Sync selected devel changes into Bioconductor devel
 

 Add GitHub links to DESCRIPTION
 

 Bump version
 

 Minor modifications of plotting function parameters and vignette instructions in response to peer review. Need to repair tests.
 

 update benchmarkinsight3 object and analysis
 

 updated V01
 

 Update v00_overview_trio.Rmd
 

 add benchmark study script
 

 update script
 

 Merge pull request #93 from rformassspectrometry/jomain

Add copy-on-replace functionality 

 refactor: implement functionality to enable copying Python MS data
 

 docs: build pkgdown site and update README (v1.27.7)
 

 add installation procedure on vignette
 

 Bump version: 3.19.11 → 3.99.0
 

 Use string args for %:::% to avoid global variable NOTE

Bare symbol SBMLR in SBMLR %:::% readSBML triggers R CMD check
"no visible binding" note. Use string form instead.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
 

 Add SBMLR to Suggests to fix undeclared import warning

R CMD check warns about requireNamespace and %:::% usage of SBMLR
when it's not listed in DESCRIPTION.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
 

 docs rebuild
 

 Merge branch 'master' of github.com:saezlab/OmnipathR into devel
 

 Merge branch 'devel'
 

 Merge branch 'devel'
 

 Update vignette
 

 Update vignette to fit pkgdown requirements
 

 epiRomics 0.99.5: add getters/setters for epiRomicsS4 S4 slots

Implement public getter and setter methods for all slots of the
epiRomicsS4 class so users can access object contents without
obj@slot or methods::slot(obj, "slot").

New accessor API (10 methods):

- annotations(x) / annotations(x) <- value   (new generic)
- meta(x)        / meta(x) <- value          (new generic)
- txdb(x)        / txdb(x) <- value          (new generic)
- organism(obj)  / organism(obj) <- value    (extends BiocGenerics)
- genome(x)      / genome(x) <- value        (extends GenomeInfoDb)

Every setter invokes validObject() so invalid assignments (for
example an empty-string genome) fail fast with a clear error.

Documentation:
- Each accessor has its own Rd page with runnable examples
  (no dontrun / donttest).
- New ?epiRomicsS4-accessors overview topic summarises every
  getter/setter pair in one table.
- ?epiRomicsS4-class cross-references each accessor via @seealso
  and documents each slot with an explicit "Access via ..." note.
- Roxygen prose across helper files that referred to
  database@meta or @annotations now references meta() /
  annotations() instead.
- Every roxygen @examples block that used methods::slot() now
  uses the matching getter.

Vignettes:
- getting-started-with-epiRomics.Rmd: 7 methods::slot() calls
  replaced with annotations(); explanatory paragraph added
  before first use.
- articles/full-analysis-with-epiRomics.Rmd: 22 methods::slot()
  calls replaced with annotations(); same explanatory paragraph
  added.
- Shipped tarball contains 0 methods::slot() references in any
  user-facing vignette, man page, or example.

Deprecation helper:
- .warn_renamed() in R/zzz-deprecated.R emits a one-time session
  tip pointing users at the new accessor API the first time any
  deprecated epiRomics_* alias fires.
- Fixed test-deprecated-aliases.R (was asserting against the
  pre-0.99.4 .Deprecated() behaviour and therefore failed under
  the message()-based rename helper introduced in 0.99.4). The
  harness now asserts the message() condition and resets
  .warn_renamed() state at the top of the block. No package
  code was changed by this test fix.

Tests:
- New tests/testthat/test-accessors.R with 20 test_that blocks
  / 50 assertions covering: getters on hg38 + mm10 fixtures,
  getters on fresh empty objects, setter round-trip, setter
  object class preservation, validObject-triggered errors on
  empty genome / empty txdb, and existsMethod / isGeneric checks
  for the extended BiocGenerics / GenomeInfoDb generics.
- Full suite: 261 tests / 607 assertions passing, 0 failures,
  0 errors, 7 skips (Windows-only + optional non-model-organism
  TxDb packages).

