Complete data package documentation updates
 

 fix link syntax
 

 add ref in readme
 

 use other workflow
 

 update gha
 

 Bumped version and date, streamlined README, fixed license.
 

 Merge pull request #347 from tidyomics/dispersion_estimation

Dispersion estimation 

 Merge pull request #348 from tidyomics/fix/granges-as-tibble-ci

Fix aggregate_duplicates GRanges CI failure on Bioconductor devel 

 Enhance glmmTMBcore function to utilize fixed edgeR phi for dispersion estimation, ensuring consistent parameter handling across gene models.
 

 Merge branch 'dispersion_estimation' of https://github.com/tidyomics/tidybulk into dispersion_estimation
 

 Fix aggregate_duplicates GRanges conversion on Bioconductor devel.

as_tibble() on GRanges now hits broken S4Vectors List dispatch; convert via as.data.frame() first so ubuntu CI passes.

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

 add dependencies
 

 update dev directory
 

 add check for identify abundant
 

 docs
 

 new seqPGEN2GDS()
 

 chore: record roxygen2 8.0.0 via Config/roxygen2/version

roxygen2 8.0.0 (used to regenerate the man pages) replaces the deprecated
RoxygenNote field with Config/roxygen2/version. Metadata only.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01QDhb4MiXhMbNpT7sggqnXe
 

 docs: regenerate seahtrue-package.Rd to include maintainer in Authors

The generated package-level Rd was stale relative to DESCRIPTION Authors@R
(Vincent de Boer, role aut+cre with ORCID). roxygen2::roxygenise() restores
the author entry. No code or NAMESPACE change.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01QDhb4MiXhMbNpT7sggqnXe
 

 ci: build seahtrue wasm against webR v0.5.2 (R 4.5.1) to match the book

library(seahtrue) failed in the book with "there is no package called
'seahtrue'". Root cause: webR wasm binaries are R-version specific and live
under bin/emscripten/contrib//. The book (the_book_of_seahtrue) uses
the quarto-live extension, which bundles webR v0.5.2 = R 4.5.1, so its runtime
fetches packages from contrib/4.5/. Building with ghcr.io/r-wasm/webr:main
produced an R 4.6 binary under contrib/4.6/ only, so the book's webR could not
find seahtrue (deps like tidyverse still resolved because repo.r-wasm.org
serves contrib/4.5).

`:main` is unreleased R 4.6, which no released webR / quarto-live runtime can
load, so it can never work for the book. Pin the build image to a released
webR whose R version matches the book. Expose it as a workflow_dispatch input
(default ghcr.io/r-wasm/webr:v0.5.2) so it can track the book's quarto-live
webR version without editing the file. The verify step already globs any
contrib// dir, so it now asserts the binary lands under 4.5.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01QDhb4MiXhMbNpT7sggqnXe
 </pre>
    </div>
  
    

      Package: seahtrue

      Commit: ba2856cbbb65ebb40dfc82b44a424c55298dd80a

      Author:  vcjdeboer <vcjdeboer@gmail.com> 

      Date: 2026-09-05 19:13:14 +0200

      Commit message:


	  
		
 ci: disable pak sysreqs so seahtrue wasm binary actually builds

The previous commit removed make_vfs_library, but the real blocker is
upstream of it: rwasm::add_pkg builds seahtrue's wasm binary by first
installing its R deps into host R via pak (rwasm R/build.R:
pak::pkg_install("deps::")). In the latest webR container pak's
"Installing system requirements" step runs `sh -c apt-get -y update`,
which fails and aborts the pak subprocess. rwasm wraps that call in try()
and treats a failed wasm build as a warning, so the step exited 0 while
producing no seahtrue binary (emscripten PACKAGES 404).

Host apt system requirements are irrelevant to a wasm cross-build (deps
come as PPM binaries; seahtrue is NeedsCompilation: no), so set
PKG_SYSREQS=false to skip pak's sysreqs/apt-get handling entirely. Also
add a verification step that fails the job if seahtrue is missing from the
emscripten PACKAGES index, so a green run can no longer hide a failed build.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01QDhb4MiXhMbNpT7sggqnXe
 </pre>
    </div>
  
    

      Package: seahtrue

      Commit: e3b1ccc4da64523bd3c88a99df5bc26b3b24a6ff

      Author:  vcjdeboer <vcjdeboer@gmail.com> 

      Date: 2026-09-05 19:05:55 +0200

      Commit message:


	  
		
 ci: build wasm repo without VFS image to fix webR deploy

The v3 reusable workflow (r-wasm/actions .../deploy-cran-repo.yml@v3)
always runs rwasm::make_vfs_library after add_pkg. In the latest webR
image that step fails: its pak install reports seahtrue's deps "not
available", leaving file_packager with "Nothing to do!" ('Function not
implemented'), which aborts the deploy.

