could be imported as counts.

Also: provenance records VISTA, R and engine versions; the code-economy
vignette computes its tallies; docs and NEWS updated.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: lisaClust

      Commit: ff5cefd9bfc244daaa1701cfe7f9e752a3502961

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

      Date: 2026-10-21 06:40:33 +1100

      Commit message:


	  
		
 1.21.9: lisa() and lisaClust() take cellWeights (a vector of cell weights or a soft cell type membership matrix), in the shared core

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 
    
  
    

      Package: spicyR

      Commit: 7010b892ad3b670ea0c9d305bfad34b354c0146d

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

      Date: 2026-10-21 06:40:39 +1100

      Commit message:


	  
		
 1.99.32: cellWeights (a vector of cell weights or a soft cell type membership matrix) in spicy(), kontextualEngine() and getPairwise(); weighted random-labelling sums in the core

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 
    
  
    

      Package: plyxp

      Commit: 7ffccf79d670b59be2ff6e5f4a0bfbb8739f984c

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-20 17:48:24 -0400

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: plyxp

      Commit: 5dbc9b82da33bfb44f9b3c6c93f2ec649782538a

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-20 17:47:33 -0400

      Commit message:


	  
		
 After testing, I remembered that .assays is reserved in masks...
 
    
  
    

      Package: plyxp

      Commit: 68493c8a38797155cd3ed517f4f0cfab37152469

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-20 17:34:07 -0400

      Commit message:


	  
		
 Update DESCRIPTION
 
    
  
    

      Package: plyxp

      Commit: d07a8a2fa80653acdfc7b76536ece393812b186e

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-20 17:33:38 -0400

      Commit message:


	  
		
 Speedup optim 5: dont walk names twice, call both functions in each
iteration
 
    
  
    

      Package: plyxp

      Commit: da64def46bc818af4d313a70791a888af4c03ed5

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-20 17:01:12 -0400

      Commit message:


	  
		
 Speedup optim 5: `enexpr` is slow, but I believe we are always passing
in a quoted value, thus this is redundant.... I think
 
    
  
    

      Package: plyxp

      Commit: 9b150a3cbfc487c40570abb0bf10424c68b2351d

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-20 16:59:52 -0400

      Commit message:


	  
		
 speedup optim 4: plyxp_group_ids2 uses `[[` alot, convert object to list
for faster operator
 
    
  
    

      Package: plyxp

      Commit: e6be03521fed0ebfdd0c2bd114335ed9213f5210

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-20 16:59:01 -0400

      Commit message:


	  
		
 speedup optim 3: expand_groups2 is slow due to appending new values, use
df0 on fully constructed list
 
    
  
    

      Package: plyxp

      Commit: a3701adae3a6fc85b205bd3b0e8076729da47cf5

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-20 16:58:05 -0400

      Commit message:


	  
		
 speedup optim 2: calling tibble is slow - construct raw data.frame with
`df0`
 
    
  
    

      Package: plyxp

      Commit: b82d5ded7a33d2e9cf291106a4035ee959b54673

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-20 16:56:37 -0400

      Commit message:


	  
		
 speedup optim 1: dont use `withDimnames = TRUE` default...
 
    
  
    

      Package: plyxp

      Commit: cc25b97a95c6bb77a0e6b2aa170122cc21fc1d06

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-20 12:57:34 -0400

      Commit message:


	  
		
 testing various parts of the S4 vctrs interface
 
    
  
    

      Package: plyxp

      Commit: 77056e837e74b07794dcc2af2887ed9efb10cbca

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-20 12:56:33 -0400

      Commit message:


	  
		
 air syntax format
 
    
  
    

      Package: plyxp

      Commit: 8ab722650239613f4bfc9870eadaa4ab4ddb5d41

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-20 12:56:17 -0400

      Commit message:


	  
		
 work in progress
 
    
  
    

      Package: plyxp

      Commit: 9bbc42353d9efc2cadbdcf0dccb86987f530ee88

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-20 12:55:47 -0400

      Commit message:


	  
		
 vctrs-S4-cast could be better. We could try to register methods from the
default system if it exists...
 
    
  
    

      Package: plyxp

      Commit: cb8e6dd4a9b6934705342d3fbaf8cc43d9df9855

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-20 12:40:25 -0400

      Commit message:


	  
		
 ensuring active bindings are read only
 
    
  
    

      Package: plyxp

      Commit: 20e05ec67ef0335f6f15afb2aa01f1e2211f2e62

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-20 12:40:04 -0400

      Commit message:


	  
		
 vec_phantom is used in printing, for code cov
 
    
  
    

      Package: plyxp

      Commit: cb5f3c3e28285c002e684b801c86e9948759d2da

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-20 12:39:30 -0400

      Commit message:


	  
		
 testing different branches of simple slice
 
    
  
    

      Package: plyxp

      Commit: 7de2cf311855f9b374f16f04c143f3a574f9d7d8

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-20 12:39:16 -0400

      Commit message:


	  
		
 Test we can rename rows and cols with mutate
 
    
  
    

      Package: plyxp

      Commit: bf4e556103d7ef07888f0a2fb912768f172d25e8

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-18 15:52:06 -0400

      Commit message:


	  
		
 Forgot to commmit these tests
 
    
  
    

      Package: plyxp

      Commit: 1a0278cdb13b3285ef0f9228c4ed6625b8a7862e

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-18 15:51:48 -0400

      Commit message:


	  
		
 many random tests for S4Vectors and vec_* generics
 
    
  
    

      Package: plyxp

      Commit: 2c870861c690f567c94d71f5cb6d87cbc4462911

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-18 15:51:14 -0400

      Commit message:


	  
		
 had a typo
 
    
  
    

