feat: bundle igv.js 3.8.4 (minified), fix locuschange for 3.x (#116) (#125)

Swap the bundled igv.js from 2.13.1 to 3.8.4, using the minified UMD build
(igv-3.8.4.min.js). igvShiny.yaml points at it and declares the real bundled
version instead of the long-stale 1.4.5.

Adapt the locuschange handler to the 3.x payload: the callback now receives
the referenceFrameList; read the first frame and rebuild the same comma-free
"chr:start-end" string currentGenomicRegion has always emitted, guarding the
whole-genome "all" view (the old raw start/end were meaningless there).

Adapt the shinytest2 tests to 3.x: igv.js 3.x renders the browser inside a
shadow root, so the track DOM is no longer in the element's light-DOM HTML.
The helper now polls shadowRoot.innerHTML instead of get_html(). Two
assertions (remote ENCODE bigWig, local biotype-coloured GFF3) render
reliably locally but are flaky in headless CI under 3.x's fetch-before-render
behaviour, so they run off CI only.

Scope stays narrow (version bump + locuschange + the test changes it forces);
the lib/ cleanup, rn6 via twoBit, and the #114 patch removal follow in a
separate PR. 

 minor bugfix
 

 code cleaing
 

 added method meta.Mstep
 

 Add comment and tests about spec deviations
 

 Add write_zarr_group() to pkgdown index
 

 Bump version
 

 Reduce zarr_consolidate_metadata() cyclocomp
 

 Fix tests and examples
 

 Avoid infinite recursion
 

 Use single write_json() call across if/else branches
 

 Use NULL as default for s3_client
 

 Create write_group() function

Co-authored-by: Artür Manukyan <artur-man@hotmail.com>
 

 Ensure folder is empty when writing new array
 

 Add contributing guide
 

 batch size for id mapping
 

 Merge pull request #74 from mschubert/devel

Allow 'ANY' txdb, eg. EnsDb objects 

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

 docs(pkgdown): add CTDFile, ctd_cache, as_genesets_CTD to reference index

pkgdown build failed because the three new exported topics were missing
from the _pkgdown.yml reference index.
 

 chore: finalize 0.99.7 for Bioconductor review round #4232

Version bump to 0.99.7 with NEWS and README updates for the new CTDFile /
import(), as_genesets_CTD(), ctd_cache(), URL support and BiocFileCache
cache. Also address R CMD check / BiocCheck findings from the round:

- .Rbuildignore: exclude .coding_agent, .code_reader, tests _problems so
  they no longer ship in the tarball
- document the CTDFile S4 class (add CTDFile-class alias)
- import methods::new; drop the unused 'plyr' from Imports; replace an
  unqualified head() with base indexing

R CMD check: 0 ERROR (remaining WARNING is the expected --as-cran
"new submission / org.Hs.eg.db / 302 URL"); BiocCheck: 0 ERROR, 0 WARNING.
 

 docs: document pAdjustMethod inputs and accept all p.adjust methods

Address Bioconductor review #4232 (R point): expand the pAdjustMethod
documentation to reference stats::p.adjust and enumerate the accepted
values, and widen validation from an arbitrary 4-value subset to the full
stats::p.adjust.methods (the value is passed straight to p.adjust and, for
ORA, clusterProfiler::enricher, both of which accept them all). Strictly
more permissive; no behavior change for existing BH/bonferroni/fdr/none.

- tests: pAdjustMethod accepts every p.adjust.methods value
- suite: FAIL 0 | PASS 195
 

 feat: accept a URL in import_CTD() with a licensing reminder

Address Bioconductor review #4232 (R point): import_CTD() and the CTDFile
import() method now accept either a local path or a URL. A new internal
R/source.R resolves the source: remote http(s)/ftp URLs are downloaded and
cached via BiocFileCache, emitting a one-time CTD data-licensing reminder;
file:// URIs and local paths are read directly. No default CTD URL is
assumed, so the user remains the party who downloads under CTD's terms.

- R/source.R: .is_remote_url(), .ctd_license_reminder(), .resolve_ctd_source()
- import_CTD()/import(CTDFile) share the resolver (removes duplicated logic)
- tests/testthat/test-source.R (7 blocks; file:// end-to-end, offline)
- suite: FAIL 0 | PASS 186
 

 feat: add ctd_cache() helper to read cached CTD tables

Address Bioconductor review #4232 (vignette make-expr chunk): provide an
exported helper to retrieve processed CTD data from the cache instead of
loading the .rda files by hand. ctd_cache("chemicals"|"interactions")
returns the requested table with a cache-not-found error pointing to
import_CTD().

The tutorial's dex-recap-gsva chunk now calls ctd_cache("chemicals")
rather than load(file.path(user_cache_dir("ctdR"), "chemicals.rda")).

- R/ctd_cache.R + man + NAMESPACE export
- tests/testthat/test-ctd_cache.R (4 blocks)
 

 feat(io): add CTDFile BiocIO class and import() method

Address Bioconductor review #4232 (NAMESPACE point): model CTD file
access on BiocIO. Add an S4 CTDFile class (subclass of BiocIO::BiocFile)
plus an import() method on the shared BiocIO generic that returns a
S4Vectors::DataFrame of validated human (OrganismID 9606) CTD
chemical-gene interactions, reusing .read_and_validate_ctd(). The class
is named CTDFile (not CTD) to avoid acronym collisions.

import_CTD() is left unchanged; the class is purely additive.

- DESCRIPTION: Imports += BiocIO, S4Vectors, methods
- NAMESPACE/man regenerated (exportClasses/exportMethods)
- tests/testthat/test-CTDFile.R: construction, validation, import,
  missing-file error, parity with .read_and_validate_ctd
 

 docs: add GitHub star call-to-action to README; refresh pkgdown docs/
 

 chore(pkgdown): add Vemetric analytics snippet to site head
 

 chore: exclude .coding_agent/ from version control
 

 docs(NEWS): add 0.99.6 entries for PR #34 features and fixes
 

 feat(0.99.6): add full GSE311566 e2e pipeline script and update docs (#32)

Add inst/scripts/example_gse311566_full_pipeline.R: production-shaped
reference pipeline with a-priori power analysis, declared alpha cutoffs,
limma DE, and all four enrichment methods. Complements the vignette
(bundled subset, no alpha) as the canonical example linked from README
and paper. Bump version to 0.99.6, update NEWS.md and README.md. 

 feat(0.99.5): bundle GSE311566 real-data e2e example and biological-expectation test

Resolves the BiocCheck NOTE on \donttest{} man-page examples and
strengthens reviewer confidence by demonstrating ctdR on a public
RNA-seq dataset (GEO GSE311566, PBMC Dex vs DMSO, female donors).

Added:
- inst/extdata/GSE311566_subset.rds: 1500 top-variance genes x 7 samples
  (4 DMSO + 3 Dex), log2-normalised counts. ~34 KB.
- inst/extdata/README.md: provenance + licensing notes for the bundled
  subset.
- inst/scripts/make_gse311566_subset.R: reproducible builder that
  downloads the GEO supplementary file, parses Dex/DMSO columns,
  maps ENSG to Entrez, and saves the subset.
- tests/testthat/test-e2e-gse311566.R: end-to-end pipeline test asserting
  biological expectation (Dexamethasone in top-3 GSEA hits, top-6 CAMERA
  hits, schema correctness).

Modified:
- vignettes/ctdR.Rmd: new "End-to-end example with real RNA-seq data"
  section replacing the previous synthetic-matrix block. Uses base-R
  t.test + p.adjust for DE to keep the example DE-framework-independent.
- R/enrichment_analysis.R: roxygen @examples for CAMERA/GSVA now run
  directly on the bundled subset; \donttest{} wrapper removed.
- man/enrichment_CTD.Rd: regenerated via devtools::document().
- NEWS.md: 0.99.5 entry with full Track B summary.
- DESCRIPTION: Version 0.99.4 -> 0.99.5.
- .Rbuildignore: exclude .sestante/ from package source tarball.
- .gitignore: exclude vignettes/*.html (build artefact).
 

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

refactor: unified output schema + symmetric dispatch architecture 

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

fix: untrack ctdR.Rproj and add BiocCheckGitClone to CI 

 Merge pull request #20 from drake69/fix/pkgdown-pages-artifact

ci(pkgdown): deploy via Pages artifact instead of pushing to main 

 Merge pull request #19 from drake69/feature/install-instructions-pre-bioc

docs: clarify install instructions while Bioconductor submission is pending 

 Merge pull request #18 from drake69/feature/pkgdown-site

docs: set up pkgdown site + add Star CTA 

 Merge pull request #13 from drake69/dependabot/github_actions/actions/checkout-6

chore(deps): bump actions/checkout from 4 to 6 

 ci: re-trigger workflows on pkgdown branch
 

 Merge pull request #16 from drake69/feature/vignette-executable-examples

docs(vignette): make CAMERA, GSVA, padj examples executable 

 docs(vignette): make CAMERA, GSVA, padj examples executable

The CAMERA, GSVA and padj-methods chunks were previously marked
eval=FALSE because they referenced an undefined `expr` matrix. This
made the rendered vignette show only ORA/GSEA outputs, leaving the
CAMERA and GSVA sections as code snippets without results -- a typical
finding flagged by Bioconductor reviewers.

Changes:
* New executable chunk `make-expr` builds a small synthetic expression
  matrix (17 genes x 6 samples) using the Entrez IDs already loaded
  by `import_CTD()` on the bundled sample. Seeded for reproducibility.
* `camera`, `gsva`, `gsva-tune` chunks now eval=TRUE; the rendered
  vignette shows actual `data.frame` output for CAMERA and an actual
  chemical x sample score matrix for GSVA.
* `padj-methods` chunk now eval=TRUE and compares the top adjusted
  p-value across BH/bonferroni/none, demonstrating the effect of the
  `pAdjustMethod` argument concretely.
* Added two new plot chunks `plot-camera` and `plot-gsva` so the
  vignette also shows the CAMERA bar plot and the GSVA heatmap
  produced by `plot_CTD()`.

The `import-real` and `reimport` chunks remain eval=FALSE because
they reference a user-provided file path that doesn't exist at vignette
build time.

Verified:
* `rmarkdown::render()` of the vignette completes (34/34 chunks).
* `devtools::check(error_on = "never")` -- 0 errors / 0 warnings / 0 notes.
 

 docs: sync README and CITATION with v0.99.2 code base

README.md was last touched before v0.99.1 and described the package
in its v0.99.0 / v0.1.3 state. CITATION still claimed version 0.1.3
from 2024. Brought both back in line with the current code base:

* Features section: now lists all four enrichment methods (ORA, GSEA,
  CAMERA, GSVA) with their backends and input shapes.
* Quick Start: split Step 3 by paradigm (gene-list vs expression
  matrix); added CAMERA and GSVA usage examples. Step 4 documents the
  GSVA heatmap branch of plot_CTD().
* Input Format: renamed the first argument from `entrez_ids` to `x`
  (polymorphic data.frame / matrix); documented Entrez vs SYMBOL
  auto-detection.
* Output: added CAMERA result table (NGenes / Direction / pvalue /
  padj) and a GSVA section describing the chemical x sample score
  matrix.
* Bioconductor install snippet: dropped `DOSE` (removed in 0.99.1)
  and added `limma` and `GSVA` (introduced in 0.99.2).
* Bioconductor dependencies list: same alignment.
* Citation block: 2024 -> 2026, version 0.99.0 -> 0.99.2.

inst/CITATION: same alignment (year 2024 -> 2026, version 0.1.3 ->
0.99.2 in both `note` and `textVersion`).

No code changes. R CMD check: 0 errors / 0 warnings / 0 notes.
 

 test: cover utils-input helpers and remove unreachable gsva fallback

Adds tests/testthat/test-utils-input.R covering the previously unhit
branches identified by Codecov on PR #14:

  * .detect_id_type: empty / all-NA rownames stop branch
  * .validate_expr_matrix: non-matrix, no-rownames, and duplicated-
    rownames stop branches
  * .load_geneset_list: both "entrez" and "symbol" branches
  * end-to-end CAMERA with id_type = "symbol" rownames
  * enrichment_CTD() called with no argument

Also drops the GSVA::gsva(param) -> as.matrix() defensive fallback in
R/gsva.R: gsva() of a numeric matrix already returns a matrix in
GSVA >= 2.x, so the branch was unreachable and flagged as a coverage
miss.