"The book of seahtrue" loads packages via webR directly from the CRAN-like
_site repo URL (its _quarto.yml `webr: repos:`) and does not use a VFS
library image, so make_vfs_library is unnecessary. Replace the reusable
workflow call with a custom job that runs only rwasm::add_pkg (compress=TRUE,
matching the working v3 default) inside ghcr.io/r-wasm/webr:main, then
uploads _site and deploys to Pages. No toolchain pinning; stays on latest
webR/wasm.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01QDhb4MiXhMbNpT7sggqnXe
 
    
  
    

      Package: seahtrue

      Commit: f410dedeea8c5a7ddecab96281f56aef538014ef

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2026-09-05 18:33:33 +0200

      Commit message:


	  
		
 Merge pull request #80 from vcjdeboer/webr-actions-v3

ci: upgrade r-wasm/actions v2 to v3 (fix webR build) 
    
  
    

      Package: seahtrue

      Commit: 5342a1bfc53b92f095dcbaa6385ecf8a2c95aa24

      Author:  vcjdeboer <vcjdeboer@gmail.com> 

      Date: 2026-09-05 18:30:52 +0200

      Commit message:


	  
		
 ci: upgrade r-wasm/actions v2 -> v3 to fix webR build (pkgdepends #462)

v2's build-rwasm code.R reinstalled the latest pkgdepends (0.9.1), which
has upstream bug r-lib/pkgdepends#462 (res_one_row_df: nrow must equal 1)
when resolving a package's full dependency graph against the r-wasm repo.
v3 drops that reinstall and uses the patched pkgdepends baked into the
webR image, fixing the deploy.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01WRiaazotsabW2TZ499LLr4
 
    
  
    

      Package: seahtrue

      Commit: c2b17b17a4bb322715d1fd274494f92980889fd2

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2026-09-05 15:37:29 +0200

      Commit message:


	  
		
 Merge pull request #79 from vcjdeboer/webr-drop-biocstyle

Drop BiocStyle vignette dep so webR build resolves 
    
  
    

      Package: seahtrue

      Commit: 739dec563ac5e2cf1be23a51299e5dd22fe5e0a4

      Author:  vcjdeboer <vcjdeboer@gmail.com> 

      Date: 2026-09-05 15:28:06 +0200

      Commit message:


	  
		
 fix: drop BiocStyle vignette dependency so webR build resolves

Switch the vignette output from BiocStyle::html_document to
rmarkdown::html_document and remove BiocStyle from Suggests. rwasm
cannot resolve the Bioconductor-only BiocStyle without a Remotes hint
(which BiocCheck disallows), which broke the webR/gh-pages build.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01WRiaazotsabW2TZ499LLr4
 
    
  
    

      Package: seahtrue

      Commit: d574d78247a1400512e00b3308a141e55b3adff0

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2026-09-05 15:03:02 +0200

      Commit message:


	  
		
 Merge pull request #78 from vcjdeboer/bioc-space-improvements

Harden bioenergetic space API + Bioconductor readiness 
    
  
    

      Package: seahtrue

      Commit: 5b7318da9f484daf20c7d66e6df8e0e37d265959

      Author:  vcjdeboer <vcjdeboer@gmail.com> 

      Date: 2026-09-05 14:23:26 +0200

      Commit message:


	  
		
 fix: regenerate revive_output_donor_A dataset to drop stale validate/settings dependency

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01WRiaazotsabW2TZ499LLr4
 
    
  
    

      Package: seahtrue

      Commit: 6d51754cf58daaed0d1eeca89b26e0460a933d40

      Author:  vcjdeboer <vcjdeboer@gmail.com> 

      Date: 2026-09-05 13:57:53 +0200

      Commit message:


	  
		
 feat: allow custom atp_factors in calculate_space

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01WRiaazotsabW2TZ499LLr4
 
    
  
    

      Package: seahtrue

      Commit: e2577b5d28b9b08baa935530deacd8f49b001c78

      Author:  vcjdeboer <vcjdeboer@gmail.com> 

      Date: 2026-09-05 13:50:47 +0200

      Commit message:


	  
		
 docs: clarify space plot width uses amrot_ecar by design vs metric max_ecar

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01WRiaazotsabW2TZ499LLr4
 
    
  
    

      Package: seahtrue

      Commit: 55802310d738f9058c17a57e9bae85825c84c5a8

      Author:  vcjdeboer <vcjdeboer@gmail.com> 

      Date: 2026-09-05 13:35:20 +0200

      Commit message:


	  
		
 chore: bump version to 1.7.1, remove Remotes field, finalize NEWS

Prepares the branch for a maintainer-run Bioconductor sync:
- Version 1.1.0.9001 -> 1.7.1 (valid x.y.z, > devel 1.7.0, keeps odd
  devel minor), fixing the BiocCheck invalid-version-format ERROR.
- Removed the Remotes: bioc::BiocStyle field (not allowed for
  Bioconductor packages); BiocStyle remains in Suggests.
- Replaced the temporary BiocCheck working checklist in NEWS.md with
  real user-facing release notes for the development version.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01WRiaazotsabW2TZ499LLr4
 
    
  
    

      Package: seahtrue

      Commit: 500c9b9c6e1576aef5fd638da41bfeff7c4a0b21

      Author:  vcjdeboer <vcjdeboer@gmail.com> 

      Date: 2026-09-05 13:12:50 +0200

      Commit message:


	  
		
 test: add coverage for revive_xfplate, calculate_space, and space plots

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01WRiaazotsabW2TZ499LLr4
 
    
  
    

      Package: seahtrue

      Commit: 32039ac0825fde14ab806a5deb0e34e8e6021810

      Author:  vcjdeboer <vcjdeboer@gmail.com> 

      Date: 2026-09-05 10:10:41 +0200

      Commit message:


	  
		
 refactor: consistent naming for space API (args snake_case, SFI wording)

Rename calculate_space() function-local arguments OCR_var/ECAR_var to
ocr_var/ecar_var (signature defaults, body uses, roxygen @param), and
update the corresponding generated man page. No exported column names
are affected: supply_index and all other output columns are unchanged.
SFI wording in comments/roxygen was already consistent
("Supply Flexibility Index (SFI)") - no change needed there.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01WRiaazotsabW2TZ499LLr4
 
    
  
    

      Package: seahtrue

      Commit: 4b90c6dfc09b23b4dd450a1ccbd9dfeb01a98101

      Author:  vcjdeboer <vcjdeboer@gmail.com> 

      Date: 2026-09-05 10:03:09 +0200

      Commit message:


	  
		
 refactor: extract bioenergetic space/trajectory API into space_xfplate.R

Pure move of calculate_space, plot_bioenergetic_space, and
plot_bioenergetic_trajectory (with their roxygen docs) from
plot_xfplate.R into a new R/space_xfplate.R, separating the
bioenergetic-space feature from the QC/sketch plot functions.
No logic changes; NAMESPACE and DESCRIPTION are unchanged. The three
moved man/*.Rd files pick up an updated "edit documentation in" source
pointer reflecting the new file.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01WRiaazotsabW2TZ499LLr4
 
    
  
    

      Package: seahtrue

      Commit: 532ac747edc4019e55434d97cc49c3bba44b1e95

      Author:  vcjdeboer <vcjdeboer@gmail.com> 

      Date: 2026-09-05 09:55:21 +0200

      Commit message:


	  
		
 feat: warn on and document calculate_space canonical name contract

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01WRiaazotsabW2TZ499LLr4
 
    
  
    

      Package: seahtrue

      Commit: 8ecb0f7078ea84167a73d7d63c7cd013a87920dc

      Author:  vcjdeboer <vcjdeboer@gmail.com> 

      Date: 2026-09-05 09:51:42 +0200

      Commit message:


	  
		
 test: tighten calculate_space missing-column test to assert cli message

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01WRiaazotsabW2TZ499LLr4
 
    
  
    

      Package: seahtrue

      Commit: c307868fe19abd549c26d8b0500b7ef4e348401b

      Author:  vcjdeboer <vcjdeboer@gmail.com> 

      Date: 2026-09-05 09:49:02 +0200

      Commit message:


	  
		
 feat: validate calculate_space inputs with clear cli errors

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01WRiaazotsabW2TZ499LLr4
 
    
  
    

      Package: seahtrue

      Commit: 64dbed1c7c0cc4d29963b65e8acd820d7aa3ce3c

      Author:  vcjdeboer <vcjdeboer@gmail.com> 

      Date: 2026-09-05 09:46:18 +0200

      Commit message:


	  
		
 docs: record BiocCheck baseline after Phase 1 hygiene

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01WRiaazotsabW2TZ499LLr4
 
    
  
    

      Package: seahtrue

      Commit: 5e22daf68ba6f75592353d5f53ce5a2323028360

      Author:  vcjdeboer <vcjdeboer@gmail.com> 

      Date: 2026-09-05 09:35:03 +0200

      Commit message:


	  
		
 fix: make R source ASCII-only and remove stray .DS_Store files

- Replace em dash in glue::glue() strings (R/read_xfplate.R) with —
  unicode escapes so R/ is pure ASCII while the rendered message is
  byte-identical.
- Replace non-ASCII prose in roxygen comments (subscript O2, micro sign
  ug, right arrow) with plain ASCII equivalents in R/assertions_read.R
  and R/plot_xfplate.R, and regenerate the matching man/*.Rd pages.
  (Unicode escapes only apply inside R string literals, not comments,
  so ASCII substitution is used there instead to avoid corrupting
  generated Rd/help text.)
- Fix .gitignore case typo (.DS_store -> .DS_Store) and add
  ^.*\.DS_Store$ to .Rbuildignore. No .DS_Store files were actually
  present/tracked in this worktree.
- Add ^\.git$ to .Rbuildignore: R CMD check's "hidden files and
  directories" NOTE was actually caused by the .git entry being
  bundled into the source tarball, not .DS_Store.