      Package: plyxp

      Commit: a3ac3536275739f6df9678496d523d2a908e0a84

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-18 15:45:40 -0400

      Commit message:


	  
		
 various tests for standard methods
 
    
  
    

      Package: plyxp

      Commit: 2adcfae841e08d475c34e65a2b306ff86bc7fa66

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-18 15:45:02 -0400

      Commit message:


	  
		
 misc
 
    
  
    

      Package: plyxp

      Commit: 6717cafccb569df8ac864ad569467457f05e4691

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-18 15:44:13 -0400

      Commit message:


	  
		
 Update test_printing.R
 
    
  
    

      Package: plyxp

      Commit: 22766c9652ece26e1553ae839cb2a94b997c12a5

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-18 15:44:03 -0400

      Commit message:


	  
		
 Update test_S4_list_unchop.R
 
    
  
    

      Package: plyxp

      Commit: 2a2aa80ba0ce261de5b5f647ff5deacf2a251c7a

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-18 15:43:43 -0400

      Commit message:


	  
		
 found bug in standard assignment, testing that binding values works as
expected
 
    
  
    

      Package: plyxp

      Commit: 83d42571797e35260156691c157eea153596d267

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-18 15:42:33 -0400

      Commit message:


	  
		
 taking inspiriation from biocmask side project
 
    
  
    

      Package: plyxp

      Commit: 3b94753a5ee2a7b903cebfaca7eca9a909500b2e

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-18 15:42:03 -0400

      Commit message:


	  
		
 improving slicing indices
 
    
  
    

      Package: plyxp

      Commit: 784a8c4aa1e0822a9e017f205ecd9459ad663dd6

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-18 15:41:42 -0400

      Commit message:


	  
		
 This is not yet needed and was not much used
 
    
  
    

      Package: plyxp

      Commit: 0045199afec9827423684e92c4b70f232862873e

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-18 15:40:32 -0400

      Commit message:


	  
		
 these sets of functions were removed a while ago
 
    
  
    

      Package: plyxp

      Commit: a5bd1f635f0517cdc7b1de827827717033599e7a

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-18 15:40:12 -0400

      Commit message:


	  
		
 logical bug, missing argment. testing other branches
 
    
  
    

      Package: plyxp

      Commit: 7c789a15e6978ce2a2c95a53330c6fc2ed177588

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-16 15:53:08 -0400

      Commit message:


	  
		
 Update vctrs-S4-chop.R
 
    
  
    

      Package: plyxp

      Commit: 94cba9a50e8c84104b602d13a2fbc6e9fccd26b7

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-16 15:51:47 -0400

      Commit message:


	  
		
 testing error paths
 
    
  
    

      Package: plyxp

      Commit: 8bf91f908539cc06fc3786efa5e024608705e02b

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-16 15:51:33 -0400

      Commit message:


	  
		
 never test the branch of no args or just columns
 
    
  
    

      Package: plyxp

      Commit: 1325abef420d629ad24f460bd4247744d3a337e6

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-16 15:51:00 -0400

      Commit message:


	  
		
 Many more group tests, including group_split
 
    
  
    

      Package: plyxp

      Commit: 5c2dd525c47db107226c9b0886ca99a7eb79764b

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-16 15:50:37 -0400

      Commit message:


	  
		
 testing that we can rename content
 
    
  
    

      Package: plyxp

      Commit: 739a232abe1f8a43bb31eb309ffa280944914d93

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-16 15:50:15 -0400

      Commit message:


	  
		
 testing peek_ctx and poke_ctx. So far not used too often. questioning
its relevance
 
    
  
    

      Package: plyxp

      Commit: cbae63bb23da382ab7fb9026ff69e41889aa4a24

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-16 15:49:39 -0400

      Commit message:


	  
		
 vec_init and vec_cast are not yet exported. This may need to change -
however the base amount of support seems to be working.
 
    
  
    

      Package: plyxp

      Commit: 146d214263f04665f348e557fdf462686891100d

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-16 15:47:25 -0400

      Commit message:


	  
		
 Unused at the moment
 
    
  
    

      Package: plyxp

      Commit: 1418437b1a797a84a3da604525a1730159a9d6c3

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-16 15:42:19 -0400

      Commit message:


	  
		
 fixing build to use BiocGeneric functions
 
    
  
    

      Package: plyxp

      Commit: 9af43ed597d82d0d490b7adad67622cc8a76fb75

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-15 17:38:01 -0400

      Commit message:


	  
		
 Update test_plyxp_utils.R
 
    
  
    

      Package: plyxp

      Commit: 7b9abb33f51c2098b9ce15ff9e1629e6c44a6dd8

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-15 17:26:36 -0400

      Commit message:


	  
		
 edit plyxp_evaluate to remove `nams` argument. It was unused for a long
time.

Also adding common plyxp_quo helper functions
 
    
  
    

      Package: plyxp

      Commit: 97645ad9b8e9fe9576e8b5e5fb52af2c36ce865f

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-15 15:49:04 -0400

      Commit message:


	  
		
 Revert 'some work'...

This commit reverts 23cdc8aebed7950d7f85865041d91f0bfbebdfb6

prior commit implements col_data/row_data generics for internal use. Not
ready for devel/bioc
 
    
  
    

      Package: plyxp

      Commit: 1d16f710889670d5800bbf18301ccfe005ad5754

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-15 15:42:47 -0400

      Commit message:


	  
		
 testing plyxp_on()
 
    
  
    

      Package: plyxp

      Commit: 517aff791cbe5f14a7afb43c6b3c5f3d21457d66

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-15 00:21:17 -0400

      Commit message:


	  
		
 formatting
 
    
  
    

      Package: plyxp

      Commit: 3996c87fb0c4d6a3212e02211b884f4d8f730a92

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-15 00:21:11 -0400

      Commit message:


	  
		
 Update NEWS
 
    
  
    

      Package: plyxp

      Commit: a9a50f87b248783922fc97d3e83e2ff36d34235b

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-15 00:11:10 -0400

      Commit message:


	  
		
 shouldnt have used roxygen tag here...
 