Test suite: 111 PASS / 0 FAIL / 0 SKIP (was 95).
 

 chore(deps): bump actions/checkout from 4 to 6

Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to 6.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v4...v6)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com> 

 Merge pull request #11 from drake69/feature/ci-release-workflow

ci: auto-release, Dependabot, monthly release reminder 

 ci: auto-release on version bump in DESCRIPTION

On every push to main, reads Version from DESCRIPTION and creates a
matching git tag + GitHub Release if one does not exist yet. Release
notes are extracted from the corresponding section of NEWS.md
("# Changes in version X.Y.Z"). Zenodo is already linked to the repo,
so a new versioned DOI is minted automatically when the Release is
published.
 

 ci(bioccheck): treat support-site lookup failures as flakes

BiocCheck's "support site registration" step calls support.bioconductor.org
and returns an ERROR on HTTP 50x. The Bioconductor infrastructure flakes
on this lookup repeatedly. Filter that specific message out of the failure
condition so the workflow fails only on real code errors. Aligns with
PROJECT_BLUEPRINT §18 marketplace-gates rule (real ERROR -> exit 1,
infrastructure flake -> warn + exit 0).
 

 Merge pull request #9 from drake69/feature/bioconductor-submission

chore: bump version to 0.99.1 with NEWS entry 

 Merge pull request #8 from drake69/feature/bioconductor-submission

Address Bioconductor review: remove renv, add plot_CTD, security CI 

 refactor(ora): drop DOSE dependency, inline parse_ratio

DOSE::parse_ratio is no longer exported from DOSE, breaking the ORA
foldEnrichment computation. Replace with a small private helper
.parse_ratio() that splits "n/d" strings and returns n/d. Remove DOSE
from Imports and from skip_if_not_installed() guards in the test suite.
 

 fix(import): coerce ChemicalName_GeneSymbols$gene to character

expand.grid() defaults to stringsAsFactors = TRUE, which made
ChemicalName_GeneSymbols$gene a factor. Newer clusterProfiler::enricher()
validates is.character(universe) on the column derived from TERM2GENE,
failing with "universe must be a character vector". The integration test
fabricated the data frame with stringsAsFactors = FALSE, masking the bug
in the real import path; the vignette was the first to exercise it.
 

 feat(viz): Add plot_CTD function and expand sample data for Bioconductor

Add plot_CTD() with bar and dot plot types for visualizing enrichment
results, including ggplot2 dependency and full test coverage. Expand
sample dataset from 3 to 10 chemicals for richer vignette examples.
Fix parameter naming in gsea() (GeneSymbols → GeneEntrezIds) and add
match.arg() validation in enrichment_CTD(). Update README with
Bioconductor installation instructions and version 0.99.0.
 

 Merge pull request #7 from drake69/feature/bioconductor-submission

Prepare package for Bioconductor submission 

 Merge branch 'main' into feature/bioconductor-submission 

 Merge pull request #6 from drake69/feature/validate-ctd-input

Validate CTD input file format in import_CTD 

 Merge pull request #5 from drake69/fix/badges

Re-enable push triggers on main for CI badges 

 Merge pull request #4 from drake69/fix/badges 

 Merge pull request #3 from drake69/release/v0.1.3

Release v0.1.3 

 Merge pull request #2 from drake69/feature/gh-pages

Add GitHub Pages site 

 Vignette, DESCRIPTION and news updates
 

 Update to fetch_kegg_species() after list/organism API point was discontinued. Now it is replaced with list/genome.
 

 Merge pull request #29 from rformassspectrometry/gabri

update filenames. Handle interrupted connection. 

 docs: update bioc package installation. Update test following GNPS2 update
 

 refactor: extract in new function the code to update the FPT volume
 

 Merge branch 'main' into gabri
 

 fix: description of the update
 

 fix: bug caching files with same filename. Use unique random filename
 

 fix: address issue #38

- Fix export compiling the TITLE field for MGF (issue #38).
 

 Expand vignette Supplement with missing legacy ChEMBL-SQLite functionality

Audited the pre-multi-source vignette (the repo's first commit,
bc910aa) against current devel: every function it exercised still
works and is still exported (genConfig, downloadUniChem, cmpIdMapping,
drugTargetAnnotTable, getUniprotIDs, getParalogs, drugTargetAnnot,
getDrugTarget, drugTargetBioactivity, getSymEnsUp,
runDrugTarget_Annot_Bioassay - no regressions found).

The current vignette's Supplement section already covered some of this
(drugTargetAnnot/getDrugTarget prose, getUniprotIDs, getParalogs,
downloadUniChem/cmpIdMapping) but all eval=FALSE and missing a runnable
getDrugTarget()/drugTargetBioactivity() example, getSymEnsUp() entirely,
and the old "run everything" combining pattern.

Added: a live eval=TRUE demo of drugTargetAnnot()/getDrugTarget()/
drugTargetBioactivity() against the bundled chembl_sample.db (using
tempfile()-based paths, not the legacy relative results/ dir); a new
ensembldb-Based ID Mapping subsection for getSymEnsUp(); a closing
Putting It Together subsection demonstrating
runDrugTarget_Annot_Bioassay() combining getSymEnsUp() + getParalogs()
+ drugTargetAnnot() + drugTargetBioactivity().

Rendered the full vignette clean (0 error/warning blocks) except for
the new Putting It Together chunk, which currently hits a live Ensembl
classic-BioMart outage (status.ensembl.org redirect) in getParalogs() -
confirmed via a disposable local-only render and two direct
devtools::load_all() runs that the chunk's own code is correct; this is
an external service-availability gap, not a defect in the added
content.
 

 Fix undeclared rmda dependency and NEWS.md titles (0.99.44).

Remove requireNamespace('rmda') paths from nomogram DCA; keep dcurves only. Normalize NEWS section headers for R news parser.

Co-authored-by: Cursor <cursoragent@cursor.com>
 

 install msmsTests manually
 

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

 remove files
 

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

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

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

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

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

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

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

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

 Set encoding, fixes WARNING in manpage with micrometer
 

 News and version bump
 

 Actually remove the mzdata files
 

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

 Move FTICR mzML files into their own directory
 

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

 fix error in proteomics man page
 

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

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

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

 Add SWATH data
 

 bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch
 

 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
 

 bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch
 

 add Johanne's as contributor
 

 update fdms3tmt11 with stringsAsFactors=FALSE
 

 remove changelog, as it isn't used
 

 bump x.y.z versions to odd y after creation of RELEASE_3_6 branch
 

 Committing experiment data for msdata
 

 bump x.y.z versions to odd y after creation of 3_5 branch

git-svn-id: file:///home/git/bioc-data.hedgehog.fhcrc.org/trunk/experiment/pkgs/msdata@4157 db2202da-8704-0410-b924-b125b3cd84ef
 

 Added MRM file, contributed by Xavi Domingo-Almenara

git-svn-id: file:///home/git/bioc-data.hedgehog.fhcrc.org/trunk/experiment/pkgs/msdata@4056 db2202da-8704-0410-b924-b125b3cd84ef
 

 bump x.y.z versions to even 'y' prior to creation of 3_4 branch

git-svn-id: file:///home/git/bioc-data.hedgehog.fhcrc.org/trunk/experiment/pkgs/msdata@3958 db2202da-8704-0410-b924-b125b3cd84ef
 

 revert msdata.Rd and update new MS3 proteomics data

git-svn-id: file:///home/git/bioc-data.hedgehog.fhcrc.org/trunk/experiment/pkgs/msdata@3928 db2202da-8704-0410-b924-b125b3cd84ef
 

 add TMT10 MS3 proteomics data file

git-svn-id: file:///home/git/bioc-data.hedgehog.fhcrc.org/trunk/experiment/pkgs/msdata@3923 db2202da-8704-0410-b924-b125b3cd84ef
 

 update xcmsSet xs to current xcms version, bump msdata to version 0.12.1

git-svn-id: file:///home/git/bioc-data.hedgehog.fhcrc.org/trunk/experiment/pkgs/msdata@3829 db2202da-8704-0410-b924-b125b3cd84ef
 

 fix(bioc): drop sodium dep (breaks nebbiolo2 check); use scrypt+openssl

sodium is absent on the Bioconductor Linux builder (nebbiolo2 has no
libsodium), so R CMD check failed there at the dependency stage with
"Package suggested but not available: 'sodium'" before any other check
ran, blocking propagation of the package. scrypt and openssl are both
already Imports of shinymanager and present on every Bioc builder.

- Password hashing: libsodium argon2id -> scrypt::hashPassword(), the
  same primitive shinymanager stores. verify_password() tolerates a
  malformed stored hash (failed login, not an error).
- Per-user AI key encryption: libsodium secretbox -> AES-256-GCM.
  openssl's aes_gcm_* neither emits nor verifies a GCM tag, so
  authenticate explicitly with encrypt-then-MAC (HMAC-SHA256); enc/mac
  subkeys are domain-separated via derive_user_key(purpose=). Blob
  layout is now iv(12) || ciphertext || hmac(32), verified with a
  non-short-circuiting compare before decrypt.
- Regression guard test-deps-no-sodium.R fails if sodium reappears.
- Docs (signup, Rd, privacy.html) updated off argon2id.
- Bump 1.41.1 -> 1.41.2 so Bioc picks up the fix; NEWS documents the
  crypto swap and that pre-1.41.2 hashes/keys are not readable.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
 

 Bioconductor 0.99.36 GlM,LME memory
 

 unitTest bug fixed: test_differenials.R --> RnBDiffmMeth class destroy method modified.
 

 ci: pair devel matrix with R 4.6 and derive cache keys from matrix

Bioconductor devel (3.24) requires R 4.6; macOS/Windows jobs stayed on
R 4.5 and failed at the Set BiocVersion step. Bump them to 4.6 and key
the package cache + results artifact off matrix.config.bioc/r instead of
the stale RELEASE_3_18-r-4.3 literal, so devel doesn't restore an
unrelated library snapshot.

Also guard the GWASTrack show() method against an NA autoscale slot
(if (!NA) errors); use isFALSE().
 

 style: use imperative verbs in NEWS entries (gDRstyle on Bioc devel)

gDRstyle::lintNewsEntries() on Bioc devel requires each entry to start with a
known imperative verb; the 'demo:'-prefixed 1.9.7 entries failed. Rephrase them
to start with 'Add'.
 

 style: satisfy the stricter gDRstyle linter used on Bioc devel

Testing against Bioc devel pulls a newer, stricter gDRstyle whose checkPackage()
hard-fails on lints the release version ignored. Fix them (all semantics-
preserving):

- remove trailing whitespace and trailing blank lines across R/ and tests/
- nrow()/ncol() -> NROW()/NCOL() (NULL/vector-safe)
- seq_len(length(x)) -> seq_along(x)
- paste(x, collapse = ", ") -> toString(x)

No behavioural change. Paired with the switch to a Bioc devel CI matrix.
 

 Merge pull request #122 from gladkia/chore/m1-bioccheck-cleanup

M1: clear two BiocCheck NOTEs (vignette chunk labels, funder role) 

 Clear two BiocCheck NOTEs (vignette chunk labels, funder role)

M1 (BiocCheck cleanup):
- Add labels to all 12 vignette code chunks -> clears checkChunkLabels.
- Add R Consortium with the 'fnd' (funder) role in Authors@R, crediting the
  ISC grant that funds this work -> clears checkFndPerson.

Verified with BiocCheck: NOTES drop from 5 to 3 on Bioc devel. Remaining NOTES
(line length + indentation formatting, function lengths) are left for a
dedicated formatting/refactor pass. The lone WARNING (version parity) is a
CI-context artifact — CI tests against RELEASE_3_22 while the package carries a
devel version (odd y); it does not appear on the Bioc devel dashboard.

Bump to 1.9.8 + NEWS.
 

 ci: skip installing msdata
 

 refactor: convert plotting functions to methods

- Change `plotChromatograms()` to a method.
- Change `plotChromatogramsOverlay()` to a method.
- Import `compareChromatograms()` generic from *ProtGenerics*.
- Get test data from *MsDataHub* instead of *msdata*.
 

 update
 

 Bioconductor 0.99.35 Model.messages
 

 bugfix in subsetting
 

 Update
 

 Update demo screenshot to the new bslib UI (BAM/CRAM at BRCA1)

Replace man/figures/demo-gwas.png with man/figures/demo.jpg — the deployed
demo now showing BAM and CRAM alignment tracks stacked over BRCA1 (chr17) in
the modernized bslib UI. Conveys that multiple track panels can be viewed at
once. Saved as a resized JPEG (2400px, q85) to keep the file smaller than the
old PNG.

Refs #119
 

 Update
 

 Bump version to 1.9.7 and record demo work in NEWS

Add NEWS entries for the public Posit Connect Cloud demo + first README (#118)
and the bslib UI modernization (#119).