Verified via R CMD build + R CMD check --no-manual: both the
non-ASCII WARNING and hidden-files NOTE are gone; overall check
Status: OK.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01WRiaazotsabW2TZ499LLr4
 
    
  
    

      Package: seahtrue

      Commit: d3ec297dfd7cfc452936424a0b9d43b162bcd8de

      Author:  vcjdeboer <vcjdeboer@gmail.com> 

      Date: 2026-09-05 09:18:39 +0200

      Commit message:


	  
		
 fix: register NSE column names to clear no-visible-binding NOTEs

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01WRiaazotsabW2TZ499LLr4
 
    
  
    

      Package: seahtrue

      Commit: 72093ee37766a73f5edcdad4356d82601f8417d8

      Author:  vcjdeboer <vcjdeboer@gmail.com> 

      Date: 2026-09-05 09:02:31 +0200

      Commit message:


	  
		
 fix: use linewidth instead of deprecated ggplot2 size for line geoms

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01WRiaazotsabW2TZ499LLr4
 
    
  
    

      Package: seahtrue

      Commit: d0fec7dcb23fd1f4dd9c311198bc84fcd25ca03c

      Author:  vcjdeboer <vcjdeboer@gmail.com> 

      Date: 2026-09-05 09:01:04 +0200

      Commit message:


	  
		
 style: use cli instead of cat for user-facing output in master.R

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01WRiaazotsabW2TZ499LLr4
 
    
  
    

      Package: seahtrue

      Commit: da318749052b2023b87cabd04b6a63139ce954f1

      Author:  vcjdeboer <vcjdeboer@gmail.com> 

      Date: 2026-09-05 09:00:34 +0200

      Commit message:


	  
		
 build: exclude prototype qmd and tooling dirs from package build

Also excludes the .superpowers/ workspace at the package root
(docs/superpowers does not exist in this tree; the stray SDD
workspace lives at top level, so ^\.superpowers$ was added
alongside the four specified patterns to actually satisfy the
build-exclusion verification).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01WRiaazotsabW2TZ499LLr4
 
    
  
    

      Package: seahtrue

      Commit: 06648642c966d6c226cd21c9ae0afa7b4b9e141a

      Author:  vcjdeboer <vcjdeboer@gmail.com> 

      Date: 2026-09-05 08:55:00 +0200

      Commit message:


	  
		
 docs: add Bioconductor-readiness & space-API hardening plan

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01WRiaazotsabW2TZ499LLr4
 
    
  
    

      Package: seahtrue

      Commit: 40d3d0671e59ed4471b5d4715cb993fcd4fc7439

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2026-01-26 17:10:44 +0100

      Commit message:


	  
		
 Update package reference to seahtrue@devel 
    
  
    

      Package: seahtrue

      Commit: eaaf624c8745da6bac3019f2d4369d8dd780a40d

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2026-01-26 16:36:09 +0100

      Commit message:


	  
		
 Remove webr-image specification from workflow 
    
  
    

      Package: seahtrue

      Commit: d8b5b29736ced2407b8824ace6a9f7c345b19cbd

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2026-01-26 16:22:53 +0100

      Commit message:


	  
		
 Update workflow to deploy devel branch and webr image 
    
  
    

      Package: seahtrue

      Commit: 24e0e650ac0852e3464db26e93cf507e445426c1

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-11-07 11:33:57 +0100

      Commit message:


	  
		
 fix: handle string "N/A" values in O2_mmHg and pH before NA replacement

Some Seahorse or Excel exports encode missing sensor readings as the literal
string "N/A" instead of true NA. This caused type coercion issues and false
numeric values during QC. The verify_xf_raw() function now:

- Detects "N/A", "NaN", and empty string "" entries
- Converts them to proper NA_real_ before numeric checks
- Replaces remaining NA values with 0 and logs cli messages

Prevents downstream errors from Excel-style string N/A values.
 
    
  
    

      Package: seahtrue

      Commit: d2dd85c2668cba6454d493b9b724c9fa4d7a411e

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-11-07 11:22:02 +0100

      Commit message:


	  
		
 fix: replace NA values in O2_mmHg and pH with zero during raw verification

Adds automatic NA handling in verify_xf_raw():
- Detects and replaces NA in O2_mmHg or pH with 0
- Prints informative cli messages when replacements occur
Prevents downstream numerical errors caused by missing sensor readings.
 
    
  
    

      Package: seahtrue

      Commit: 61f06657345b0697e3a008ff5a513ebcc02f4d2e

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-11-07 11:01:11 +0100

      Commit message:


	  
		
 fix: xf_rate_test to xf_rate
 
    
  
    

      Package: seahtrue

      Commit: c80d6a4cbd1716cb9b3aa52e97e2ff150d8bd093

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-11-07 10:47:12 +0100

      Commit message:


	  
		
 fix: robust background correction check using xf_rate

Replaces fragile logic that caused NA and type errors when Background wells
were missing or contained non-numeric OCR values. The new block:

- Uses xf_rate instead of xf_rate_test in the main function
- Handles missing 'ocr' column gracefully
- Coerces OCR to numeric safely (suppresses warnings)
- Returns TRUE/FALSE/NA/"no_background" consistently

Prevents 'missing value where TRUE/FALSE needed' errors during background correction detection.
 