    
  
    

      Package: plyxp

      Commit: 5e2ebb641e46b0a2227fc137d6285f4d99126a5d

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-15 00:10:33 -0400

      Commit message:


	  
		
 More tests for test coverage and no errors. Can improve these more later
 
    
  
    

      Package: plyxp

      Commit: ccf0b7e5521f05278ce6a6fbaceafde085a49c8f

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-15 00:09:30 -0400

      Commit message:


	  
		
 Allow new quosure to mimic its parent quosure transform value
 
    
  
    

      Package: plyxp

      Commit: 8e03a4a19f54a269dcf0c4a7ca85fc4e7626c4f9

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-15 00:09:00 -0400

      Commit message:


	  
		
 switching on incorrect value.
 
    
  
    

      Package: plyxp

      Commit: d74d57252dfd828523236d3587710642a789e4c4

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-15 00:08:28 -0400

      Commit message:


	  
		
 air formatting
 
    
  
    

      Package: plyxp

      Commit: 633620510ed7618380e4192abeebe0c280665fae

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-15 00:07:47 -0400

      Commit message:


	  
		
 some additional test coverage
 
    
  
    

      Package: plyxp

      Commit: a52ff181b3f43b75ef0a6e387cc4ecbf7358252a

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-14 23:38:48 -0400

      Commit message:


	  
		
 plyxp_quos defaults to exclude empty. ungroup now retains empty quos and
has granular behavior
 
    
  
    

      Package: plyxp

      Commit: 184141d57b6900663bf6324549c575b76ea42009

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-14 21:33:59 -0400

      Commit message:


	  
		
 tests and reformat news
 
    
  
    

      Package: plyxp

      Commit: c045fd2f86d33fca791f0cba38aa3305c8d2f5df

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-14 21:31:06 -0400

      Commit message:


	  
		
 enabled .features and .samples as grouping options
 
    
  
    

      Package: plyxp

      Commit: 14c057bc78fabceb7acc3e603a7b275c2a0edbdd

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-14 21:07:28 -0400

      Commit message:


	  
		
 found a bug! `.add` should work now
 
    
  
    

      Package: plyxp

      Commit: 340e8b3bc182153c42b0e1883acd7cdc04d95208

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-14 20:24:21 -0400

      Commit message:


	  
		
 An unused function. It should be removed soon
 
    
  
    

      Package: plyxp

      Commit: d08b5d733812d6c87b4cfabb8f8407c155946deb

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-14 15:04:29 -0400

      Commit message:


	  
		
 likely wont be used, commenting out
 
    
  
    

      Package: plyxp

      Commit: 3ee7af20527e744106e1c26ef364254d54203961

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-14 15:04:18 -0400

      Commit message:


	  
		
 small refactor
 
    
  
    

      Package: plyxp

      Commit: 866829a4043c6ec949d9bf428a134a53474357a7

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-14 15:03:57 -0400

      Commit message:


	  
		
 formatting
 
    
  
    

      Package: plyxp

      Commit: 642a8c14332f74a12d0292d740bb4f1de04c33b0

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-14 15:02:32 -0400

      Commit message:


	  
		
 enforce_matrix() is no longer needed. replaced with enforce_2d_size()
 
    
  
    

      Package: plyxp

      Commit: d64dc0c462ef66502e78862d325aaaf549ec658f

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-14 15:01:03 -0400

      Commit message:


	  
		
 with 0c648906b39c3f5426f4311ec6f3cac357573143, we changed how
environments were made available.
 
    
  
    

      Package: plyxp

      Commit: efe3285fb00d625f652f9ddd9c71e8f9808a1322

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-14 14:59:01 -0400

      Commit message:


	  
		
 this function is no longer used, it was inlined to .bind_self
 
    
  
    

      Package: gDRcore

      Commit: 52202c8b93fb0f362b5c3283db5a39f0a2778b71

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

      Date: 2026-10-20 22:49:54 +0200

      Commit message:


	  
		
 Merge pull request #217 from gdrplatform/GDR-3718

test: fit co-dilution experiments through the pipeline and on refit 
    
  
    

      Package: gDRcore

      Commit: b4af88170a9502f9b4e1beb7dbf1db994952ecad

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

      Date: 2026-10-20 21:27:25 +0200

      Commit message:


	  
		
 Merge remote-tracking branch 'origin/main' into GDR-3718

# Conflicts:
#	NEWS.md
 
    
  
    

      Package: gDRcore

      Commit: 1d98dfb55604dbce2091c1f16842eecf13a02edd

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

      Date: 2026-10-20 16:49:02 +0200

      Commit message:


	  
		
 test: check that a refit replaces the stored processing metadata
 
    
  
    

      Package: gDRcore

      Commit: 607e4da4ef5041dfae451317aff66c1f16eb143c

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

      Date: 2026-10-19 17:24:59 +0200

      Commit message:


	  
		
 chore: update the package date
 
    
  
    

      Package: gDRcore

      Commit: 4cecb033b9e5c1057ea28832ab2d1a412d14da79

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

      Date: 2026-10-19 09:46:18 +0200

      Commit message:


	  
		
 test: fit co-dilution experiments through the pipeline and on refit
 
    
  
    

      Package: gDRcore

      Commit: 8a25f099eb15bb972168dfb3563b5db929491309

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

      Date: 2026-10-20 21:26:17 +0200

      Commit message:


	  
		
 Merge pull request #216 from gdrplatform/GDR-3586

fix: restore CIScore_50/80 and the single-agent arm fit for combinations 
    
  
    