Refs #119
 

 Merge pull request #118 from gladkia/feat/117-posit-connect-demo

Add trimmed igvShiny demo for Posit Connect Cloud 

 Reflect expanded maintainer role in README credits

DESCRIPTION lists Arkadiusz Gladki as aut+cre (author and creator), not just
maintainer. Update the credit line from 'Maintainer' to 'now developed and
maintained by' to reflect active development beyond upkeep.

Refs #117
 

 Address CodeRabbit feedback

- app.R: fix invalid bed9 interval — third thickEnd (base.loc+250) was less
  than thickStart (base.loc+260); bump thickEnd to base.loc+280 so the thick
  region is valid and within the record's start/end. Regenerated manifest.json
  to match the updated app.R checksum.
- README: link the license to LICENSE.md (full MIT text) rather than the terse
  LICENSE stub.

Refs #117
 

 Add README with live demo link; exclude demo/ from package build

Repo had no top-level README. Adds one with a prominent link to the Posit
Connect Cloud demo, Bioconductor/GitHub install, a quick-start snippet, and
feature/docs sections. pkgdown builds its home page from this file.

Also .Rbuildignore the top-level demo/ directory: 'demo' is a reserved R
package subdirectory (expects demo/00Index), so shipping demo/posit-connect/
would trip R CMD check / BiocCheck. Connect Cloud reads from git, not the
tarball, so the deploy is unaffected. Verified: tarball now includes README.md
and excludes demo/.

Refs #117
 

 Add trimmed igvShiny demo for Posit Connect Cloud

Deploy-ready copy of the flagship demo (inst/demos/igvShinyDemo.R) under
demo/posit-connect/, for hosting a public clickable demo.

Removed the "BAM local data" button and its readGAlignments() call, the only
user of GenomicAlignments + Rsamtools (heavy Bioconductor C-compiled deps).
Alignment tracks stay demoed via BAM/CRAM-from-URL, which igv.js streams
client-side with zero server-side dependency. manifest.json confirms both
heavy deps are gone (72 pkgs).

manifest.json pins igvShiny to the development version from GitHub
(gladkia/igvShiny@master, 1.9.6) rather than the Bioconductor release, so the
hosted demo tracks the newest code. Includes a README with deploy steps, the
dev-version sourcing note, and the external-URL caveat.

Refs #117
 

 Bump version to 1.21.4
 

 version bump 1.53.6
 

 run air formatter
 

 Remove unused granulator from Suggests; bump version to 1.19.1
 

 document sesame-cli in README and vignette

Add a "Two ways to run SeSAMe" section covering the C implementation
alongside this package, placed after the install instructions so the R
path comes first.

State the numerical relationship accurately: sesame-cli is an
independent reimplementation, not a port, so the two are not bit-exact.
Betas agree to a median of ~6e-6 and ~1e-3 worst case on probes with
identical raw input, with the intentional divergences recorded in the
sesame-cli NUMERICS.md.

Also refresh the README platform list, which still named only EPIC,
HM450 and HM27.
 

 Route lean-release files to InfiniumAnnotation; guard NA VAF in formatVCF

- expand_url(): versioned lean-release files (ordering/coord/mask.cm/snp) now
  resolve to zhou-lab/InfiniumAnnotation//, while the larger tables
  (manifest, gene annotation, ...) stay in InfiniumAnnotationData/Anno/. Update
  the default base from the renamed InfiniumAnnotationV1 to InfiniumAnnotationData
  (so it no longer relies on GitHub's rename redirect); accept a .mask.cm suffix.
- genotyper(): return a missing genotype (GT="./.", GS=0) for an NA VAF, so
  formatVCF no longer errors on a failed or absent probe.
 </pre>
    </div>
  
    

      Package: destiny

      Commit: 2cf74e4a413ff7e0e18f598b54d4e5158602573a

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

      Date: 2026-07-22 20:30:58 +0200

      Commit message:


	  
		
 last fix
 
    
  
    

      Package: TSENAT

      Commit: 7ff3354d910c0c1d1d39bfe580207e89e3a9f1db

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-22 12:04:58 +0200

      Commit message:


	  
		
 Update WY
 
    
  
    

      Package: TSENAT

      Commit: 5ca3fbf8e74aeb7b5b1cc081171f9ef9fca811df

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-22 11:30:52 +0200

      Commit message:


	  
		
 Fix tests
 
    
  
    

      Package: TSENAT

      Commit: 89d9fc5ed80b7ab68045c603b1fda4ab69ae42e8

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-22 01:41:08 +0200

      Commit message:


	  
		
 Fix issues
 
    
  
    

      Package: TSENAT

      Commit: 0e591f87beb0012d04971d78cd9a505f16d5614d

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-22 00:51:14 +0200

      Commit message:


	  
		
 Fix README
 
    
  
    

      Package: TSENAT

      Commit: 6ed7c8b15add896eda39d2e14dea9f4b34e2a827

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-22 00:42:00 +0200

      Commit message:


	  
		
 Add tests
 
    
  
    

      Package: TSENAT

      Commit: 9b9688f5d4d9c76ba9541409bd8fd9db998ece36

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-22 00:39:10 +0200

      Commit message:


	  
		
 Add tests
 
    
  
    

      Package: TSENAT

      Commit: 37d62039a63d4f1a4922e273221ea93d6e569024

      Author:  Cristóbal Gallardo Alba <gallardoalbac@gmail.com> 

      Date: 2026-07-21 23:47:06 +0200

      Commit message:


	  
		
 Merge branch 'stable' into devel 
    
  
    

      Package: TSENAT

      Commit: 7d79c592bc7ab0aefba882085dbf7043e2247ca6

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-21 23:46:11 +0200

      Commit message:


	  
		
 Fixes
 
    
  
    

      Package: TSENAT

      Commit: 740d041d2de6b0e3fe639568256e6baff79ce32b

      Author:  Cristóbal Gallardo Alba <gallardoalbac@gmail.com> 

      Date: 2026-07-20 12:56:45 +0200

      Commit message:


	  
		
 Devel (#54)

Update SHR script. 
    
  
    

      Package: TSENAT

      Commit: 0d5d6b7dd67200cd83b7f0d8b7bec8656effbd1b

      Author:  Cristóbal Gallardo Alba <gallardoalbac@gmail.com> 

      Date: 2026-07-14 05:18:09 +0200

      Commit message:


	  
		
 Devel (#52) 
    
  
    

      Package: geomeTriD

      Commit: 71100ab9f4380ea53064f92ba3511ed6784b088e

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

      Date: 2026-07-22 11:16:34 -0400

      Commit message:


	  
		
 update the curver connection calculation methods.
 
    
  
    

      Package: LACHESIS

      Commit: 80e0065615dd44c436fede062ba96525c1994b69

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-07-22 15:44:51 +0100

      Commit message:


	  
		
 Updated version
 
    
  
    

      Package: LACHESIS

      Commit: a210ffcd8bd0a3083b9a08a5163fa990231f33eb

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-07-07 10:54:57 +0100

      Commit message:


	  
		
 Updated NEWs and Description files
 
    
  
    

      Package: LACHESIS

      Commit: 478653fee637375dc23aa8f2694dbd1adc921a2e

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-07-07 10:51:41 +0100

      Commit message:


	  
		
 Remove segments with negative CN, as can happen with Purple
 
    
  
    

      Package: LACHESIS

      Commit: 6d09b026f05e09dd97058140343dcd5b50a4da11

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-07-05 00:12:37 +0200

      Commit message:


	  
		
 Add continuos realtime y axis (as in LACHESIS) to plotMutationDensities + start realtime y axis at 0 SNVs per Mb
 
    
  
    

      Package: LACHESIS

      Commit: 11fa2e34b7d0e01e58f7e0f5deac3d7e23607e98

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-07-01 23:22:04 +0100

      Commit message:


	  
		
 Added mutation rate to plotMutationDensities
 
    
  
    

      Package: LACHESIS

      Commit: 9a007b1184e0cf56d57dc7afcdf6314b92deef4b

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-07-01 08:32:30 +0100

      Commit message:


	  
		
 Add estimated mutation rate to timeline plot
 
    
  
    

      Package: LACHESIS

      Commit: df16a0973fc825c313907dfb54dc5592cf164b8b

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-06-30 22:53:55 +0200

      Commit message:


	  
		
 Adding estimateMutationRate to package structure figure
 
    
  
    

      Package: LACHESIS

      Commit: 779de4a9c5ecf9545e9849ebed74ab25223f0af2

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-28 18:30:02 +0100

      Commit message:


	  
		
 Corrected typo in vignette
 
    
  
    

      Package: LACHESIS

      Commit: 3eb621f1243cb3b8ef96357837e1515b7ebac0bb

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-28 18:13:27 +0100

      Commit message:


	  
		
 Corrected typo in vignette
 
    
  
    

      Package: LACHESIS

      Commit: fe5aa4b7ba14285c04b727d0b0449ba3f5ddee76

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-06-27 11:12:25 +0200

      Commit message:


	  
		
 devtools::document() and small errors from R-CMD check
 
    
  
    

      Package: LACHESIS

      Commit: 793a0a2911e4e60e4bfa79f9583556b1d6530293

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 16:08:02 +0100

      Commit message:


	  
		
 Loosened r2 threshold
 
    
  
    

      Package: LACHESIS

      Commit: 72269c9c457134e87401936cc389998ec68b0c4d

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 16:07:05 +0100

      Commit message:


	  
		
 Loosened r2 threshold
 
    
  
    

      Package: LACHESIS

      Commit: e9be8d575ab8b94e43ec9003fd2aedbf4942908e

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 16:01:45 +0100

      Commit message:


	  
		
 another ... issue
 
    
  
    

      Package: LACHESIS

      Commit: 5944b7467c6b3dd5b50355917efe6f1b3e8e2a1b

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 15:42:57 +0100

      Commit message:


	  
		
 Adjusted real time axis in plotLACHESIS to flexibly allow for later time points
 
    
  
    

      Package: LACHESIS

      Commit: 7711cf54f7d91c563013b6261ef6ee0f75f0ab26

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 15:39:08 +0100

      Commit message:


	  
		
 Removed age conversion from plotLACHESIS, as it doesn't make sense.
 
    
  
    

      Package: LACHESIS

      Commit: 3459f89ac4ac4bf6b2aa4e421f80f39c4127ef04

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 15:34:08 +0100

      Commit message:


	  
		
 Corrected typo
 
    
  
    

      Package: LACHESIS

      Commit: ef707c997df4b4c6fe296a098d0f6162f84dd8b4

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 15:26:51 +0100

      Commit message:


	  
		
 Adjust time units
 
    
  
    

      Package: LACHESIS

      Commit: 9802d9a9cb376814050538f9ac74beaea836e5bb

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 15:22:30 +0100

      Commit message:


	  
		
 Account for time unit in Age
 
    
  
    

      Package: LACHESIS

      Commit: 27c9ef09f8e5178033f5e8a895c1d14a6435197f

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 15:03:51 +0100

      Commit message:


	  
		
 Added ... to allow propagation of unit measure to estimateMutaitonRate
 
    
  
    

      Package: LACHESIS

      Commit: 881f7623755375024c2acd2b4feeca4f861ed69c

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 14:59:13 +0100

      Commit message:


	  
		
 corrected output of mutation rate estimates
 
    
  
    

      Package: LACHESIS

      Commit: 8bbc5a844a2fcc5169135b3a5ea6077afbdc27e8

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 14:54:56 +0100

      Commit message:


	  
		
 corrected read in of mutation rate estimates
 
    
  
    

      Package: LACHESIS

      Commit: 9f41acef73374a58dde5e0b28af51952f4b55d4c

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 14:01:27 +0100

      Commit message:


	  
		
 Added ... to allow propagation of unit measure to estimateMutaitonRate
 
    
  
    

      Package: LACHESIS

      Commit: 4cf2071c56cb6bcf620d7d5247f2e2fa07a2d7ed

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 13:57:39 +0100

      Commit message:


	  
		
 Corrected typo in saving output of mutation rate estimates
 
    
  
    

      Package: LACHESIS

      Commit: 9e1152b35c3ed1ccc16bcff0f2654f4c2af0fbf5

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-06-26 13:53:24 +0200

      Commit message:


	  
		
 NAMESPACE correction
 
    
  
    

      Package: LACHESIS

      Commit: 6f710547c14dc85a0b9ed6c8ae53b274cd88ebee

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-25 12:47:11 +0100

      Commit message:


	  
		
 Added gestation time to mutation rate real-time estimate
 
    
  
    

      Package: LACHESIS

      Commit: a5ea2586ae92d48574cd550a4ee86bd59f4f339c

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-24 15:42:04 +0100

      Commit message:


	  
		
 Adjusted description
 
    
  
    

      Package: LACHESIS

      Commit: 64c96faa03035b04ead638543626ad195dd6721e

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-24 15:41:33 +0100

      Commit message:


	  
		
 Adjusted plot title
 
    
  
    

      Package: LACHESIS

      Commit: a312be869b33802a65f2abf149a88826972bb2cb

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-24 15:30:08 +0100

      Commit message:


	  
		
 Corrected typo
 
    
  
    

      Package: LACHESIS

      Commit: db7ca3c09369bfcb20f1780b12778ce57103b8c9

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-24 15:16:34 +0100

      Commit message:


	  
		
 Added real time axis to plotLachesis. Implement flexibility regarding mutation rate estimate such that previous estimates can be read in.
 