    
  
    

      Package: seahtrue

      Commit: ab70f41a32a9950cb78fdffae3d9a523494f4691

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-11-07 09:43:48 +0100

      Commit message:


	  
		
 fix: remove flagged background wells before group join to prevent normalization errors
 
    
  
    

      Package: seahtrue

      Commit: ea331f54eb0a233a54db511b3ef05d3168af8ac4

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-06-27 16:04:27 +0200

      Commit message:


	  
		
 Update README.md 
    
  
    

      Package: seahtrue

      Commit: 32555b99bf1ac828bbd91017be59979c910a6d7d

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-05-19 10:59:04 +0200

      Commit message:


	  
		
 fix: fixed more global variables and function calls
 
    
  
    

      Package: seahtrue

      Commit: 91d00ae0232543dcb4894ca4eb2790744b7fe06d

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-05-19 10:43:11 +0200

      Commit message:


	  
		
 fix: excluded state
 
    
  
    

      Package: seahtrue

      Commit: 497c2b64961859ead6304c2c3d329b1bafc238d8

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-05-19 10:30:37 +0200

      Commit message:


	  
		
 fix: .data$state over function state
 
    
  
    

      Package: seahtrue

      Commit: 29f4f36f2a54d8853f3a26bace381c9cc782661f

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-05-19 10:15:18 +0200

      Commit message:


	  
		
 refactor: devtools::check() and namespace update
 
    
  
    

      Package: seahtrue

      Commit: 0ef11cf50194ea00a1753d44945eae334f945a68

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-05-19 09:02:38 +0200

      Commit message:


	  
		
 feat: space plots added
 
    
  
    

      Package: seahtrue

      Commit: d934a7a8b386f37c7e7d2f806cdafac0b690ada4

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-04-01 11:48:08 +0200

      Commit message:


	  
		
 Merge branch 'devel' of github.com:vcjdeboer/seahtrue into devel
 
    
  
    

      Package: seahtrue

      Commit: 0c7bde4067c4f58e3986b2befbedaec38e511691

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-04-01 11:46:26 +0200

      Commit message:


	  
		
 refactor: update version
 
    
  
    

      Package: seahtrue

      Commit: 211757a344ada6540b960fde6023210624f59214

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-04-01 11:42:06 +0200

      Commit message:


	  
		
 Update webr.yml 
    
  
    

      Package: seahtrue

      Commit: 9c0ee004848c62f707893c18cd1056c65d5273bc

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-04-01 11:37:48 +0200

      Commit message:


	  
		
 Update webr.yml 
    
  
    

      Package: seahtrue

      Commit: d322fd9ee0bb51f2b0471532f55ff2d5c1cc06da

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-04-01 11:33:18 +0200

      Commit message:


	  
		
 refactor: cell_n NA was dealed with, don't need validation anymore
 
    
  
    

      Package: seahtrue

      Commit: 1addafd3c6a71e5d65328524ddd6ab28e53c736a

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-04-01 11:31:49 +0200

      Commit message:


	  
		
 refactor: final validate leftover removed
 
    
  
    

      Package: seahtrue

      Commit: 5fd2e98f89658fd299fdc3b520c3aa50c23610bc

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-04-01 10:43:18 +0200

      Commit message:


	  
		
 fix: change NA handling for normzalization reads
 
    
  
    

      Package: seahtrue

      Commit: 85ea8df163ccfea5de179b8d79c7ee81f43a1e97

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-04-01 10:23:04 +0200

      Commit message:


	  
		
 refactor: get rid of slow validate package, now jsut tidy functions for evaluating qc
 
    
  
    

      Package: seahtrue

      Commit: 19049442aaa00b1e51f9a4dd4e7543c266889c31

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-04-01 10:22:09 +0200

      Commit message:


	  
		
 feat: include instrument type
 
    
  
    

      Package: seahtrue

      Commit: 30c90f1f2db681b0215a6014b3fc680346a405bb

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-03-30 22:57:26 +0200

      Commit message:


	  
		
 fix: typo in column name in alert
 
    
  
    

      Package: seahtrue

      Commit: 5b1a544c45f3e22b126f1b163f8a7ac672d3d1b2

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-03-30 22:55:47 +0200

      Commit message:


	  
		
 refactor: conditional tidyxl use. tidyxl not available in webr, move to suggests. REAL commit
 
    
  
    

      Package: seahtrue

      Commit: ada6a83c9e67e8379193c7fe441a7027fddcee9f

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-03-30 22:53:51 +0200

      Commit message:


	  
		
 refactor: conditional tidyxl use. The todyxl is not available for webr, so need to move it to suggests
 
    
  
    

      Package: seahtrue

      Commit: 9cf4f89e19d798c9a9a67fcac557d36eeb7d31e1

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-03-30 21:36:36 +0200

      Commit message:


	  
		
 Merge remote-tracking branch 'upstream/RELEASE_3_20'
 
    
  
    

      Package: seahtrue

      Commit: 8cf365ab96a6fc1936adc5bfa04d2b00f4e90111

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-03-30 11:19:31 +0200

      Commit message:


	  
		
 Update webr.yml 
    
  
    

      Package: seahtrue

      Commit: f7b2cf5198256ae227dbf773ad99c72e293d8de7

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-03-30 11:17:22 +0200

      Commit message:


	  
		