      Package: gDRcore

      Commit: c0bca21388e5d0a8923c78e6f8f7a2009a4bf76a

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

      Date: 2026-10-20 16:48:58 +0200

      Commit message:


	  
		
 perf: read CIScore from the isobolograms in one grouped pass
 
    
  
    

      Package: gDRcore

      Commit: 9a23e3df2a382259c156db9d8f230484d6e63ce7

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

      Date: 2026-10-19 17:24:59 +0200

      Commit message:


	  
		
 chore: update the package date
 
    
  
    

      Package: gDRcore

      Commit: de83ea423f009d15ca82128dfe2b3d7a367b4d71

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

      Date: 2026-10-19 08:54:50 +0200

      Commit message:


	  
		
 fix: restore CIScore_50/80 and the single-agent arm fit for combinations
 
    
  
    

      Package: gDRutils

      Commit: 95cc0ac7b301580467a58c199d647116d5a0a25c

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

      Date: 2026-10-20 21:24:24 +0200

      Commit message:


	  
		
 Merge pull request #207 from gdrplatform/GDR-3718

fix: add a co-dilution fit profile and allow refitting a processed SE 
    
  
    

      Package: gDRutils

      Commit: 6886f232b269da20794fd9965ea0903fd190aa55

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

      Date: 2026-10-19 17:24:58 +0200

      Commit message:


	  
		
 chore: update the package date and the changelog entry
 
    
  
    

      Package: gDRutils

      Commit: 6e015a81c2f1895b7fa56ffecaff34a966066ee2

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

      Date: 2026-10-19 09:45:53 +0200

      Commit message:


	  
		
 fix: set SE metadata over an entry that holds a sessionInfo
 
    
  
    

      Package: gDRutils

      Commit: d9a847c6576794014d4ef253a31e89ae5207d4d0

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

      Date: 2026-10-19 09:45:53 +0200

      Commit message:


	  
		
 fix: add a co-dilution fit profile
 
    
  
    

      Package: methylclock

      Commit: 665c17d786a3dfd1910fe2a4d752867dc62e3cc9

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

      Date: 2026-10-20 20:33:26 +0200

      Commit message:


	  
		
 bump version to 1.99.4
 
    
  
    

      Package: methylclock

      Commit: 791d7cab7b41196b9b92e8a5a6dde14ec3da69df

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

      Date: 2026-10-20 20:33:13 +0200

      Commit message:


	  
		
 State telomere length unit and NEOage tissue

The clock catalog now states that the TL clock estimates telomere length in kilobases, the unit of the terminal restriction fragment measurements it was trained on (Lu et al. 2019). The four NEOage rows describe their training tissue as "buccal epithelium (preterm infants)", matching the PedBE wording. Catalog regenerated; no computational change.
 
    
  
    

      Package: DuckDBSpatial

      Commit: 036c2d9d7462258dcb129e64a45dbecb312c22ef

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

      Date: 2026-10-20 11:04:21 -0700

      Commit message:


	  
		
 feat: accept in-memory sf objects in st_join/st_join_table (0.99.8)

st_join.DuckDBTable/st_join_table only accepted lazy DuckDBTable/
DuckDBDataFrame objects for x/y. Closes a real gap flagged by a user
comparing against duckspatial::ddbs_intersects(), which accepts sf
objects on either side.

New internal .as_duckdb_table() materializes an in-memory sf object (or
a data.frame with an sfc or raw-WKB-list geometry column -- the latter
matching the shape as.data.frame() on a DuckDBDataFrame's own geometry
column produces) by converting its geometry to WKT (the same idiom
.geom_to_sql() already uses for a single geometry), copying it into a
temp DuckDB table via copy_to(), then casting back to native GEOMETRY
with ST_GeomFromText(). Temp-table naming reuses DuckDBArray's
PID+counter convention to avoid the dbplyr::unique_table_name()
global-RNG collision class fixed there in 0.99.9. Chosen over
writeGeoParquet()+tempfile since that would pull in nanoparquet as a
hard dependency and add disk I/O for what's typically the small side of
a join.

Three independent review passes (two rounds, four reviewer agents total)
caught and fixed real problems before this shipped:
- The redirect errors added to .geom_to_sql() pointed at spatialMatch()/
  spatialJoin(), which don't exist in this package (those are
  BiocDuckDB-level MultiAssaySpatialExperiment methods) -- corrected to
  layerSpatialMatch(), st_join(), and st_join_table().
- .as_duckdb_table()'s raw-WKB branch crashed on any NULL entry (the
  common case of a DuckDBDataFrame's own geometry column, which
  represents missing geometries as NULL), since sf::st_as_sfc.WKB()
  asserts every element is raw with no NULL tolerance. Fixed by
  substituting an empty geometry per NULL entry, wrapped in the same
  tryCatch-to-friendly-error pattern writeGeoParquet() already uses.
- Hardened the generated ST_GeomFromText("") SQL against a geometry
  column name containing a literal double quote.

Also removed .spatialMatch_sql()'s dead else branch (DuckDBDataFrame-
spatial.R): it attempted the same DuckDBDataFrame(as.data.frame(table))
call that didn't actually work, but its only caller (layerSpatialMatch())
never reaches it with a non-DuckDBTable table, taking a separate
in-memory sf::st_intersects() path instead -- unreachable, untested dead
code.

Added regression tests for all of the above, including sf-on-either-side
joins, the NULL-geometry fix, and the corrected error-message text. Full
test suite: 0 failures.
 