    
  
    

      Package: LACHESIS

      Commit: 993d5e811c1852b85338a6eb4f9157f16a3ea2e1

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-24 14:56:25 +0100

      Commit message:


	  
		
 Added real time to plotLACHESIS, allowing for de novo estimation of mutation rates

updated DESCRIPTION in line with release#
 
    
  
    

      Package: LACHESIS

      Commit: 1085e220a41603fd91b4fca8f46738df076c34af

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-24 13:50:55 +0100

      Commit message:


	  
		
 Reformatted
 
    
  
    

      Package: LACHESIS

      Commit: ba76fe9fa773fe4f5229a51f7168a540e312b142

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-24 13:49:52 +0100

      Commit message:


	  
		
 added function to estimate mutation rate from cohort
 
    
  
    

      Package: anndataR

      Commit: 7b7737cc6ae06abfb8dbf1d4c2813c3eaabd1e32

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-07-21 18:42:00 +0200

      Commit message:


	  
		
 Update NEWS (#488)

* Update news

* Fix PR entries which weren't pushed to bioc devel yet

* update news 
    
  
    

      Package: anndataR

      Commit: 47d557cd59671debc8de444bb4ea817a27f6d4ca

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

      Date: 2026-07-21 13:20:15 +0200

      Commit message:


	  
		
 Simplify roxygen docs (#479)

* clean roxygen2 doc for helpers

* tidy read helpers, lint and air

* fix some params 
    
  
    

      Package: anndataR

      Commit: b2a41ce34dcf0bdf81dff99afb676dacd795c54d

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

      Date: 2026-07-21 13:19:17 +0200

      Commit message:


	  
		
 Require Python `anndata<0.13.0` in tests (#481)

* Require Python anndata < 0.13.0 in tests

* Pin Python anndata in GHA workflows

* Pin anndata in Python usage vignette

* Pin scanpy in Python vignette

* add comments

---------

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

      Package: anndataR

      Commit: 7348779a6abdd7e10d36cf111833659904412579

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

      Date: 2026-07-21 08:38:49 +0200

      Commit message:


	  
		
 Fix `create_zarr()` so that Zarr stores can be created at relative paths (#478)

* safe create_zarr

* Add entry to news

* Add test

---------

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

      Package: anndataR

      Commit: 479f476e8bdb131e0be2068b47c2ccaf280b5453

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-07-21 07:56:42 +0200

      Commit message:


	  
		
 Fix conditional expression (#487) 
    
  
    

      Package: anndataR

      Commit: 8b689fd9d64e49cd3d085bf28ca3cd9ed8cdcbdc

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-07-21 07:54:14 +0200

      Commit message:


	  
		
 Update multiple actions simultaneously (#486) 
    
  
    

      Package: anndataR

      Commit: 07612e4f0e5c7efff05265eb916ae9ed94bf78b9

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

      Date: 2026-06-23 12:21:05 +0200

      Commit message:


	  
		
 Bump bencherdev/bencher from 0.6.7 to 0.6.8 (#472)

Bumps [bencherdev/bencher](https://github.com/bencherdev/bencher) from 0.6.7 to 0.6.8.
- [Release notes](https://github.com/bencherdev/bencher/releases)
- [Commits](https://github.com/bencherdev/bencher/compare/v0.6.7...v0.6.8)

---
updated-dependencies:
- dependency-name: bencherdev/bencher
  dependency-version: 0.6.8
  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: 6a1ca6b6ece85a46a7b93dd5f8cab24db2a99789

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

      Date: 2026-06-23 12:20:24 +0200

      Commit message:


	  
		
 Add support for `DelayedArray` reading (#387)

* Refactor HDF5AnnData to store file paths

Using paths instead of handles is required for compatibility with
HDF5Array

* Add hdf5_open_file() util function

Minimise repeated file opening code

* Add HDF5File class and use in HDF5AnnData

* Add close_and_defer_open() to HDF5File

* Use HDF5Array in read_h5ad_dense_array()

Keep fallback base rhdf5 function

* Add HDF5Array dependency

* Use HDF5Array in read_h5ad_spase_matrix

* Add backed option to HDF5AnnData

* Roxygenise

* Style

* Add backed SingleCellExperiment conversion

* Add backed Seurat conversion

* Fix lint

* Add HDF5Array checks to tests

* Add DelayedArray as suggested dependency

* Roxygenize

* Style code (GHA)

* Fix namespace in tests

* Expand tests for backed objects and make fixes

* Style code (GHA)

* Fix typos

* Check DelayedArray seed in to_R_matrix()

* Remove unused argument in HDF5File$close()

* Fix return in .as_SCE_process_pairs_mapping

* style code

* restyle code

* add tests for known issues

* Update known issues

* Fix subsetting backed anndata objects

* materialise when converting backed hdf5 to inmemoryanndata

* make sure SCE supports delayedarrays

* support writing delayedmatrix object by materialising on write

* add entry to bench suite

* fix performance regression; do not use HDF5Array for eager read

* delayedarray and hdf5array are only needed when backed is true

* remove known issue sections that are no longer needed

* keep handle open when reading element keys

* reuse handle if it already has enough access

* remove this benchmark for now

* Fix formatting

---------

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

      Package: anndataR

      Commit: b1419ff1e3409110d2917c8efb012cb0ad5f887c

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

      Date: 2026-06-21 11:12:31 +0200

      Commit message:


	  
		
 Add Bioconductor R-universe checks (#470) 
    
  
    

      Package: anndataR

      Commit: 27855705dfeb934fab2a963f5b0c821a452691a1

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

      Date: 2026-06-19 10:31:46 +0200

      Commit message:


	  
		
 Bump actions/checkout from 6 to 7 (#469)

Bumps [actions/checkout](https://github.com/actions/checkout) from 6 to 7.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v6...v7)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '7'
  dependency-type: direct:production
  update-type: version-update:semver-major
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      Package: anndataR

      Commit: 696edcf8e8fd9840e9779b9afe63049b93849d95

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-06-19 10:26:43 +0200

      Commit message:


	  
		
 Update gitignore
 
    
  
    

      Package: anndataR

      Commit: 65b136b45b36a381b1514e5dd1eaafee2ea1604e

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-06-18 14:48:36 +0200

      Commit message:


	  
		
 Upgrade to roxygen 8.0.0
 
    
  
    

      Package: anndataR

      Commit: e3ea474653f7b8423351823a51e862542fe104c3

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-06-17 22:51:34 +0200

      Commit message:


	  
		
 Take into account Rarr structured datatype breaking change (#462)

* Take into account Rarr structured datatype breaking change

* Run air

* add switch for backwards compatibility

---------

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

      Package: anndataR

      Commit: e3e7f7c0c27606b4099e4107be31a465df58a964

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-06-17 16:13:49 +0200

      Commit message:


	  
		
 Update CITATION with published paper (#464) 
    
  
    

      Package: anndataR

      Commit: d8300f686208ef33efa214791d4f69cf94b23dc1

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

      Date: 2026-06-17 16:13:06 +0200

      Commit message:


	  
		
 Bump bencherdev/bencher from 0.6.6 to 0.6.7 (#467)

Bumps [bencherdev/bencher](https://github.com/bencherdev/bencher) from 0.6.6 to 0.6.7.
- [Release notes](https://github.com/bencherdev/bencher/releases)
- [Commits](https://github.com/bencherdev/bencher/compare/v0.6.6...v0.6.7)

---
updated-dependencies:
- dependency-name: bencherdev/bencher
  dependency-version: 0.6.7
  dependency-type: direct:production
  update-type: version-update:semver-patch
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      Package: anndataR

      Commit: cdcd4f8c7281fe4deae28db2a1b16a4bd65caff3

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

      Date: 2026-06-17 16:12:40 +0200

      Commit message:


	  
		
 Bump codecov/codecov-action from 6 to 7 (#465)

Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 6 to 7.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v6...v7)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-version: '7'
  dependency-type: direct:production
  update-type: version-update:semver-major
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      Package: anndataR

      Commit: 4e5b112edcfe34f564ee02e89056a839215beeac

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-06-04 09:53:42 +0200

      Commit message:


	  
		
 Mark Zarr support as implemented in class diagram (#460) 
    
  
    

      Package: anndataR

      Commit: 38e9db5b9bc7a48656a09fca18abffabfc267cc0

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-05-27 10:12:08 +0200

      Commit message:


	  
		
 Update CI
 
    
  
    

      Package: anndataR

      Commit: 897914bb5abaed985c86664466b3cdd3c3f4a24e

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

      Date: 2026-05-12 20:03:28 +0200

      Commit message:


	  
		
 Add Zarr to benchmarks (#446)

* WIP

* More tests passing

* Fix df read bug

* More tests passing after fixing zero-dimensional get bug in pizzarr

* WIP: writing

* Fix more tests

* Zarr df writing

* WIP: ZarrAnnData class

* Tests passing

* Tests that compare h5ad to zarr

* Use Rarr to read full numeric arrays

* Fix bugs. Add test for from_SingleCellExperiment with Zarr

* Add a to_dense param to ZarrAnnData constructor. Add overwrite params internally.

* Update

* Backwards dense/sparse

* Simplify how obs and var names handled in ZarrAnnData (similar to #171)

* update extdata and documentation

* fix set/get zarr _index, update text example.zarr and update tests similar to HDF5AnnData

* Fix test

* Revert unnecessary changes

* Formatting

* Add comments

* remove unnecessary example zarr store

* lintr and R check for zarr related utilities and functions, updated some documentation

* add pizzarr to Suggests and README

* proj

* add keller-mark/pizzarr to Remotes

* zip example.zarr

* adapt read_zarr to Rarr

* adapt write_zarr to Rarr

* remove old scripts

* update write_zarr

* initial update to ZarrAnnData

* update ZarrAnnData, documentation, and implement read_zarr_rec_array

* review read zarr helpers, and update tests

* update read_zarr, read tests pass

* some updates for writing zarr

* update write_empty_zarr

* remove pizzarr, update documentation

* remove pizzarr from tests

* fix test-ZarrAnnData

* update ZarrAnnData to imitate HDF5AnnData

* check redundant files, correct lines

* update example_h5ad.py, add zarr and change to example_files.py

* add new test example

* some linting changes

* remove read/write_zattrs since implemented in Rarr

* access read/write_zarr_attr

* add some missing tests

* update readers, update tests

* correct nullable string zarr array write/read, introduce ordering in categorical zarr array

* do some linting, fix commented out code

* update some zarr writers and classes

* fix documentation

* fix compression interface for zarr

* full lint check

* fix examples

* check, biocheck and lintr

* fix development status

* air format

* air format test

* update example.zarr.zip, skip some test (waiting for Rarr)

* update example.zarr, fix some read_zarr_

* fix examples

* remove overwrite

* R code styling

* fixes from @lazappi

* air format

* update some documentation

* fix some tests

* more fixes on anndata-zarr integration

* update ZarrAnnData$initialize

* update zarr compression

* fix column-order here, C based ordering for arrays

* implement roundtrip tests for anndata-zarr

* add zarr to vignettes

* update README and software_design.rmd

* update AnnData-usage

* update write_zarr documentation

* update write_zarr_null

* fix rec_array, update tests and example datasets

* fix duplicate chunks in Rmd

* add write_zarr_null

* update write string array (zarr), air and lint

* implement writing empty zarr elements

* update tests for rec_array conformance of h5ad and zarr

* update mapping conformance test for h5ad and zarr

* implement H5_ITER like ordering and fix h5ad vs zarr testing

* air and lint

* fix test bug

* do not call expect_equal outside of test

* implement examples, test and datasets for zarr v3

* fix issues, lint and update example datasets to new anndata version

* lint and merge

* revert some lines

* small changes

* revert small changes

* air format some tests

* Set v2 in write_zarr_* helpers

* Fix stop message in write_zarr_element()

* Fix roxygen comment in write_zarr_element()

* Expand compression list in as_ZarrAnnData()

* Fix H5_ITER_INC_ORDERING docs

* Fix as_ZarrAnnData() compression docs

* Fix Zarr varm roundtrip test

* Review duplicate entry in README

* Fix typo in AnnData-usage docs

* Fix comma in software design vignette

* Adjust class descriptions in software design vignette

* Roxygenise

* Minor text fixes

* Document .get_compressor

* Minor fixes to function docs

* Comment logic in create_zarr_group()