 Update webr.yml 
    
  
    

      Package: seahtrue

      Commit: 36fb73fc457b80027deef53a840b409faa75ce75

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-03-30 11:11:13 +0200

      Commit message:


	  
		
 Update webr.yml 
    
  
    

      Package: seahtrue

      Commit: 1964b37f62fedc8f49095039ab066bd70bac3066

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-03-30 11:00:28 +0200

      Commit message:


	  
		
 Update webr.yml 
    
  
    

      Package: seahtrue

      Commit: c74e4a1e26dfff211b5815feb03f1851cc7307e3

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-03-30 10:58:01 +0200

      Commit message:


	  
		
 Update webr.yml 
    
  
    

      Package: seahtrue

      Commit: af244868d461c50839d33766b724a182790451ce

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-03-30 10:50:16 +0200

      Commit message:


	  
		
 Update webr.yml 
    
  
    

      Package: seahtrue

      Commit: b33b684987ce84d94dee8bd40a7c1e2df50a16ca

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-03-30 10:49:00 +0200

      Commit message:


	  
		
 Update webr.yml 
    
  
    

      Package: seahtrue

      Commit: b88178da67eac19bbdb09a91e7ebd5dfa4d9f2c9

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2025-03-30 10:44:33 +0200

      Commit message:


	  
		
 Create webr.yml 
    
  
    

      Package: seahtrue

      Commit: 1be0d45b84fcdbe2dabee93ee05673d370fc775c

      Author:  Vincent de Boer <vcjdeboer@gmail.com> 

      Date: 2024-12-03 07:22:45 +0100

      Commit message:


	  
		
 Merge pull request #75 from PabRod/main

Declare bioconductor dependencies source 
    
  
    

      Package: seahtrue

      Commit: 64388f171108b2d2aac4e74e8f527dc2c6dc597d

      Author:  Pablo Rodríguez Sánchez <pablo.rodriguez.sanchez@gmail.com> 

      Date: 2024-11-29 12:56:27 +0100

      Commit message:


	  
		
 Use less operative systems

Latest release for the 3 most popular ones is enough
 
    
  
    

      Package: seahtrue

      Commit: 359868a1cf3235f409ee431ff9701b901235369d

      Author:  Pablo Rodríguez Sánchez <pablo.rodriguez.sanchez@gmail.com> 

      Date: 2024-11-29 12:40:41 +0100

      Commit message:


	  
		
 Add basic GitHub action
 
    
  
    

      Package: seahtrue

      Commit: fded42ebc3652ead30f1ebfa8de37d7f3e6df45c

      Author:  Pablo Rodríguez Sánchez <pablo.rodriguez.sanchez@gmail.com> 

      Date: 2024-11-28 15:31:40 +0100

      Commit message:


	  
		
 Declare bioconductor dependencies source

Otherwise the installation has to be completed manually
 
    
  
    

      Package: epialleleR

      Commit: 1124a6a2da6410653e71b66b48765b8ce6bed32d

      Author:  Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no> 

      Date: 2026-09-05 14:10:29 +0200

      Commit message:


	  
		
 + better plotting, acknowledgements
 
    
  
    

      Package: epialleleR

      Commit: 074df9c7c2a07965c7ad488f9b439fd2f0568ebe

      Author:  Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no> 

      Date: 2026-09-05 14:07:25 +0200

      Commit message:


	  
		
 + better plotting, acknowledgements
 
    
  
    

      Package: epialleleR

      Commit: b9b055c38a6a65d86ff42424cbf23578f2add1bb

      Author:  Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no> 

      Date: 2026-09-05 14:06:38 +0200

      Commit message:


	  
		
 + better plotting
 
    
  
    

      Package: epialleleR

      Commit: 579a7f54bacad67af4b8c2f4f146a19fb162fae5

      Author:  Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no> 

      Date: 2026-09-05 14:06:04 +0200

      Commit message:


	  
		
 + doi
 
    
  
    

      Package: epialleleR

      Commit: 5499433b71a7e3da432406412730ddbce9411faa

      Author:  Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no> 

      Date: 2026-09-04 17:32:03 +0200

      Commit message:


	  
		
 non-ASCII fix
 
    
  
    

      Package: alabaster.vcf

      Commit: d88aa63410e779f0b99b8d3db27e1b81156c7bfb

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

      Date: 2026-09-05 16:35:39 +1000

      Commit message:


	  
		
 Simplified README to point to landing page, fixed license, updated NEWS.

Also bumped version and date for a new release.
 
    
  
    

      Package: alabaster.vcf

      Commit: 77c3cd4fb32dfbe978204eefe53ad08f33b72297

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

      Date: 2026-09-05 16:35:05 +1000

      Commit message:


	  
		
 Officially deprecate the stageObject(), loadObject() methods.

Almost everyone should already be using saveObject and loadObject anyway.

Also fixed the manpage links to include the package name of external functions.
 
    
  
    

      Package: alabaster.base

      Commit: ee547d7c0681b28f1a6497743a2559dc25fd1130

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

      Date: 2026-09-05 16:00:47 +1000

      Commit message:


	  
		
 Include alabaster.vcf::readVCF in readObject dispatch for vcf_experiment.
 