    
  
    

      Package: BiocDuckDB

      Commit: b2a9c29347875328747406aca3cf208872431a75

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

      Date: 2026-10-20 09:31:36 -0700

      Commit message:


	  
		
 fix: correct spatialJoin's sparse path for two out-of-core DuckDBDataFrames (0.99.27)

spatialJoin(DuckDBDataFrame, DuckDBDataFrame) with its default
sparse = TRUE called DuckDBSpatial::st_intersects_table(x, y), which only
ever accepted y as a single scalar geometry (sfc/sfg/WKT) -- it has no
case for another lazy table. It always errored with "unsupported
geometry type: DuckDBDataFrame" when both sides were out-of-core,
defeating the whole point of the sparse, stay-lazy path (the
sparse = FALSE branch, a full attribute join via sf::st_join(), already
worked fine). It also silently ignored the join= predicate argument on
this branch regardless.

Fixed by switching to DuckDBSpatial::st_join_table() (new in DuckDBSpatial
0.99.8), a real two-table SQL join producing a sparse (id_x, id_y) pair
table instead of embedding y as a literal, which also correctly threads
join= through this time.
 
    
  
    

      Package: DuckDBSpatial

      Commit: 847fc37dd8b70a61f7aafb7f6d6266031b720499

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

      Date: 2026-10-20 09:16:22 -0700

      Commit message:


	  
		
 feat: add st_join_table for sparse joins between two lazy spatial tables (0.99.8)

st_intersects_table() only ever supported testing x against a single
reference geometry -- its y goes through .geom_to_sql(), which has no
case for another lazy table -- so there was no way to get a sparse match
table between two out-of-core layers short of materializing the full
attribute join via st_join(). This blocked spatialJoin(DuckDBDataFrame,
DuckDBDataFrame) in BiocDuckDB, whose sparse=TRUE branch called
st_intersects_table(x, y) and always errored with "unsupported geometry
type: DuckDBDataFrame" when both sides were out-of-core.

Added st_join_table(x, y, join = st_intersects, sparse = TRUE), modeled on
the existing st_join.DuckDBTable: same INNER JOIN ... ON (...)
approach and the same .st_predicate_sql_name() mapping to honor join=,
but projecting a sparse (id_x, id_y) row-pair table instead of full
attributes.
 </pre>
    </div>
  
    

      Package: CEMiTool

      Commit: 325dddd3fc11c4c18eec095ae1f968aedf561f40

      Author:  Pedro Russo <pedrostrusso@gmail.com> 

      Date: 2026-10-20 09:06:05 -0300

      Commit message:


	  
		
 Version bump
 
    
  
    

      Package: CEMiTool

      Commit: 3630f2a726ec1e290cb6558ad40802ded423bfb9

      Author:  Pedro Russo <pedrostrusso@gmail.com> 

      Date: 2026-10-20 09:02:13 -0300

      Commit message:


	  
		
 Mirroring changes in master to devel
 
    
  
    

      Package: OmnipathR

      Commit: 9ce957c453451091c2d2ac65a94746c5b8a95b5e

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-20 12:23:32 +0100

      Commit message:


	  
		
 Bump version: 4.1.0 → 4.1.1
 
    
  
    

      Package: OmnipathR

      Commit: 644c8a1280a5ec8cf7dc75713af05ab06a3a5fbe

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-13 02:45:11 +0100

      Commit message:


	  
		
 NEWS for 4.1.1

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: 730cb57407b77a3095252f681d6d577c372a910c

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-13 02:44:37 +0100

      Commit message:


	  
		
 CITATION: ASCII quotes, so that readCitationFile() reads it

BiocCheck reads the file without a declared encoding and gives a
warning for non-ASCII characters.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: 4af5333194c429fd99ff19faf24580ad7fdd34be

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-13 00:54:40 +0100

      Commit message:


	  
		
 docs rebuild

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: ee5ad33716fbe7738990c52ef86c9a36cef67783

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-13 00:54:40 +0100

      Commit message:


	  
		
 resources: use a cached resource list for one hour at most

Resources are added to and removed from the server often, so a resource
list older than one hour is downloaded again.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: f57ef9609c83810a158c54113184b0dac6fee2f4

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-13 00:54:40 +0100

      Commit message:


	  
		
 omnipath_cache_remove: max_age and min_age remove only the matching versions

When status was not given, the version filter kept no version at all, so
omnipath_cache_remove(max_age = 30) emptied the whole cache instead of
removing what is older than 30 days. Without status, versions of any state
are now kept. The manual now describes status as it works: the states to
keep.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: e561784371addd03657df181fdee1e7ca01c3425

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-13 00:11:42 +0100

      Commit message:


	  
		
 Live web service tests do not run on Bioconductor build machines

A short outage of the OmniPath web service must not fail the Bioconductor
build. Other machines, our daily build server included, still run them.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: c714f9dfb8f66191bf12582ded0e6a7946a53518

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-13 00:11:42 +0100

      Commit message:


	  
		
 resources: download with retries and cache, fix category filter

resources() read the resource list with readLines(), with no retry and no
cache, on every query that names resources. One failed connection failed
the query. It now uses the package downloader, like the other functions.
The generic_categories argument looked for a key that the service does not
send, so it always gave an empty result. It now reads the key categories.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: ba43e096a988ee4d47955a66313c8ad09ccc411d

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-12 23:08:14 +0100

      Commit message:


	  
		
 docs rebuild

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: 38528ff92def0e4d302c75e931c6caf14321e1df

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-12 23:08:14 +0100

      Commit message:


	  
		
 Runnable examples for 29 more manual pages

Examples of functions that download data run again: on build servers these
functions return early, so the examples stay fast. Small offline helpers
have new examples. The cache and configuration examples work on a temporary
directory, and never change the user's cache or configuration.
wikipathways_metabolites_sparql() returns early on build servers like the
other download functions. The show_network() example calls show_network().