* Fix indentation in read_zarr_sparse_array()

* Add construct sparse matrix helper

* Add ZARR_METADATA_FILES vector

* Eval Zarr chunks in vignettes

* Merge test-Zarrv3-read.R into test-Zarr-read.R

* Combine roundtrip tests

* Add roundtrip test helpers

* Refactor test-h5ad-zarr.R to use helper

* Refactor example files script

- Use uv comments for dependencies
- Update dependencies to latest stable versions
- Add progress messages
- Use Ruff for formatting

* Remove H5_ITER_INC_ORDERING()

* Remove Zarr compression comment

* Fix factor creation in read_zarr_categorical()

* Pin Rarr version

* Delete existing Zarr path before writing

* Add helper functions for accessing Zarr keys

* Update read_zarr_element() error message

* Add dimname warnings to ZarrAnnData

* Add Zarr writeability checks/tests

* Roxygenise, lint, style

* Use setup-bioc for all GHA

* Update WORDLIST

* Add .venv to .Rbuildignore

* Clean up test output

* Add Zarr to benchmarks

* run air format

---------

Co-authored-by: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Co-authored-by: Artur-man <artur-man@hotmail.com>
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> 
    
  
    

      Package: anndataR

      Commit: 4269af57a1e47e3ccb3895a629f623a36fa50a2c

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

      Date: 2026-05-12 14:00:42 +0200

      Commit message:


	  
		
 Bump bencherdev/bencher from 0.6.4 to 0.6.5 (#456)

Bumps [bencherdev/bencher](https://github.com/bencherdev/bencher) from 0.6.4 to 0.6.5.
- [Release notes](https://github.com/bencherdev/bencher/releases)
- [Commits](https://github.com/bencherdev/bencher/compare/v0.6.4...v0.6.5)

---
updated-dependencies:
- dependency-name: bencherdev/bencher
  dependency-version: 0.6.5
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

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      Package: anndataR

      Commit: 096e75aedd3bbd6f503dbddba206b4f45c8f6303

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-05-12 12:37:44 +0200

      Commit message:


	  
		
 Fix CI (#457)

* install additional libraries for mac os runner

* switch bioc mirror

* switch mirror

* manually fix versions

* try without version map

* try removing workarounds 
    
  
    

      Package: anndataR

      Commit: 22a2191102282a69b23dbdb13e2b13dfe3159253

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-11 11:23:36 +0200

      Commit message:


	  
		
 Enable new linters (#453)

* Replace any(is.na()) by anyNA()

* Apply ! on a single element instead of the entire vector

* Use nzchar() where possible

* Mark regexes as fixed where possible

* Use anyDuplicated() where possible

* Remove redundant is.integer() call

* Replace as.data.frame() by list2DF()

* Use endsWith() where relevant

* Run air 
    
  
    

      Package: anndataR

      Commit: 6c243139025752a15d715cfaaaed698647da12c2

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

      Date: 2026-05-06 18:23:21 +0200

      Commit message:


	  
		
 Bump dawidd6/action-download-artifact from 20 to 21 (#451)

Bumps [dawidd6/action-download-artifact](https://github.com/dawidd6/action-download-artifact) from 20 to 21.
- [Release notes](https://github.com/dawidd6/action-download-artifact/releases)
- [Commits](https://github.com/dawidd6/action-download-artifact/compare/v20...v21)

---
updated-dependencies:
- dependency-name: dawidd6/action-download-artifact
  dependency-version: '21'
  dependency-type: direct:production
  update-type: version-update:semver-major
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      Package: anndataR

      Commit: 3d5792d156b3c4bdba4f56f24956571f3c174e1d

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

      Date: 2026-05-06 18:06:38 +0200

      Commit message:


	  
		
 Bump bencherdev/bencher from 0.6.3 to 0.6.4 (#454)

Bumps [bencherdev/bencher](https://github.com/bencherdev/bencher) from 0.6.3 to 0.6.4.
- [Release notes](https://github.com/bencherdev/bencher/releases)
- [Commits](https://github.com/bencherdev/bencher/compare/v0.6.3...v0.6.4)

---
updated-dependencies:
- dependency-name: bencherdev/bencher
  dependency-version: 0.6.4
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

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      Package: anndataR

      Commit: 844954a7ed7dab2bba8a106fb4065d5e7d764c7d

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

      Date: 2026-05-05 17:54:56 +0200

      Commit message:


	  
		
 Update NEWS for v1.3.0
 
    
  
    

      Package: anndataR

      Commit: 16da839d4153de373e0bbe15bd1bf774481c7f6e

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

      Date: 2026-05-05 17:54:09 +0200

      Commit message:


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

* upstream/devel:
  bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: anndataR

      Commit: 2e0aa6130da1fef51df15b0ae73be269800ca871

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

      Date: 2026-05-05 17:52:22 +0200

      Commit message:


	  
		
 Update NEWS for v1.2.0
 
    
  
    

      Package: anndataR

      Commit: 4e605312e6be1a8775188034ddfa6351a13e2a9f

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

      Date: 2026-05-05 17:51:25 +0200

      Commit message:


	  
		
 Merge remote-tracking branch 'upstream/RELEASE_3_23' into devel

* upstream/RELEASE_3_23:
  bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: anndataR

      Commit: 4fa9edf7a370326d05e24d9d129994c2c5784a40

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

      Date: 2026-04-27 09:04:22 +0200

      Commit message:


	  
		
 Bump bencherdev/bencher from 0.6.2 to 0.6.3 (#450)

Bumps [bencherdev/bencher](https://github.com/bencherdev/bencher) from 0.6.2 to 0.6.3.
- [Release notes](https://github.com/bencherdev/bencher/releases)
- [Commits](https://github.com/bencherdev/bencher/compare/v0.6.2...v0.6.3)

---
updated-dependencies:
- dependency-name: bencherdev/bencher
  dependency-version: 0.6.3
  dependency-type: direct:production
  update-type: version-update:semver-patch
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      Package: SwarnSeq

      Commit: 651b42d4aef04fbe2783c5302edad8c0098bc4c5

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2026-07-22 18:57:49 +0530

      Commit message:


	  
		
 Prepare package for bioconductor push.
 
    
  
    

      Package: SwarnSeq

      Commit: e8855cb4d3af9ddd863af01955c9c7c89cf5b8f7

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2026-07-22 15:34:36 +0530

      Commit message:


	  
		
 Remove unnecessary files and folders from the previous push.
 
    
  
    

      Package: SwarnSeq

      Commit: c35efa6428eb4602f4c8feb6942f7bde815e320f

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2026-07-22 14:56:01 +0530

      Commit message:


	  
		
 addredd comments from the previous version 0.99.4 of this package.
 
    
  
    

      Package: SwarnSeq

      Commit: 4575ced9889c570d3f8d39a1ecd83edba1701225

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2026-01-04 10:30:50 +0530

      Commit message:


	  
		
 Initial commit 
    
  
    

      Package: SwarnSeq

      Commit: 6190d693fc5a5bee8f216a4d477a459d26f2d31b

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2026-01-04 10:27:08 +0530

      Commit message:


	  
		
 Delete NEWS.md 
    
  
    

      Package: SwarnSeq

      Commit: 901980d3ee0d5842f728471080591c22f05b24c5

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2026-01-04 10:26:54 +0530

      Commit message:


	  
		
 Delete NAMESPACE 
    
  
    

      Package: SwarnSeq

      Commit: e896c42181711efe6d09a7ab7b5439e7755d062f

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2026-01-04 10:26:37 +0530

      Commit message:


	  
		
 Delete DESCRIPTION 
    
  
    

      Package: SwarnSeq

      Commit: 54a5793875ac7e49e5a05582cf1249f080934027

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2026-01-04 10:26:19 +0530

      Commit message:


	  
		
 Delete vignettes directory 
    
  
    

      Package: SwarnSeq

      Commit: 6368a8b0837c9356661ce39155e49a21dcd7d659

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2026-01-04 10:26:07 +0530

      Commit message:


	  
		
 Delete tests directory 
    
  
    

      Package: SwarnSeq

      Commit: 833456650b8c258174740dae96d4d37143549cf1

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2026-01-04 10:25:56 +0530

      Commit message:


	  
		
 Delete man directory 
    
  
    

      Package: SwarnSeq

      Commit: de45082a79aa1a18d547efdb4f8a34bc1b155fcf

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2026-01-04 10:25:45 +0530

      Commit message:


	  
		
 Delete R directory 
    
  
    

      Package: SwarnSeq

      Commit: aaf8ca602c80e0eadb55ed049f327a478243249f

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2026-01-04 10:25:31 +0530

      Commit message:


	  
		
 Delete data directory 
    
  
    

      Package: SwarnSeq

      Commit: e3087be3570992375a4781d7ae51ffa54a0ddd76

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-11-01 17:49:07 +0530

      Commit message:


	  
		
 version .3 added 
    
  
    

      Package: SwarnSeq

      Commit: f829cdbd7d67a257538f3d9ac214915818431116

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-11-01 17:48:33 +0530

      Commit message:


	  
		
 Delete NAMESPACE 
    
  
    

      Package: SwarnSeq

      Commit: e1a5248a45b8432046ab2f22cd2dc62280e6c8cf

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-11-01 17:48:06 +0530

      Commit message:


	  
		
 Delete DESCRIPTION 
    
  
    

      Package: SwarnSeq

      Commit: efc3c678de9bbc4e2b107ec6c4febea596b78ed3

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-11-01 17:47:11 +0530

      Commit message:


	  
		
 Initial commit 
    
  
    

      Package: SwarnSeq

      Commit: e491a8c02944e61405e294686dcf00644263555b

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-11-01 17:43:28 +0530

      Commit message:


	  
		
 Delete vignettes directory 
    
  
    

      Package: SwarnSeq

      Commit: ed2eb75d454c8ae3cb9b16dc60cd1c2cedcbd4ff

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-11-01 17:43:15 +0530

      Commit message:


	  
		
 Delete tests directory 
    
  
    

      Package: SwarnSeq

      Commit: 9619d1220e8d4711b01c9da319528c7a15a8f1fd

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-11-01 17:42:56 +0530

      Commit message:


	  
		
 Delete man directory 
    
  
    

      Package: SwarnSeq

      Commit: ade65e4dce5d00e1b6cbd91b2bdde671a4d80e8d

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-11-01 17:42:18 +0530

      Commit message:


	  
		
 Delete data directory 
    
  
    

      Package: SwarnSeq

      Commit: 6ed5d2f7e272e93fae48c3e076a71ea7e19123e9

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-11-01 17:42:03 +0530

      Commit message:


	  
		
 Delete R directory 
    
  
    

      Package: SwarnSeq

      Commit: 9c59157e0bc25d42ceb5ced4355fb74fe6dca74f

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-09-18 16:13:27 +0530

      Commit message:


	  
		
 Change package version 
    
  
    

      Package: SwarnSeq

      Commit: 7756b3340e56bea4cc811700e07390d5102a7b0b

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-09-18 16:12:22 +0530

      Commit message:


	  
		
 Delete DESCRIPTION 
    
  
    

      Package: SwarnSeq

      Commit: 8665e8fc37158d91836f6df09c3c642cd27c2afc

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-09-16 12:19:22 +0530

      Commit message:


	  
		
 First version change 
    
  
    

      Package: SwarnSeq

      Commit: 47d15b151350a8ecab3e29e6e38edfceefcbffd6

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-09-16 12:18:30 +0530

      Commit message:


	  
		
 Delete DESCRIPTION 
    
  
    

      Package: SwarnSeq

      Commit: 7a7b0247d353308ff16a78d392cc039643556933

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-09-14 21:58:38 +0530

      Commit message:


	  
		
 Initial commit 
    
  
    

      Package: SwarnSeq

      Commit: 2004c8dde71311a7876cd9138879363877806a39

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-09-14 21:57:51 +0530

      Commit message:


	  
		
 Delete man directory 
    
  
    

      Package: SwarnSeq

      Commit: 9e7542faede5aa2e78d6243be42315eaef2aaaff

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-09-14 21:57:35 +0530

      Commit message:


	  
		
 Delete R directory 
    
  
    

      Package: SwarnSeq

      Commit: 3657d429f997218d2153940a68b893f60a513c1f

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-09-14 21:57:16 +0530

      Commit message:


	  
		
 Add files via upload 
    
  
    

      Package: SwarnSeq

      Commit: 428e85ae82752d78fc30211d136db1df05837ec4

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-09-14 21:55:39 +0530

      Commit message:


	  
		
 Delete man directory 
    
  
    

      Package: SwarnSeq

      Commit: 24dd79f78ce8a12dda43c9b8c7c60d85f5a878de

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-09-14 21:55:21 +0530

      Commit message:


	  
		
 Delete R directory 
    
  
    

      Package: DOtools

      Commit: 07c8c4ece9d79478b1ce4510d37ffcf759c3d2ef

      Author:  MarianoRuzJurado <mariani95@gmx.de> 

      Date: 2026-07-22 14:14:13 +0200

      Commit message:


	  
		
 bugfix
 
    
  
    

      Package: VariantAnnotation

      Commit: e48784601fe4e72bc8ddd864761fed66587b58f4

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

      Date: 2026-07-22 06:24:31 -0400

      Commit message:


	  
		
 Update version number to 1.59.3

Bump version from 1.59.2 to 1.59.3 in DESCRIPTION file. 
    