Quality gates:
- R CMD check --as-cran: 0 ERRORs, 0 WARNINGs, 1 NOTE
  ("New submission" — expected).
- BiocCheck: 0 ERRORs, 0 WARNINGs, 9 NOTES — all pre-existing
  and stylistic, none introduced by this change.
- Both vignettes rebuild cleanly with the new accessor API.

Internal @slot usage inside non-exported helpers is unchanged;
the sweep replaced @ access only in user-facing surfaces
(vignettes, examples, roxygen prose).

Backward compatibility: slot names, slot types, class validity,
and the constructor signature are unchanged, so existing user
objects continue to work without modification.
 

 Fixing unit tests
 

 Allow custom seed in sigmoidal fit.
 

 Migrate Author/Maintainer fields to Authors@R format in DESCRIPTION.
 

 updt vignette
 

 version bump
 

 Merge pull request #29 from NICHD-BSPC/v0.99.11

V0.99.11

(Hopefully) some final touches before Bioc release:

feature: Pattern analysis 'cluster membership' table allows gene selection and addition to scratchpad.
bugfix: PCA plot race conditions when checking for rld slot with a pre-loaded dataset.
feature: landing page now shows clickable project and analysis tables 

 updt intro tour for new proj/analysis tbls
 

 sort proj df
 

 handle sorted proj/analysis tbl
 

 add global and analysis tbls
 

 fix indent
 

 use file.path not paste fr paths
 

 mv current obj loc in ui
 

 add modal for getting project info
 

 add new test for tbl gene selection
 

 return gene sel frm pattern plt; add to scratchpad
 

 fix pca-plot bug for race conditions
 

 Bump version from 1.13.3 to 1.13.4 

 Revert "feat(chemoproteomics): Integrate sample size calculation for dose response experiments (#181)"

This reverts commit 7261a055f8bc1f41a1790980106730ea0021eaa4.
 

 feat(visualization-code): Add event handler for edge deletion (#186) 

 Merge the feat(statistical inference): dynamic update of the metadata table for dose response curves (#182) 

 Version bump
 

 Drop Windows
 

 Fix loess span
 

 Update server links in README
 

 Add workflow badges
 

 Add pkgdown configuration
 

 Add GitHub Actions via biocthis
 

 http -> https in quantitativeproteomics URL 

 fix: harden unichem source parsing
 

 deprecate
user requested
 

 Bump version
 

 Add Bioconductor build status, availability, and download badges to README
 

 chore: version bump
 

 fix: inconsistent vignette title
 

 chore: ignore quarto temp files
 

 fix: import methods and memoise
 

 Update perform_non_parametric() tests because of changes in stats::wilcox.test() (#8)

* Update tests to not consider changing behavior of wilcox.test in R-devel when exact = TRUE

Do exact = FALSE for testing basic functionality of 
perform_non_parametric()after more changes to stats::wilcox.test in R 
4.6 devel. We are still testing with one test that alternative 
confidence levels can be reported.

* Bump version and reset cache [nocache] 

 version bump for vignette
 

 fix(constructors): initialize chr tibble with typed columns

Initialize chr as tibble(rt = numeric(), intensity = numeric())
instead of tibble() so that column types are defined even when
no matching scans are found, preventing downstream type errors.

Bump version to 0.99.21.
 

 fix: add missing peak_density slot doc to resolve codoc mismatch

Add the @slot peak_density roxygen entry to lcmsPlotDataContainer so the
generated Rd file matches the S4 class definition. This resolves the R CMD
check WARNING about a code/documentation mismatch for the slot list.
 

 feat: add lp_peak_density and related improvements (#29)

Add lp_peak_density() for peak density plots mirroring xcms::plotChromPeakDensity():
sample indices on the y-axis within the kernel density range, coloured
peak points per sample, density line overlay, and optional feature-group
rectangles simulated via the density-descent algorithm. Features are
inherited from lp_chromatogram() when not supplied explicitly. Supports
rt_unit, bw, min_fraction, min_samples, sample_groups, max_features, and
auto-faceting for multiple m/z windows.