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: 8907449f2bb545a0288ddc3d7a295544ab55f5f0

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-12 23:08:14 +0100

      Commit message:


	  
		
 subnetwork: select the vertices with V(), add examples to graph helpers

subnetwork() called igraph_vs(), which does not exist, so the function
failed on every call. It now selects the given nodes with V(), or all nodes
when none is given. ensure_igraph(), subnetwork() and graph_interaction()
have offline examples.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: 466c2a7025d7723bfa2bfba0fd3126581becf1fa

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-12 23:02:28 +0100

      Commit message:


	  
		
 Vignettes build when a third-party server does not answer

Chunks that download from g:Profiler, UniProt, the OBO Foundry or a
publisher show the error instead of stopping the vignette build. The text
next to each such chunk tells the reader why the output can be missing.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: 9c6de4f542099aeb253f1c25b85fa68239d42c01

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-12 23:01:20 +0100

      Commit message:


	  
		
 Build-server detection also reads OMNIPATHR_BUILDSERVER

A local R CMD check under any user can now skip the slow examples the same
way as the Bioconductor and Saez Lab build servers.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: a7c05f9a876c08a8e0e33d9c32a930fbf2cf3491

      Author:  jannikfranken <Jannik8513@gmail.com> 

      Date: 2026-09-30 15:34:36 +0200

      Commit message:


	  
		
 `oma_organisms`: robust to header changes, re-download malformed cache

OMA now serves its species table from Zenodo with 5 comment lines and a
column header row instead of 3 comment lines. The hard-coded `skip = 3L`
made readr return a single column table, without `ncbi_tax_id`, which
broke the organism name translation (`taxon_name`, `latin_name`, etc.).

Now all lines starting by "#" and the header row are removed, the columns
are read with fixed names and types, and the result is validated. If the
table is malformed (e.g. a previously cached bad parse), the cache entry
is removed and the file is downloaded again.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: 5897de4085b65dd462b4da5fcdfce7b7cea20883

      Author:  jannikfranken <Jannik8513@gmail.com> 

      Date: 2026-09-28 16:29:02 +0200

      Commit message:


	  
		
 KEGG: use list/genome, the list/organism endpoint returns 400

The KEGG REST endpoint `list/organism` has been retired and now fails
with HTTP 400. This broke `kegg_organisms()`, `kegg_organism_codes()`
and, through the argument validation in `kegg_query()`, any KEGG call
that checks organism codes (e.g. `kegg_conv("compound", "pubchem")`).

- `kegg_request()` now transparently requests `list/genome` whenever
  `list/organism` is asked for, so `kegg_list("organism")`,
  `kegg_request("list", "organism")` and `kegg_organisms()` work again.
- New internal `kegg_genome_to_organisms()` reshapes the two column
  output of `list/genome` ("T01001", "hsa; Homo sapiens (human)") by
  splitting the second field on "; " into `kegg_name` and `latin_name`.
- Removed the obsolete `list/organism` entry from `KEGG_COLUMNS`.
- Updated the `kegg_list()` docs to the new return shape.

Breaking change: the organism table now has 3 columns (`genome`,
`kegg_name`, `latin_name`) instead of 4. The `phylogeny` column is
dropped, as `list/genome` does not provide it; nothing in OmnipathR
used it. The code remains in the 2nd column, so `kegg_organism_codes()`
is unaffected.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: MetaboCoreUtils

      Commit: 3f40f43f37002a0deee0715af1edb2294ddfc78d

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

      Date: 2026-10-20 11:37:37 +0200

      Commit message:


	  
		
 Merge pull request #89 from rformassspectrometry/jomain

feat: add parameter nomatch to translate() 
    
  
    

      Package: MetaboCoreUtils

      Commit: 9077c8175e5a34cb47b7d67841365ffd42b325d0

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

      Date: 2026-10-19 07:24:21 +0200

      Commit message:


	  
		
 feat: add parameter nomatch to translate()

- Add parameter `nomatch` to the `translate()` function to configure the
  behaviour if a name could not be translated/matched. Add also parameter
  `warning` that allows to disable warning messages.
 
    
  
    

      Package: geneslator

      Commit: e7b7161780f2f622eb3614cec05e012af3eca3c6

      Author:  GMicale <gmgmicky@gmail.com> 

      Date: 2026-10-20 11:08:31 +0200

      Commit message:


	  
		
 Updated README
 
    
  
    

      Package: geneslator

      Commit: 10aae9e9cbacd29d346b4d6d0f473a4342a6b05c

      Author:  GMicale <gmgmicky@gmail.com> 

      Date: 2026-09-24 19:19:39 +0200

      Commit message:


	  
		
 Merge branch 'main' of github.com:knowmics-lab/geneslator
 
    
  
    

      Package: geneslator

      Commit: b825a4f5fb156f01fad889fcde03b9f0e6f71f77

      Author:  Giovanni Micale <gmgmicky@gmail.com> 

      Date: 2026-09-04 17:10:34 +0200

      Commit message:


	  
		
 Update README.md 
    
  
    

      Package: biomaRt

      Commit: ba00684e7d8282b927ea8d650f96d218483d6ce4

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-19 09:38:41 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: biomaRt

      Commit: 3d1eaf5520af3e09583664594fe28d9d309b77d9

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-19 09:53:09 +0200

      Commit message:


	  
		
 Use fetch = FALSE in vignette as well
 
    
  
    

      Package: biomaRt

      Commit: f88dd09c86169861e243b5cc6f958fa3de6c6a1c

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-19 09:38:26 +0200

      Commit message:


	  
		
 Avoid hits on ensembl latest release
 
    
  
    

      Package: gDR

      Commit: c98efa763cefe1baa5946a5187791a139f363210

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

      Date: 2026-10-20 09:45:05 +0200

      Commit message:


	  
		
 Merge pull request #70 from gdrplatform/GDR-3728

fix: show one legend per page in the Incucyte analysis report 
    
  
    