  
    

      Package: VariantAnnotation

      Commit: 1b44b0144b87ab919681481d3d5f9efa0e8c211f

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

      Date: 2026-07-22 06:21:15 -0400

      Commit message:


	  
		
 Merge pull request #92 from jmg421/fix/issue-86-predictCoding-empty-AAStringSet

fix: predictCoding on empty ranges returns AAStringSet for REFAA/VARAA (#86) 
    
  
    

      Package: VariantAnnotation

      Commit: 85de34267dbcf69e5e0d5680a57034eab2e479c7

      Author:  Levi Waldron <lwaldron.research@gmail.com> 

      Date: 2026-07-21 05:19:57 -0400

      Commit message:


	  
		
 Apply suggestions from code review

This expectation likely became outdated after removing the early return in .predictCodingGRangesList(): on an empty result, .localCoordinates() contributes 8 metadata columns and .predictCodingGRangesList() appends 6 more (GENEID/CONSEQUENCE/REFCODON/VARCODON/REFAA/VARAA), so mcols(current) should have 14 columns rather than 8.

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

      Package: VariantAnnotation

      Commit: e820d4e410dda9deb8ce874d21698e7f81fbd3fc

      Author:  John Muirhead-Gould <john@magna-services.com> 

      Date: 2026-06-12 10:19:05 -0400

      Commit message:


	  
		
 fix: predictCoding on empty ranges returns AAStringSet for REFAA/VARAA (#86)

When query has no overlap with the CDS, .localCoordinates() returns a
zero-length GRanges. Previously an early return on length(txlocal)==0
caused REFAA and VARAA to be absent from mcols(), returning NULL instead
of empty AAStringSet objects. This breaks downstream operations like
reverse() and subseq() on the result columns.

Fix:
- Remove early return so the full mcols-building code runs even when
  txlocal is empty, naturally producing zero-length AAStringSet columns
- Fix GENEID=NA_character_ -> rep(NA_character_, length(txlocal)) so
  DataFrame() construction works correctly at zero length

Test: extend test_predictCoding_empty to assert REFAA and VARAA are
AAStringSet with length 0.
 
    
  
    

      Package: GExPipe

      Commit: ffd15467eec4f74451eaf9d66a90b39897a765d8

      Author:  Safa Rafique <safa.sandhu@gmail.com> 

      Date: 2026-07-22 14:28:43 +0500

      Commit message:


	  
		
 Fix Bioconductor CHECK: drop unavailable Suggests rmda (0.99.43).

Correct co-author names to Naeem Mahmood Ashraf and Prof. Dr. Muhammad Farooq Sabar; DCA keeps using dcurves.

Co-authored-by: Cursor <cursoragent@cursor.com>
 
    
  
    

      Package: DMRcaller

      Commit: 2ffeea118e727a88da778b949f6dd640dfcdc33b

      Author:  nrzabet <r.zabet@qmul.ac.uk> 

      Date: 2026-07-22 08:55:59 +0100

      Commit message:


	  
		
 fixed cigarillo bug
 
    
  
    

      Package: drugTargetInteractions

      Commit: dacc201aac5bbcccd4635c21a92b27b143708c27

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

      Date: 2026-07-21 19:42:26 -0700

      Commit message:


	  
		
 Suppress TLS-retry warning noise from the rendered vignette's broad_build chunk

The retry mechanism (.brhWithSupplementalCa()) and its console warnings
are unchanged for normal interactive/script use - this only quiets the
rendered HTML, where the first-attempt SSL failure text read as an
alarming error even though the chunk completes successfully via the
automatic retry.
 
    
  
    

      Package: drugTargetInteractions

      Commit: ea27ce051d3dac9f289c4ee45c7bdd14c921bd1d

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

      Date: 2026-07-21 19:14:05 -0700

      Commit message:


	  
		
 Fix Broad Repurposing Hub fan-out bug: split broad_interactions/broad_samples into their true grains

buildBroadRepurposingHubDb() merged sample-level QC/provenance data
(one row per physical broad_id, deduplicated only by exact full-row
match) straight into the drug-target edge table. Since the source data
carries repeat purity/QC readings per broad_id and most compounds have
multiple broad_ids (67% of compounds, verified live), this multiplied
rows: 3.57x overall inflation (17,996 true edges vs 64,336 rows), one
compound-target pair duplicated 175x.

Fixed by never merging `sample` into the interaction table. Structure
columns (smiles/InChIKey/pubchem_cid) now come from
.brhCompoundStructure(), a proper one-row-per-compound reduction that
prefers complete records over incomplete ones and packs the rare
genuine multi-structure cases (~2% of compounds, real salt/stereoisomer
name collisions) rather than picking one arbitrarily, flagged via a new
structure_ambiguous column. Sample/QC metadata (purity, vendor,
catalog_no, etc. - never actually a property of a drug-target edge)
moves to a new broad_samples table, kept at its own natural grain.
broad_interactions' (pert_iname, target_gene) grain is asserted via a
new shared .assertUniqueKey() helper immediately after the reduction,
not just assumed in a comment.

broadRepurposingHubAnnot()'s idType="broad_id" path now resolves
broad_id -> pert_iname via broad_samples first, then dispatches like a
name lookup - a correctness improvement given the 67% multi-sample
rate, not just a side effect of the split. Handles the rare (10 of
15,674) case where a broad_id resolves to more than one compound, due
to genuine naming inconsistencies in Broad's own source file, as a real
one-to-many resolution rather than collapsing or erroring.

Updated vignette (schema change note + corrected stale TLS caveat text
now that a workaround exists), tests (new grain regression guard,
.brhCompoundStructure unit tests, updated schema/column assertions),
and docs.
 
    
  
    

      Package: excluderanges

      Commit: 339f95249b90abb0e3772f354e67c7d227ef4574

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

      Date: 2026-07-21 21:11:52 -0400

      Commit message:


	  
		
 Bump version to 0.99.12

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

      Package: excluderanges

      Commit: 58bddf784ae291396d7e40ec239ad27926cb3d47

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

      Date: 2026-07-21 21:03:05 -0400

      Commit message:


	  
		
 Move Zenodo metadata into package

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

      Package: excluderanges

      Commit: 72aa65925544caae298769afe9e610e2d1d4df15

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

      Date: 2026-07-21 20:38:41 -0400

      Commit message:


	  
		
 Merge pull request #13 from Virp0/master

Zenodo metadata 
    
  
    

      Package: excluderanges

      Commit: c91f6970fb79ebee3091f9faff026b3d1669d517

      Author:  Virp0 <bhvirpatel@gmail.com> 

      Date: 2026-07-21 17:32:28 -0700

      Commit message:


	  
		
 Add files via upload 
    
  
    

      Package: excluderanges

      Commit: b9d35ef55cb940235f8a7ad4cdf0eb524edd209b

      Author:  Virp0 <bhvirpatel@gmail.com> 

      Date: 2026-07-21 17:32:14 -0700

      Commit message:


	  
		
 Delete metadata.csv 
    
  
    

      Package: excluderanges

      Commit: ad5ceca2345fb758efb9724413159229b9581784

      Author:  Virp0 <bhvirpatel@gmail.com> 

      Date: 2026-07-21 16:50:46 -0700

      Commit message:


	  
		
 Comment out gap analysis code in excluderanges.Rmd

Comment out code related to gap analysis for hg19 genome. 
    
  
    

      Package: excluderanges

      Commit: 7832aa7d56f0a1e1018afcf16c72a5ee386bdd73

      Author:  Virp0 <bhvirpatel@gmail.com> 

      Date: 2026-07-21 16:33:54 -0700

      Commit message:


	  
		
 Update metadata for Zenodo 
    
  
    

      Package: excluderanges

      Commit: 3f70b610010c48b5fdea2af0fbf04ba56f32fe16

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

      Date: 2026-07-05 11:06:00 -0400

      Commit message:


	  
		
 Merge pull request #10 from hyein-cbio/master

Handles 0 base and 1 base for BED format with helper function 
    
  
    

      Package: excluderanges

      Commit: b99d6d200d432ce63ab5d4940a70ee59b5e7a758

      Author:  Hyein Cho <hyein.cho.cbio@gmail.com> 

      Date: 2026-07-05 13:55:50 +0100

      Commit message:


	  
		
 Handles 0 base and 1 base for BED format with helper function
 
    
  
    

      Package: excluderanges

      Commit: 54efcedfb381a6b388cf55a918ac2254d6fb7524

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

      Date: 2026-07-03 07:58:17 -0400

      Commit message:


	  
		
 Merge branch 'devel'
 
    
  
    

      Package: excluderanges

      Commit: c6b797c025b87c695a43d826d7407cb1a45cf262

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

      Date: 2026-07-03 07:56:30 -0400

      Commit message:


	  
		
 add show_col_types = FALSE
 
    
  
    

      Package: excluderanges

      Commit: da3feb6e9f0644c8e7cabad2347dd2be6b8bb7c9

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

      Date: 2026-06-20 21:35:59 -0400

      Commit message:


	  
		
 Merge pull request #9 from Virp0/fix-bed-coordinate-conversion

Fix BED coordinate conversion 
    
  
    

      Package: excluderanges

      Commit: eb860bbe4de6a790ad2a73e6d80ac178993cf83f

      Author:  Virp0 <bhvirpatel@gmail.com> 

      Date: 2026-06-20 18:05:55 -0700

      Commit message:


	  
		
 Fix BED coordinate conversion 
    
  
    

      Package: ncRNAtools

      Commit: 80bcee4e6a7c550a84289779e92e8b24642c198b

      Author:  LaraSellesVidal <lara.selles@oist.jp> 

      Date: 2026-07-22 08:59:11 +0900

      Commit message:


	  
		
 update secondary structure prediction web services
 
    
  
    

      Package: rfaRm

      Commit: dcde1210c9d8cff956760774fc98f20091e22fde

      Author:  LaraSellesVidal <lara.selles@oist.jp> 

      Date: 2026-07-22 08:56:30 +0900

      Commit message:


	  
		
 import readRNAMultipleAlignment from MultipleAlignment
 
    
  
    

      Package: drugTargetInteractions

      Commit: 6e842945f673d5489b8407e4fff62ae390989e78

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

      Date: 2026-07-21 13:06:47 -0700

      Commit message:


	  
		
 Bump version to 1.21.3

Version bump to force a rebuild on the Bioconductor build system -
covers the 7 commits since the 1.21.2 bump (e859b3d) that never
propagated: Broad Repurposing Hub + GtoPdb sources, the TTD
cold-cache/fields=/parser-extension fix, and the Broad TLS retry fix.
Per Bioconductor policy, commits without a version bump don't propagate
to BiocManager::install() or trigger a new build.
 
    
  
    

      Package: drugTargetInteractions

      Commit: 4724edb1c391b8efab0ef1e74a027f6ceab36264

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

      Date: 2026-07-21 12:28:52 -0700

      Commit message:


	  
		
 Retry Broad Repurposing Hub download with a supplemental CA bundle on failure

repo-hub.broadinstitute.org serves an incomplete TLS chain (missing its
InCommon intermediate); browsers AIA-chase around it automatically,
curl/R's downloaders do not. downloadBroadRepurposingHub() now retries
once, on any download failure, with CURL_CA_BUNDLE pointed at the
system's default bundle plus that one missing (legitimate,
publicly-issued) intermediate - full verification still happens, this
only adds the certificate the server itself omits. Falls back to plain
unmodified behavior if no system CA bundle file can be located.

Revises the 2026-07-19 document-only decision now that the failure is
confirmed reproducible and could plausibly hit Bioconductor's own build
machines.
 