Fix highlight_peaks_mode = "rectangle" and "point" in lp_chromatogram():
geoms now set inherit.aes = FALSE to avoid evaluating the global
x = rt_plot aesthetic against detected_peaks (object 'rt_plot' not found),
and RT values are scaled correctly when rt_unit = "minute".

Add line_type to lp_chromatogram(), x_dim/y_dim/fill_scale to
lp_intensity_map(), and expand the peak density vignette section.

Bump version to 0.99.20.
 

 Alignment wrong gene names
 

 Merge branch 'EnesSefaAyar-master'
 

 Merge branch 'master' into master 

 Merge pull request #38 from leopoldguyot/master

Add wu2026 dataset 

 add metadata + update wu2026 script
 

 Merge branch 'UCLouvain-CBIO:master' into master
 

 update metadata for krull2024
 

 Update make-data_krull2024.R

colData fixed, protein assay sample names did not match before 

 Bump version
 

 Fixing original class detection, metadata removal, and adding a checkpoint in loadGSVAranks
 

 Added saveGSVAranks() and loadGSVAranks()
 

 Increment version number to 0.99.8
 

 Add C++ compact seqqual decode helpers with round-trip tests
 

 changed logo
 

 add installation instruction on vignette
 

 Lower R version requirement to >= 4.4.0, bump version to 0.99.10
 

 chore: bump version number
 

 fix: adapt to new ggplot2 interface
 

 Merge pull request #259 from leopoldguyot/replaceColnames

replaceColnames function 

 add dev note
 

 use org notes
 

 create replaceColnames documentation
 

 add note describing the fix
 

 rebuild documentation
 

 merge all conflicts
 

 add link to contrib and CoC
 

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

 add verbose argument to .splitSE
 

 fix: typo in pkgdown workflow
 

 Version bumped
 

 docs: added contribution section in README
 

 fix: 'healed' some merging scars
 

 test: fixed some unit tests
 

 .formatColData(): simplify

remove quantCols argument since it is not used,
and the rownames should be derived from colData$quantCols and colData$runCol
 

 .formatColData: clarify rownames logic
 

 udate news
 

 fix: fixed fnames when reading QFeatures and added unit tests
 

 [FIX] - joinAssays allows for fcol and automatically generates the assayLinks
 

 fix conflicts
 

 fix conflicts
 

 fix conflicts
 

 new createPrecursorId function
 

 description_updated
 

 description file updated
 

 Merge pull request #5 from CyanolabFreiburg/main

Merge pull request #15 from lyoussar/main 

 Merge pull request #4 from CyanolabFreiburg/main

merging 

 Merge pull request #12 from lyoussar/main

Merge pull request #3 from CyanolabFreiburg/main 

 Merge pull request #11 from lyoussar/main

merging 

 Merge pull request #10 from lyoussar/master

Master 

 Merge pull request #9 from lyoussar/master

update_version 

 Shortened chr4_subset_a_thal to 1 MB
 

 Removed annotateGRanges function as it was not being used anywhere
 

 fix: support alternate column names for chromosome fields in pairs parsing
 

 fix: add distance parameter to join_overlap_left functions
 

 bump to 1.13.1
 

 Merge pull request #117 from gdrplatform/GDR-3351

chore: migrate from qs to qs2 package (GDR-3351) 

 chore: update Dockerfile to install qs2 instead of qs (GDR-3351)
 

 chore: migrate from qs to qs2 package (GDR-3351)
 

 docs: fix truncated add_intermediate_data title, reoxygenate (GDR-3351)
 

 chore: address reviewer feedback for GDR-3351 qs2 migration

- pipeline_helpers.R: update save_intermediate_data and
  read_intermediate_data docstrings from qs to qs2
- utils.R: update add_intermediate_data title from qs to qs2
 

 chore: migrate from qs to qs2 package (GDR-3351)
 

 chore: merge origin/main and resolve conflicts
 

 docs: use explicit .qs2 filenames in get_synthetic_data examples (GDR-3351)
 

 docs: regenerate man pages after GDR-3351 qs2 migration updates
 

 fix: index list.files result for Ligand pattern in test-merge_SE (GDR-3351)
 