      Package: gDR

      Commit: 8ebe3144c8670a34c1df3718b45b412ec6e26c3a

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

      Date: 2026-10-19 13:38:58 +0200

      Commit message:


	  
		
 fix: show one legend per page in the Incucyte analysis report
 
    
  
    

      Package: limma

      Commit: 595fd2c4d7fe23168182dfbc4486eea5bc4cb8ae

      Author:  Mikael Jagan <jaganmn2@gmail.com> 

      Date: 2026-10-20 00:17:02 -0400

      Commit message:


	  
		
 no longer using methods-internal class
 
    
  
    

      Package: geNetClassifier

      Commit: 781ddcfba595cc5f3076c88257eaeda45ec44553

      Author:  Mikael Jagan <jaganmn2@gmail.com> 

      Date: 2026-10-20 00:07:58 -0400

      Commit message:


	  
		
 no longer using methods-internal class
 
    
  
    

      Package: S4Vectors

      Commit: 904dc54db14b1e9fa111e3d9e66ba135f5911b7a

      Author:  Mikael Jagan <jaganmn2@gmail.com> 

      Date: 2026-10-20 00:00:23 -0400

      Commit message:


	  
		
 no longer using methods-internal class
 
    
  
    

      Package: Category

      Commit: adc36989fed922abd0e34197565f79bf1c4d3b6e

      Author:  Mikael Jagan <jaganmn2@gmail.com> 

      Date: 2026-10-19 23:29:27 -0400

      Commit message:


	  
		
 no longer using methods-internal class
 
    
  
    

      Package: igblastr

      Commit: 0b6fab6efd2a12a47d93c25b47514454c848fb44

      Author:  J. Kim <juyeongkim@users.noreply.github.com> 

      Date: 2026-09-18 13:27:26 -0700

      Commit message:


	  
		
 Build and push docker image for igblastr (#12)

* Build and push docker image for igblastr

* Ignore `RELEASE_3_22` branch 
    
  
    

      Package: sesame

      Commit: c304730fac5a4e97e8e15028f94c6fad56b435ef

      Author:  Wanding Zhou <zhouw3@email.chop.edu> 

      Date: 2026-10-19 16:50:17 -0400

      Commit message:


	  
		
 1.31.7: heatmap annotation tracks (zwdzwd/sesame#220), follow-up fixes

#220 (Pancreas-Pratik) adds CpG-context and Ensembl Regulatory Build tracks
under the visualizeRegion() heatmap, built on first use and cached in
BiocFileCache; biomaRt is in Suggests and needed only for the regulatory
track. On top of the merge:

- @param for show.cgi, show.regulatory, show.beta.legend and
  show.annotation.legend, which R CMD check flagged as undocumented.
- NAMESPACE regenerated by roxygen; imports and exports are unchanged.
- A plain visualizeRegion() call is silent again: it no longer prints
  "Heatmap annotations not requested."
- sesameAnno_buildHeatmapAnnotations() checks for biomaRt before reading
  the manifest, so a missing package fails before any download.
- The regulatory legend title is "Ensembl Regulatory Build Feature" in
  every layout; the beta legend label takes sample.name.fontsize instead
  of an empty argument.

R CMD check: 0 errors, 0 warnings (R 4.6.0, sesameData 1.31.1).
 
    
  
    

      Package: sesame

      Commit: 4109d7d99b167166552359313c46adeed4c15559

      Author:  Wanding Zhou - Bioinformatics <zhouwanding@gmail.com> 

      Date: 2026-10-19 16:21:20 -0400

      Commit message:


	  
		
 Merge pull request #220 from Pancreas-Pratik/devel

Add heatmap annotations to visualizeRegion 
    
  
    

      Package: sesame

      Commit: 522b2e9ba7538a63310eb93c77c3cce5d0b6c385

      Author:  Pratik Mehta <pratikmehta00@gmail.com> 

      Date: 2026-09-23 15:08:28 -0400

      Commit message:


	  
		
 Address review comments: add CpG and Ensembl regulatory heatmap annotations
 
    
  
    

      Package: sesame

      Commit: 57926125eada5b3a774742008532e6d511051212

      Author:  Pratik Mehta <pratikmehta00@gmail.com> 

      Date: 2026-09-20 10:27:18 -0400

      Commit message:


	  
		
 Add heatmap annotations to visualizeRegion
 
    
  
    

      Package: BreastSubtypeR

      Commit: 67d982cb324ec376ea599929eb41837a50fd09b3

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 14:43:28 +0200

      Commit message:


	  
		
 Merge pull request #174 from JohanHartmanGroupBioteam/fix/prepublication-review-1.5.8

Correct clean-session Shiny behavior and clarify unpublished 1.5.8 maintenance findings 
    
  
    

      Package: BreastSubtypeR

      Commit: 840b190524d989a7f9c2aaa7cf43888196ec5822

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 11:11:44 +0200

      Commit message:


	  
		
 Clarify maintenance provenance and remove unused plotting dependency
 
    
  
    

      Package: BreastSubtypeR

      Commit: 0ec9682928dc81edb090e624cdc8fc50f0afc5b8

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 10:58:31 +0200

      Commit message:


	  
		
 Represent undefined additional ROR-PC categories as missing values
 
    
  
    

      Package: BreastSubtypeR

      Commit: 647e5c9f5b8d9f779e27baddb274fc93e14a8b75

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 10:56:00 +0200

      Commit message:


	  
		
 Fix Shiny namespace lookup and empty silent-error reporting
 
    
  
    

      Package: BreastSubtypeR

      Commit: 0921e85b2d7eeed72b4679df43fc5dce379c5087

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 07:35:15 +0200

      Commit message:


	  
		