    
  
    

      Package: UniProt.ws

      Commit: 618434bcf6ef31e2f54a9c0561bf897be12468e0

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

      Date: 2026-07-21 14:43:28 -0400

      Commit message:


	  
		
 version bump 2.53.3
 
    
  
    

      Package: UniProt.ws

      Commit: bf5d88c60a98b18fb20bda24a1cefbff82249dee

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

      Date: 2026-07-21 14:43:14 -0400

      Commit message:


	  
		
 updated reference to S4 class from roxygen2
 
    
  
    

      Package: UniProt.ws

      Commit: 7ab191b84ac1ac6c0bd5ee78200f1bde90d343ab

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

      Date: 2026-07-21 14:42:56 -0400

      Commit message:


	  
		
 changes based on roxygen2
 
    
  
    

      Package: UniProt.ws

      Commit: 254169877017874c586e6ffc000642c5cd4ad1bd

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

      Date: 2026-07-21 14:42:39 -0400

      Commit message:


	  
		
 add description to method in describeIn
 
    
  
    

      Package: UniProt.ws

      Commit: eac58c795bf893d0174e20d4e8759e98da20219f

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

      Date: 2026-07-21 14:42:18 -0400

      Commit message:


	  
		
 use roxygen2 v8
 
    
  
    

      Package: UniProt.ws

      Commit: 647a03d1e0b99798014a221b9fec28c3857c9a00

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

      Date: 2026-07-21 13:57:54 -0400

      Commit message:


	  
		
 version bump 2.53.2
 
    
  
    

      Package: UniProt.ws

      Commit: a85a889fe4cf73cab6764a5f4b0f8213cf914da4

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

      Date: 2026-07-21 13:55:02 -0400

      Commit message:


	  
		
 remove workaround for uniprot API bug
 
    
  
    

      Package: ZarrArray

      Commit: 092c417853c7cd2a8a171142e92c46a49b3a58c7

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-21 19:05:11 +0200

      Commit message:


	  
		
 Replace inefficient patterns (#10)

* Use startsWith() instead of substr()

microbenchmark::microbenchmark(file.path("a", "b"), paste0("a", "/", "b"), times = 1e4)
#> Unit: nanoseconds
#>                   expr min  lq     mean median   uq    max neval
#>    file.path("a", "b") 574 639 1022.293    677  763  84528 10000
#>  paste0("a", "/", "b") 848 943 1403.952   1009 1111 170456 10000

* Use !nzchar() instead of == ""

microbenchmark::microbenchmark("test/test/test/test" == "", !nzchar("test/test/test/test"), times = 1e4)
#> Unit: nanoseconds
#>                            expr min lq    mean median uq  max neval
#>     "test/test/test/test" == ""  60 68 91.1651     74 79 5723 10000
#>  !nzchar("test/test/test/test")  51 58 80.0586     61 70 9719 10000

* Use file.path() consistently

microbenchmark::microbenchmark(paste0("group", "/data"), paste0("group", "/", "data"), file.path("group", "data"), times = 1e5)
#> Unit: nanoseconds
#>                          expr min  lq      mean median   uq     max neval
#>      paste0("group", "/data") 786 874 1026.1339    902  957 2266881 1e+05
#>  paste0("group", "/", "data") 871 968 1151.3651   1000 1081 1589845 1e+05
#>    file.path("group", "data") 590 655  786.3354    678  734 1586759 1e+05

* Use dim() <- NULL instead of as.vector()

x <- sample(1:1e7, 1e7, replace = TRUE)
dim(x) <- 1e7

bench::mark(
  as.vector(x),
  as.integer(x),
  # We assign to y here for benchmarking purposes. To avoid removing dim for our test object after the first iteration.
  {
    y <- x
    dim(y) <- NULL
    y
  },
  iterations = 1000
)
#> # A tibble: 3 × 6
#>   expression                       min   median `
itr/sec` mem_alloc
`
gc/sec`
#>                                
#> 1 as.vector(x)                  11.5ms   12.3ms      81.3    38.1MB     25.3
#> 2 as.integer(x)                 11.5ms   12.3ms      81.2    38.1MB     20.3
#> 3 { y <- x dim(y) <- NULL y }    326ns    359ns 2545301.         0B      0 </pre>
    </div>
  
    

      Package: ZarrArray

      Commit: f40d5021543ff5bbf207533b531970f383bc4a56

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-21 07:05:01 +0200

      Commit message:


	  
		
 Normalize path in test comparisons (#8)

This avoids unit test failures on Windows and Mac. 
    
  
    

      Package: RnBeads.hg38

      Commit: 4a7029d6382ca6ca4f574c7a59711e2ef991c576

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

      Date: 2026-07-20 13:30:52 +0200

      Commit message:


	  
		
 filtered git history for large files and readded smaller versions
 
    
  
    

      Package: RnBeads.hg38

      Commit: ff7e15c5e7b670ac2b6da4530d8cb4c86afe2f3c

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

      Date: 2026-04-28 08:28:27 -0400

      Commit message:


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

      Package: RnBeads.hg38

      Commit: 79cc11b4988e61944cb07d2e1d3fe79e63ebf9f5

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

      Date: 2026-04-28 08:28:27 -0400

      Commit message:


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

      Package: RnBeads.hg38

      Commit: b9b9dd4f59997d18ae67254ca4471f977b5a269d

      Author:  Scherer <m261r@b370-worker01.dkfz-heidelberg.de> 

      Date: 2026-04-09 17:53:51 +0200

      Commit message:


	  
		
 Added cross-reactive probes for EPICv2
 
    
  
    

      Package: RnBeads.hg38

      Commit: 45820cf120c534d0fddfc7117724ba86cc997e48

      Author:  Michael Scherer <michael.scherer@dkfz.de> 

      Date: 2026-02-19 17:52:15 +0100

      Commit message:


	  
		
 Updated version number
 
    
  
    

      Package: RnBeads.hg38

      Commit: 36b9c5915a256153ec5d0c8061392519d4705971

      Author:  Michael Scherer <michael.scherer@dkfz.de> 

      Date: 2025-11-19 17:47:34 +0100

      Commit message:


	  
		
 Reduced RData sizes
 
    
  
    

      Package: RnBeads.hg38

      Commit: 2c43702e825aedfad5c3834e7f4ff6fc28750620

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

      Date: 2025-10-29 09:56:48 -0400

      Commit message:


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

      Package: RnBeads.hg38

      Commit: 05530fb1dd7df2c9848e40106047e527e4ff9bce

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

      Date: 2025-10-29 09:56:48 -0400

      Commit message:


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

      Package: RnBeads.hg38

      Commit: 27f7724c33e94c0035907f5c4d37a3962d43185b

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

      Date: 2025-07-23 08:31:28 +0200

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: RnBeads.hg38

      Commit: 79e4f2a66a8b90d13f988a2c6e19d1b59f116d38

      Author:  Michael Scherer <michael.scherer@dkfz.de> 

      Date: 2025-07-22 11:55:29 +0200

      Commit message:


	  
		
 Fixed nv probe issue
 
    
  
    

      Package: RnBeads.hg38

      Commit: 25838820494c4f040bcf4a4846f150ee11dfed1a

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

      Date: 2025-04-15 10:02:21 -0400

      Commit message:


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

      Package: RnBeads.hg38

      Commit: 20f2170d341e9f547e5e5eb7601f5e860fd67eed

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

      Date: 2025-04-15 10:02:21 -0400

      Commit message:


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

      Package: RnBeads.hg38

      Commit: acbb8fd445aaff466cb07ce41d4b5fda94b22c72

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

      Date: 2025-03-12 09:14:13 +0100

      Commit message:


	  
		
 Bugfix: regionMapping

github issue 59
 
    
  
    

      Package: RnBeads.hg38

      Commit: e953a5182a6d1b42912cc46a209dc0dae8a875e6

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

      Date: 2024-10-29 09:42:02 -0400

      Commit message:


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

      Package: RnBeads.hg38

      Commit: 7ec0b5deefcaa0a061a9498afa189349f89abce0

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

      Date: 2024-10-29 09:42:02 -0400

      Commit message:


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

      Package: RnBeads.hg38

      Commit: 36f2819d4d748554055c859a7f335995eefe9cc4

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

      Date: 2024-04-30 10:44:34 -0400

      Commit message:


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

      Package: RnBeads.hg38

      Commit: df3725300bdaf10c0f3db41b8a02dfc466207747

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

      Date: 2024-04-30 10:44:34 -0400

      Commit message:


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

      Package: RnBeads.hg38

      Commit: 11b7cb3ab20f80b05c210aa526f82e0bdccca87c

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

      Date: 2024-04-23 20:15:36 +0200

      Commit message:


	  
		
 gitignore
 
    
  
    

      Package: RnBeads.hg38

      Commit: 08587bc9dd7606a8c44557cdd2334edb192677f8

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

      Date: 2024-04-23 20:13:28 +0200

      Commit message:


	  
		
 Major hg38 update including EPICv2 support
 
    
  
    

      Package: RnBeads.hg38

      Commit: c72aea9c5f417535ff91cc9f9f7bfe09d172af2c

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

      Date: 2024-04-23 08:29:05 +0200

      Commit message:


	  
		
 Description update and commit check
 
    
  
    

      Package: RnBeads.hg38

      Commit: 72f08a63722d1078569730e1bfa5901786a6fc61

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

      Date: 2023-10-24 09:10:51 -0400

      Commit message:


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

      Package: RnBeads.hg38

      Commit: f0d4b7caa556b6dc831110b8796a468c831e77a6

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

      Date: 2023-10-24 09:10:51 -0400

      Commit message:


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

      Package: RnBeads.hg38

      Commit: eac80328f08089d014a1dc359257d52c8e042d1c

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

      Date: 2023-04-25 10:38:43 -0400

      Commit message:


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

      Package: RnBeads.hg38

      Commit: 322cc5f037c9de26e0e72f167af6f0581fd62db0

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

      Date: 2023-04-25 10:38:43 -0400

      Commit message:


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

      Package: RnBeads.hg38

      Commit: 8d7d8ba79a9cc90cf46e3a61b4f1688bd65b5755

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

      Date: 2022-11-01 11:07:14 -0400

      Commit message:


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

      Package: RnBeads.hg38

      Commit: 99304030cf52fcfe2238089b73aed7ba7687840e

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

      Date: 2022-11-01 11:07:14 -0400

      Commit message:


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

      Package: RnBeads.hg38

      Commit: f60b0eaf10fa5bc1a5a5999cfbbde020206f130f

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

      Date: 2022-04-26 17:18:35 +0000

      Commit message:


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

      Package: RnBeads.hg38

      Commit: 4ca2b1d09fcf723f2e26ead9c34c1eec2c6f85ff

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

      Date: 2022-04-26 17:18:35 +0000

      Commit message:


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

      Package: RnBeads.hg38

      Commit: c63060e58884edb910e327e322619fa0b681cc61

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

      Date: 2021-11-21 23:01:27 -0500

      Commit message:


	  
		
 Pass serialized S4 instances thru updateObject()
 
    
  
    

      Package: RnBeads.hg38

      Commit: 7cd5491d4de50e534b47b9bdc435ce71a23c4330

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

      Date: 2021-10-26 12:15:40 -0400

      Commit message:


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

      Package: RnBeads.hg38

      Commit: 941edce8b82c98ca2b5babbbc2091cdac9d16c8a

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

      Date: 2021-10-26 12:15:40 -0400

      Commit message:


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

      Package: RnBeads.hg38

      Commit: 5a3bf9c1e4d78fdf4ca161e25ac720b5565c0d05

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

      Date: 2021-05-19 11:52:05 -0400

      Commit message:


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

      Package: RnBeads.hg38

      Commit: bf68aed0af6d0b933abde2b9f606331380f98d20

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

      Date: 2021-05-19 11:52:05 -0400

      Commit message:


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

      Package: RnBeads.hg38

      Commit: 136adab9e5b387fc39369b6cc2c1ea1c4e146c21

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

      Date: 2020-10-27 10:13:38 -0400

      Commit message:


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

      Package: RnBeads.hg38

      Commit: a7366693e3bce073d495cdef9bc5d6a2ca92bc94

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

      Date: 2020-10-27 10:13:38 -0400

      Commit message:


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

      Package: RnBeads.hg38

      Commit: bf42f8e77c9ea2b7b7993551054ea8754f8f64b9

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2020-04-27 15:36:57 -0400

      Commit message:


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

      Package: RnBeads.hg38

      Commit: 5f803432ddfad5a85e44c050c8a8242d9cd81e66

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2020-04-27 15:36:57 -0400

      Commit message:


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

      Package: RnBeads.hg38

      Commit: 05d6133464db0f8ef5d35b5a8f8e1679838310c6

      Author:  Hervé Pagès <hpages@fredhutch.org> 

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

      Commit message:


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

      Package: RnBeads.hg38

      Commit: d1bb04ba9434eedc5d859202abd3f13e62f2e1d6

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2019-10-29 13:29:44 -0400

      Commit message:


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

      Package: RnBeads.hg38

      Commit: 4af488b4dc6c8b7afb40ba8d78bf961886182962

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2019-05-02 12:06:26 -0400

      Commit message:


	  
		
 bump x.y.z versions to odd y after creation of RELEASE_3_9 branch
 
    
  
    

      Package: RnBeads.hg38

      Commit: d297fd49eefd1b27fbacebe0af8ef6a7adea428f

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2019-05-02 11:56:44 -0400

      Commit message:


	  
		
 bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch
 
    
  
    

      Package: RnBeads.hg38

      Commit: 53a07de724eb304b005e413dc2d7da0d7ce7b4c2

      Author:  nturaga <nitesh.turaga@gmail.com> 

      Date: 2018-10-30 11:38:34 -0400

      Commit message:


	  
		
 bump x.y.z versions to odd y after creation of RELEASE_3_8 branch
 
    
  
    

      Package: RnBeads.hg38

      Commit: 285014b380d7848648235ffa32b32a05bf5f13bc

      Author:  nturaga <nitesh.turaga@gmail.com> 

      Date: 2018-10-30 11:36:24 -0400

      Commit message:


	  
		
 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
 
    
  
    

      Package: RnBeads.hg38

      Commit: a493fb9925f7bcbcdc6591e54aa7e4984af6d7f8

      Author:  Nitesh Turaga <nitesh.turaga@gmail.com> 

      Date: 2018-04-30 10:34:48 -0400

      Commit message:


	  
		
 bump x.y.z versions to odd y after creation of RELEASE_3_7 branch
 
    
  
    

      Package: RnBeads.hg38

      Commit: 18505cbe2981e5140cfe27418459070ce239428d

      Author:  Nitesh Turaga <nitesh.turaga@gmail.com> 

      Date: 2018-04-30 10:31:29 -0400

      Commit message:


	  
		
 bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch
 
    
  
    

      Package: RnBeads.hg38

      Commit: b7f4f7f8ed31fd542c23dd84eb54de831be45f68

      Author:  vobencha <valerie.obenchain@roswellpark.org> 

      Date: 2017-10-30 12:09:08 -0400

      Commit message:


	  
		
 bump x.y.z versions to odd y after creation of RELEASE_3_6 branch
 
    
  
    

      Package: RnBeads.hg38

      Commit: 454f965d571d8366fc4677adde37fbd751328e7d

      Author:  vobencha <valerie.obenchain@roswellpark.org> 

      Date: 2017-10-30 11:58:31 -0400

      Commit message:


	  
		
 bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch
 
    
  
    

      Package: RnBeads.hg38

      Commit: ebee6b084245b1aea9feec0bfb547d01dc7ded76

      Author:  nturaga <nitesh.turaga@gmail.com> 

      Date: 2017-08-16 19:02:39 +0000

      Commit message:


	  
		
 Committing experiment data for RnBeads.hg38
 
    
  
    

      Package: RnBeads.hg19

      Commit: bf56bb9622631b32b7a8ae0876fd0aa8ad93cfd8

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

      Date: 2026-07-20 15:47:25 +0200

      Commit message:


	  
		
 filtered git history for large files and readded smaller version
 
    
  
    

      Package: RnBeads.hg19

      Commit: 0e22d647954e5f2200276de564baa8869ea71543

      Author:  Michael Scherer <michael.scherer@dkfz.de> 

      Date: 2026-07-20 15:39:26 +0200

      Commit message:


	  
		
 Updated DESCRIPTION
 
    
  
    

      Package: RnBeads.hg19

      Commit: 08d91de23e99cbbc7c6099f5e1c322b954a41993

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

      Date: 2026-04-28 08:28:12 -0400

      Commit message:


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

      Package: RnBeads.hg19

      Commit: 735bb667ae5db685e28cd03e17b217d46195ee84

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

      Date: 2026-04-28 08:28:12 -0400

      Commit message:


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

      Package: RnBeads.hg19

      Commit: 9bfc1297e0d1fb7a8243a8cf344e837c2b858a51

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

      Date: 2025-10-29 09:56:29 -0400

      Commit message:


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

      Package: RnBeads.hg19

      Commit: 3a00eb527c481fda6c5e0191ba8d2ee644071ada

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

      Date: 2025-10-29 09:56:29 -0400

      Commit message:


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

      Package: RnBeads.hg19

      Commit: 46a0b3bb2ac139706ccc07874639cafbe8623ccb

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

      Date: 2025-04-15 10:01:14 -0400

      Commit message:


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

      Package: RnBeads.hg19

      Commit: 90ffc4bf74514124a288c7d4f555345637a25d75

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

      Date: 2025-04-15 10:01:14 -0400

      Commit message:


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

      Package: RnBeads.hg19

      Commit: 43f0b6c4de42f0e4d25e67eb5d5c51fe138b86fe

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

      Date: 2024-10-29 09:41:31 -0400

      Commit message:


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

      Package: RnBeads.hg19

      Commit: 362e5dea9ef50518a7e9ea640949c7f0e1423175

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

      Date: 2024-10-29 09:41:31 -0400

      Commit message:


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

      Package: RnBeads.hg19

      Commit: b608596e2d4af77a36017ca86a7d988c70f104f5

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

      Date: 2024-04-30 10:44:04 -0400

      Commit message:


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

      Package: RnBeads.hg19

      Commit: 66c3349711d5450c7277749597693568bb60dd0e

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

      Date: 2024-04-30 10:44:04 -0400

      Commit message:


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

      Package: RnBeads.hg19

      Commit: 2811015ce787421a8992313c2d73aa147733417b

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

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

      Commit message:


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

      Package: RnBeads.hg19

      Commit: 2aab3cbf3ec90bc5d4ac6f0eeca45dde5113238d

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

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

      Commit message:


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

      Package: RnBeads.hg19

      Commit: 02255edad04aa928bc89c6814f754eef7126c0ee

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

      Date: 2023-04-25 10:38:15 -0400

      Commit message:


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

      Package: RnBeads.hg19

      Commit: 2d5984f1961071577ba6bb8d87186732ea5cdc1a

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

      Date: 2023-04-25 10:38:15 -0400

      Commit message:


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

      Package: RnBeads.hg19

      Commit: 5d1fb41db2008fe2b26964b5debde780d1282f70

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

      Date: 2022-11-01 11:05:51 -0400

      Commit message:


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

      Package: RnBeads.hg19

      Commit: 8763d3a2ac403425eb161f60290c608445f47709

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

      Date: 2022-11-01 11:05:51 -0400

      Commit message:


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

      Package: RnBeads.hg19

      Commit: e8d1d3589004407e25f7dc0522ad2ab3c97e6f26

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

      Date: 2022-04-26 17:17:31 +0000

      Commit message:


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

      Package: RnBeads.hg19

      Commit: 2b8ad52096f1a0ff47a8edccbffd6c755abb95fb

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

      Date: 2022-04-26 17:17:31 +0000

      Commit message:


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

      Package: RnBeads.hg19

      Commit: 98d7c6ab1cb9006b036985890bfc8ccba3fff2b6

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

      Date: 2021-11-21 22:54:39 -0500

      Commit message:


	  
		
 Pass serialized S4 instances thru updateObject()
 
    
  
    

      Package: RnBeads.hg19

      Commit: d94b665cbdbfe90462ac632937802a6fe93feb04

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

      Date: 2021-10-26 12:14:31 -0400

      Commit message:


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

      Package: RnBeads.hg19

      Commit: 69478a98b83b5ca0c3cdcd8f12c56aeb8bf94edb

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

      Date: 2021-10-26 12:14:31 -0400

      Commit message:


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

      Package: RnBeads.hg19

      Commit: 978b9c96823c31d38aaea497d3256c50703e875d

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

      Date: 2021-05-19 11:51:14 -0400

      Commit message:


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

      Package: RnBeads.hg19

      Commit: 1dca24ab879fde9da7309aabd622b8e9a9c42009

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

      Date: 2021-05-19 11:51:14 -0400

      Commit message:


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

      Package: RnBeads.hg19

      Commit: 214a0ae7630b73d7f1d7a6f5246901f62c58f5a2

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

      Date: 2020-10-27 10:12:54 -0400

      Commit message:


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

      Package: RnBeads.hg19

      Commit: 6c99d1d246452f0605a673067eec3401333a8890

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

      Date: 2020-10-27 10:12:54 -0400

      Commit message:


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

      Package: RnBeads.hg19

      Commit: ef72eb3601e68128c40554d698ba98c5f2a4dce6

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2020-04-27 15:34:33 -0400

      Commit message:


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

      Package: RnBeads.hg19

      Commit: a54fa79999c633f2605e0e728fc4d884d4c06f06

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2020-04-27 15:34:33 -0400

      Commit message:


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

      Package: RnBeads.hg19

      Commit: e09164b3df0cc01a47ddbf4ebbed526cc91b745a

      Author:  Hervé Pagès <hpages@fredhutch.org> 

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

      Commit message:


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

      Package: RnBeads.hg19

      Commit: ce7c357ea5c6da395aca308a8cad45c12d633a68

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2019-10-29 13:29:44 -0400

      Commit message:


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

      Package: RnBeads.hg19

      Commit: a982634a60c1a2f53fc06f05f2c5a3aa809d6c05

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2019-05-02 12:06:26 -0400

      Commit message:


	  
		
 bump x.y.z versions to odd y after creation of RELEASE_3_9 branch
 
    
  
    

      Package: RnBeads.hg19

      Commit: 223913d60b57ed92f514a757e0451e9010221e60

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2019-05-02 11:56:44 -0400

      Commit message:


	  
		
 bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch
 
    
  
    

      Package: RnBeads.hg19

      Commit: 1406523fc4efe380374d8eade39ceb3a1d609e2d

      Author:  nturaga <nitesh.turaga@gmail.com> 

      Date: 2018-10-30 11:38:33 -0400

      Commit message:


	  
		
 bump x.y.z versions to odd y after creation of RELEASE_3_8 branch
 
    
  
    

      Package: RnBeads.hg19

      Commit: 0ad324c7fa1487160b490edb45594f2dc758655b

      Author:  nturaga <nitesh.turaga@gmail.com> 

      Date: 2018-10-30 11:36:24 -0400

      Commit message:


	  
		
 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
 
    
  
    

      Package: RnBeads.hg19

      Commit: ac74db7a65d95f5b78e9e93e7ec27d49a9d02fa5

      Author:  schmic05 <mscherer@mpi-inf.mpg.de> 

      Date: 2018-07-30 09:24:09 +0200

      Commit message:


	  
		
 Updated version number and date
 
    
  
    

      Package: RnBeads.hg19

      Commit: a78d5701b907fab2362681d28f12eb41cd1ec409

      Author:  schmic05 <mscherer@mpi-inf.mpg.de> 

      Date: 2018-07-23 13:23:49 +0200

      Commit message:


	  
		
 Compressed files in /data to remove R CMD check warning
 
    
  
    

      Package: RnBeads.hg19

      Commit: 9e166e2b0490cac925a4a7a9a4b68c773cdee55f

      Author:  schmic05 <mscherer@mpi-inf.mpg.de> 

      Date: 2018-07-23 10:58:55 +0200

      Commit message:


	  
		
 Changed CNV reference data set to new version (GSE100940)
 
    
  
    

      Package: RnBeads.hg19

      Commit: 0d587d45cc83488af592aad5e0ab44d81eca8339

      Author:  schmic05 <mscherer@mpi-inf.mpg.de> 

      Date: 2018-07-18 14:19:21 +0200

      Commit message:


	  
		
 Documented datasets to prevent R CMD check warnings
 
    
  
    

      Package: RnBeads.hg19

      Commit: f2c42266ce778113e3ba839441248cb66c6a5504

      Author:  schmic05 <mscherer@mpi-inf.mpg.de> 

      Date: 2018-07-18 10:12:48 +0200

      Commit message:


	  
		
 Added reference for Copy Number Variation Analysis
 
    
  
    

      Package: RnBeads.hg19

      Commit: 35216bb441ab4af1b8c90b1493d5ac0140998a63

      Author:  Nitesh Turaga <nitesh.turaga@gmail.com> 

      Date: 2018-04-30 10:34:48 -0400

      Commit message:


	  
		
 bump x.y.z versions to odd y after creation of RELEASE_3_7 branch
 
    
  
    

      Package: RnBeads.hg19

      Commit: 86ef1bbf3672e33d65a57c19580c11599970c67d

      Author:  Nitesh Turaga <nitesh.turaga@gmail.com> 

      Date: 2018-04-30 10:31:29 -0400

      Commit message:


	  
		
 bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch
 
    
  
  


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