 Merge pull request #74 from gdrplatform/GDR-3351

chore: migrate test data files from qs to qs2 format (GDR-3351) 

 docs: regenerate man pages after GDR-3351 qs2 migration updates
 

 fix: handle qs2 extension in get_test_dataset_paths (GDR-3351)
 

 bump
 

 pathProbCBN is optimized
 

 Merge pull request #5 from rockwillck/devel

Devel 

 Merge pull request #3 from rockwillck/devel

Devel 

 Merge pull request #2 from rockwillck/devel

fix title 

 edgeR 4.9.8
- Minor fix to DGEListFromTximeta()
 

 fix: use explicit $ column references for data.table dims to fix ggplot2 v4 S7 compatibility

The previous fix (e5ed286) changed dims[axis == ...] to dims[dims$axis == ...]
but left bare 'name', 'axis', and 'desc' column references in data.table
expressions. With ggplot2 v4's S7 system, these symbols resolve to S7 objects
instead of data.table column names, causing 'object name not found' errors.

Changed all occurrences of:
  dims[, name] -> dims$name
  dims[, axis] -> dims$axis
  dims[..., name] -> dims$name[...]
  thisDim[, desc] -> thisDim$desc
  thisDim[, name] -> thisDim$name

Fixes #113, related to #108, #109
 

 chore: bump version to 2.23.4 for Bioconductor build
 

 Fixing unit test
 

 And note about read_ / write_ API design
 

 some tweaks on top of Bea's edits
 

 add extra intro and related methods
 

 add example prepare_exons() and shorten into aux func
 

 bump up r version and splicelogic version
 

 another note on the Jones data
 

 add globalVars for non-standar evals Note
 

 Fix in block processing
 

 windows unsupported
 

 epiRomics 0.99.3

README and installation
- Bioconductor install first; GitHub moved under a "not recommended"
  banner and switched to BiocManager::install().
- Replaced broken top-level doc/ links with browseVignettes(),
  pkgdown site, and Bioconductor landing page.
- Aligned README R-version minimum to DESCRIPTION (R >= 4.5.0).

DESCRIPTION and NAMESPACE
- TxDb.*, org.*.db, BiocFileCache, parallel moved to Suggests with
  requireNamespace() guards at every call site.
- Full @importFrom audit across every R file; NAMESPACE regenerated.

API rename with deprecation shim
- All exported functions renamed to verb-first, no package prefix
  (build_database, plot_tracks, find_putative_enhancers, ...).
- 20 .Deprecated() aliases ship for one release cycle so existing
  users are not broken.
- Parameter renames to drop the epiRomics_ prefix throughout.

Genome handling
- genome is now a free-form string validated against the user-supplied
  TxDb via validate_genome_matches_txdb(). No hardcoded whitelist.
- Any organism with a TxDb.* and org.*.db package is supported.

Examples and vignettes
- ~0.8 MB toy dataset shipped at inst/extdata/toy/ (hg38 chr11 INS
  locus) so the Getting Started vignette runs end-to-end against
  bundled data. Full walkthrough moved to vignettes/articles/ as a
  pkgdown-only article (not built during R CMD check / install).
- inst/extdata/toy/toy_database.rds (28 KB) ships a pre-built
  epiRomicsS4 subset to chr11:1.7M-2.5M; the vignette shows
  build_database() as an eval=FALSE demonstration chunk and loads
  the pre-built object via readRDS() so R CMD build runs offline.
- Synthetic-data helpers power every man-page @example; no
  \donttest blocks remain except the network-only cache_data() call.
- Both vignettes open with visible setup, interleave prose before and
  after every code chunk, and print data-frame structure.
- Getting-started intro rewritten to frame multi-omics enhancer scope
  and contrast epiRomics against Gviz, trackViewer, Signac.
- vignettes/references.bib holds package citations.