 Merge pull request #173 from JohanHartmanGroupBioteam/maintenance/1.5.8-candidate

Prepare provisional 1.5.8 maintenance candidate and document ROR limitations 
    
  
    

      Package: BreastSubtypeR

      Commit: 107d0388ff2b596b2fedb18dcc5421f09b5e287d

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 06:45:23 +0200

      Commit message:


	  
		
 Prepare provisional 1.5.8 candidate with ROR interpretation and boundary disclosures
 
    
  
    

      Package: BreastSubtypeR

      Commit: aea84bd07b126c122b7445d34895c7a43c0ef000

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 05:43:52 +0200

      Commit message:


	  
		
 Merge pull request #171 from JohanHartmanGroupBioteam/ci/bioccheck-account-checks

Stabilize BiocCheck CI by separating maintainer account checks 
    
  
    

      Package: BreastSubtypeR

      Commit: d4198abc26711036ee77f36f80a4a2e85d1f9924

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 05:18:04 +0200

      Commit message:


	  
		
 Stabilize BiocCheck CI by separating maintainer account checks
 
    
  
    

      Package: BreastSubtypeR

      Commit: b34d561fda860d6b2b1e2d1bf0e7fd3196846106

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

      Date: 2026-10-19 05:13:48 +0200

      Commit message:


	  
		
 Merge pull request #170 from JohanHartmanGroupBioteam/docs/readme-shiny-screenshot

Synchronize README screenshot and refine publication links and logo 
    
  
    

      Package: BreastSubtypeR

      Commit: cb8123928f133393889e9e302eaa8a8d03a24227

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 04:46:21 +0200

      Commit message:


	  
		
 Increase README logo height to 120 pixels
 
    
  
    

      Package: BreastSubtypeR

      Commit: 856f0e603cc1cd4b13e7b140a8ad29de88b4bfce

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 04:43:53 +0200

      Commit message:


	  
		
 Link Editor's Choice references to the BreastSubtypeR entry
 
    
  
    

      Package: BreastSubtypeR

      Commit: 4cf3fd342d6d9026ee3cc4fa749e7528fd936f33

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 04:35:58 +0200

      Commit message:


	  
		
 Synchronize README Shiny screenshot after visualization refresh
 
    
  
    

      Package: BreastSubtypeR

      Commit: 7a1085ca489663118cbb50505770e46056cff010

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 04:25:53 +0200

      Commit message:


	  
		
 Merge pull request #169 from JohanHartmanGroupBioteam/maintenance/visualization-refresh

Refresh approved visualization styling with exact scientific preservation 
    
  
    

      Package: BreastSubtypeR

      Commit: 06ab3d61496a49fbf301c19d40fb9dc1d7729313

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 00:39:54 +0200

      Commit message:


	  
		
 Refresh approved visualization styling without changing scientific results
 
    
  
    

      Package: BreastSubtypeR

      Commit: de820e700d3de2290d8ddf6c4c1d2a275a32c16a

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

      Date: 2026-10-18 23:35:41 +0200

      Commit message:


	  
		
 Merge pull request #165 from JohanHartmanGroupBioteam/docs/documentation-refresh-oslo-20261018

docs: refresh documentation and correct OSLO example provenance 
    
  
    

      Package: BreastSubtypeR

      Commit: 7bc7e954d017ac340e1c0f72408f3e5c2af713a9

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-18 23:09:20 +0200

      Commit message:


	  
		
 docs: align Shiny workflow and add verified example screenshot
 
    
  
    

      Package: BreastSubtypeR

      Commit: 97dbcbc719e59eabb0c9880fe474df9dd697b57a

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-18 23:09:20 +0200

      Commit message:


	  
		
 Merge main into documentation refresh
 
    
  
    

      Package: BreastSubtypeR

      Commit: 38d4f5811c0793f64b53de2ed4b8ae3ceacae07c

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-18 22:33:19 +0200

      Commit message:


	  
		
 Merge pull request #167: clarify the local Shiny workflow

Clarify the local Shiny workflow and compact its presentation. 
    
  
    

      Package: BreastSubtypeR

      Commit: f6da04e571907207b6a3dc9c0448e82937fa4efe

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-18 22:03:59 +0200

      Commit message:


	  
		
 test: cover Shiny workflow and pending AUTO presentation
 
    
  
    

      Package: BreastSubtypeR

      Commit: 22a79b3e4b4ed143349496d8193e0a56c50fcc60

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-18 22:03:44 +0200

      Commit message:


	  
		
 ui: clarify AUTO state and Shiny presentation
 
    
  
    

      Package: BreastSubtypeR

      Commit: 047970d859fac312afd0f3b8465d2667d936859b

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-18 17:32:44 +0200

      Commit message:


	  
		
 docs: label release and devel build badges
 
    
  
    

      Package: BreastSubtypeR

      Commit: 463e77b1c84705242b2f91758aba73366beb435e

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-18 16:53:58 +0200

      Commit message:


	  
		
 docs: correct OSLO example expression provenance
 
    
  
    

      Package: BreastSubtypeR

      Commit: 8951b7a1fbc8e21b9087e826c84b4bbee01ab323

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-18 16:53:50 +0200

      Commit message:


	  
		
 docs: refresh README and publication recognition
 
    
  
    

      Package: BreastSubtypeR

      Commit: b90c15f9b0869e71b2c0cbfaafcb71fa2b6a3aba

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-18 16:53:43 +0200

      Commit message:


	  
		
 docs: synchronize workflow vignette
 
    
  
    

      Package: BreastSubtypeR

      Commit: 669bcb93f97f491ab58fca7064129eb3d26a26d5

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-18 16:53:35 +0200

      Commit message:


	  
		
 docs: clarify method interpretation and reference help
 
    
  
  


</div>

</div>