Tests
- Gene-mode tests in test-plot_quick_view_synthetic.R hard-assert
  requireNamespace() for org.Hs.eg.db and
  TxDb.Hsapiens.UCSC.hg38.knownGene. Package-level deps stay in
  Suggests.
- Regression tests updated for the toy chr11 window and
  pkgdown-only articles layout.

Housekeeping
- Non-standard top-level doc/ directory removed.
- Eliminated paste()/paste0() in condition signals, removed <<-,
  and trimmed residual >80-char lines.
- pkgdown site restored: _pkgdown.yml plus dedicated pkgdown
  workflow; article pattern matches vignettes/articles/.
- BiocCheck workflow runs the Bioconductor SPB sequence under
  bioconductor/bioconductor_docker:devel.
- .gitignore deduped; vignette artifact globs broadened.

Version bumped to 0.99.3.
 

 Update DESCRIPTION

R 4.5.0 dependency - R check and unit tests don't work on github actions with 4.6.0 yet
 

 Revert sonnia to dontrun
 

 adjust huggModel for basilisk helper
 

 TCR_summary to S4
 

 dontrun to donttest
 

 version bump for Bioc 3.23
 

 corrected typos
 

 Fixed unit test
 

 Lower R dependency to >= 4.5.0 to fix Bioconductor build ERROR, bump to 0.99.9
 

 Fixed a bug when ranks are stored as doubles
 

 feat(diann): Add parameter to handle labeling for protein turnover (#128) 

 Update README.md 

 Patch: Shift to mia version of scuttle function to aggregate rows by group (#820)

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

 Bumped version
 

 Add tests for SingleCellExperiment object, minor fixes
 

 git commit -m "Merge bioc/devel and bump version to 6.35.1"
 

 Merge pull request #378 from mixOmicsTeam/issue-374

PR addressing Issue #374 

 fix: remove devtools::install_github from vignette to fix Bioconductor
build error
 

 docs: update README-WhatsNew with aes_string fix note
 

 fix(plotMarkers): replace aes_string with aes
 

 style: Fix trailing space on roxygen import
 

 Fix(NAMESPACE): Add rlang .data import
 

 fix: add rlang to Imports in DESCRIPTION
 

 update examples to reflect how to plot specific studies with plotIndiv mint objects
 

 fix bug in plotIndiv mint models
 

 fixed plot subtitles for rep.space = multi with chosen study
 

 patch fix for plotIndiv mint example running on cran check
 

 install badger package in github action not in markdown
 

 update mixOmics version to reflect release version on bioconductor 3.21
 

 S4Vectors 0.49.2: Try to address error reported by ASAN + UBSAN on Mac

Error is quite cryptic:

  map_ranges_to_runs.c:408:16: runtime error: load of misaligned address
  0x000000000001 for type 'const int *', which requires 4 byte alignment

and I'm not in a position to try to reproduce it at the moment anyways
so this is just a shot in the dark.
 

 limpa 1.3.12
- EListFromLongFormatFile() uses arrow package instead of nanoparquet
 

 Doc bug fix
 

 Yet more updates to IRLBA-related libraries.
 

 Increment version number to 0.99.7
 

 Restrict expression barplot fill_by to sample-level bars
 

 BiocGenerics 0.57.1: Fix updateObject() on numeric_version objects

See https://github.com/Bioconductor/BiocGenerics/issues/23
 

 chore: rename plot title
 

 Bump version from 1.9.2 to 1.9.3 

 added anomaly model to MSstatsClean call (#14)

 

 fix(pkgdown): Fix url to the MSstatsPTM github page (#128)