    
  
    

      Package: alabaster.spatial

      Commit: 043098aac8d353c3811f3f1e74e714ba7899e826

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

      Date: 2026-09-05 15:47:56 +1000

      Commit message:


	  
		
 Officially deprecate the stageObject(), loadObject() methods.

Almost everyone should already be using saveObject and loadObject anyway.

Also fixed the manpage links to include the package name of external functions,
and streamlined the README to reference the BioC landing page.

Bumped version and date for a new release.
 
    
  
    

      Package: miRSM

      Commit: 7c5e02b01baac4f5cc072e8f2681dc6ed43dcfbf

      Author:  zhangjunpeng411 <zhangjunpeng_411@yahoo.com> 

      Date: 2026-09-05 13:37:19 +0800

      Commit message:


	  
		
 Update
 
    
  
    

      Package: miRSM

      Commit: 265527911e0310d2bc933952c67cdee8fe371cf6

      Author:  zhangjunpeng411 <zhangjunpeng_411@yahoo.com> 

      Date: 2026-09-03 20:07:05 +0800

      Commit message:


	  
		
 Update
 
    
  
    

      Package: miRspongeR

      Commit: dd51ec9a3dfa63bd0dd5561d54f285c0a7b96a1c

      Author:  zhangjunpeng411 <zhangjunpeng_411@yahoo.com> 

      Date: 2026-09-05 13:35:53 +0800

      Commit message:


	  
		
 Update
 
    
  
    

      Package: miRspongeR

      Commit: 6a92748ff3841ad4d83e9d2da5dd783098418548

      Author:  zhangjunpeng411 <zhangjunpeng_411@yahoo.com> 

      Date: 2026-09-03 19:52:45 +0800

      Commit message:


	  
		
 UPDATE
 
    
  
    

      Package: alabaster.se

      Commit: 8fe1157c1445e492ef3a07416640a6404071242f

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

      Date: 2026-09-05 15:01:04 +1000

      Commit message:


	  
		
 Bumped version and date, streamlined README to point to the BioC page.
 
    
  
    

      Package: alabaster.se

      Commit: 2bb1b28c066b86c3490b48498bb2c757b09b9973

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

      Date: 2026-09-05 15:00:12 +1000

      Commit message:


	  
		
 Officially deprecate the stageObject(), loadObject() methods.

Almost everyone should already be using saveObject and loadObject anyway.

Also fixed the manpage links to include the package name of external functions.
 
    
  
    

      Package: alabaster.sce

      Commit: c48839b334f47f56f90d6ed41925f9cae5c28709

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

      Date: 2026-09-05 14:51:36 +1000

      Commit message:


	  
		
 Minor docfixes, simplified README to point to landing page.
 
    
  
    

      Package: alabaster.sce

      Commit: 4df9ede00bed188cb47a2604965edce447219540

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

      Date: 2026-09-05 14:25:13 +1000

      Commit message:


	  
		
 Officially deprecate the stageObject(), loadObject() methods.

Almost everyone should already be using saveObject and loadObject anyway.

Also fixed the manpage links to include the package name of external functions.

Bumped version and date for a new release.
 
    
  
    

      Package: alabaster.ranges

      Commit: 67392867a1c6d0c996f7995c45d7de6bfc1acb19

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

      Date: 2026-09-05 12:38:48 +1000

      Commit message:


	  
		
 Updated NEWS, fixed LICENSE, bumped version and date.
 
    
  
    

      Package: alabaster.ranges

      Commit: 00a28478774ea8aacda44677fb51e5ba0470e0eb

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

      Date: 2026-09-05 12:19:27 +1000

      Commit message:


	  
		
 Officially deprecate the stageObject(), loadObject() methods.

Almost everyone should already be using saveObject and loadObject anyway.

Also fixed the manpage links to include the package name of external functions.
 
    
  
    

      Package: Biostrings

      Commit: fb0cd89830abd054cf2681d6bc6c929981e07b21

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

      Date: 2026-09-04 17:04:57 -0700

      Commit message:


	  
		
 Biostrings 2.81.9: Fix issue with as.data.frame.XStringSet(), improve tests
 
    
  
    

      Package: BiocBookDemo

      Commit: 45ac12ecff53c2ef7ea22c123f9d4ecfc5151408

      Author:  Jacques <jacquesserizay@gmail.com> 

      Date: 2026-09-04 23:33:51 +0200

      Commit message:


	  
		
 bump to 1.11.1
 
    
  
    

      Package: BiocBookDemo

      Commit: f62a453792b89f611ef62dbde4d0e8014d0d23ea

      Author:  Jacques <jacquesserizay@gmail.com> 

      Date: 2026-09-04 22:51:35 +0200

      Commit message:


	  
		
 fix: python code chunk styling
 
    
  
    

      Package: BiocBookDemo

      Commit: d0ebc71142a96f083228fdfd3f92f3f63e79f1c9

      Author:  Jacques <jacquesserizay@gmail.com> 

      Date: 2026-09-04 22:37:29 +0200

      Commit message:


	  
		
 fix: deeptool call
 
    
  
    

      Package: BiocBookDemo

      Commit: 214a0f6f1e70408e257c52e7753fc222f9a853c7

      Author:  Jacques <jacquesserizay@gmail.com> 

      Date: 2026-09-04 22:16:45 +0200

      Commit message:


	  
		
 fix: cooler calls
 
    
  
    

      Package: BiocBookDemo

      Commit: f3ab969763d74b832b2a39e702cb890603860606

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-09-04 15:31:53 +0200

      Commit message:


	  
		
 deps: add remotes entry for js2264/BiocBook
 
    
  
    

      Package: BiocBookDemo

      Commit: 9b22b0a5111b436e83eb7619f5df405d48f81292

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-09-04 14:55:06 +0200

      Commit message:


	  
		
 feat: try python chunks
 
    
  
    

      Package: BiocBookDemo

      Commit: 5ec6cc57d053215a555b2df43b11cd8e811afcd3

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-09-04 13:37:33 +0200

      Commit message:


	  
		
 ci: install remotes
 
    
  
    

      Package: BiocBookDemo

      Commit: ca6e15e72a8a688d06a288d108ecce45644c7c29

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-09-04 12:35:49 +0200

      Commit message:


	  
		
 fix: enable pdf
 
    
  
    

      Package: BiocBook

      Commit: 562ccc635b0c10de5985680723cd8a7e069b3700

      Author:  Jacques <jacquesserizay@gmail.com> 

      Date: 2026-09-04 23:07:54 +0200

      Commit message:


	  
		
 bump to 1.11.1
 
    
  
    

      Package: BiocBook

      Commit: ab1ec74767b683b2f58ae06f5b8be0e2befa3377

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-09-04 17:08:38 +0200

      Commit message:


	  
		
 fix: update documentation
 
    
  
    

      Package: BiocBook

      Commit: 322a1b2503af44afe551ea32e3191e2df1685fb8

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-09-04 16:24:51 +0200

      Commit message:


	  
		
 doc: enhance doc for Python integration with setup_python and micromamba support
 
    
  
    

      Package: BiocBook

      Commit: 035b6e614b14ce7659ae27d6118f8e6715ae5912

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-09-04 15:31:12 +0200

      Commit message:


	  
		
 fix: move reticulate from Suggests to Imports
 
    
  
    

      Package: BiocBook

      Commit: ae57e24ff22aca7fbee763e3a83d24b0388a8ccc

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-09-04 15:26:59 +0200

      Commit message:


	  
		
 feat: add support for Python chapters and micromamba integration
 
    
  
    

      Package: BiocBook

      Commit: 45db39041157e59e95fc5cc09126ab85bae05845

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-09-04 15:21:06 +0200

      Commit message:


	  
		
 feat: add page body directly from function call
 
    
  
    

      Package: splicelogic

      Commit: b78a80ffefe2fc5ce6be14611497113c4b3433ae

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-09-04 15:31:58 -0400

      Commit message:


	  
		
 Version bump to 1.1.4
 
    
  
    

      Package: splicelogic

      Commit: da080e700961eb07a85b7106f928a39a3c33b927

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-09-04 15:31:19 -0400

      Commit message:


	  
		
 update news to 1.1.4 and add renamed functions
 
    
  
    

      Package: splicelogic

      Commit: 6dd72f9595b7d75f982eeb3c1fedb65c0fbf792b

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-09-04 15:28:06 -0400

      Commit message:


	  
		
 rename alternative splice site functions for clarity and update documentation
 
    
  
    

      Package: splicelogic

      Commit: c612e3086961632efdad3d408c3b3b64ea28e3dc

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-09-04 14:55:36 -0400

      Commit message:


	  
		
 update news for version 1.1.3
 
    
  
    

      Package: splicelogic

      Commit: 3e2c8147ebd134e9109787fc23420a489b1e57ff

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-09-04 14:53:06 -0400

      Commit message:


	  
		
 Version bump to 1.1.3
 
    
  
    

      Package: splicelogic

      Commit: c4c1bac824dfdaadb01bf34a19690b7201ef6414

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-09-04 14:27:04 -0400

      Commit message:


	  
		
 update README
 
    
  
    

      Package: splicelogic

      Commit: 86c9d38b5476ddc39683fca6ff4fb00f42f68b61

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-09-04 14:22:13 -0400

      Commit message:


	  
		
 vignette updates and reorganization
 
    
  
    

      Package: splicelogic

      Commit: 615a016eb5798831da3f245ae496b071ce3c89d9

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-09-04 14:20:01 -0400

      Commit message:


	  
		
 Update documentation for 'type' parameter in find_events functions
 
    
  
    

      Package: splicelogic

      Commit: 43a3af54ad7a36e26980ee20c0cf11a5df55d42f

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-09-03 22:03:26 -0400

      Commit message:


	  
		
 Enhance documentation and include alternative transcription start and end site detection
 
    
  
    

      Package: splicelogic

      Commit: 603a49df90592a0b482b715b935157afe3991807

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-09-03 22:03:01 -0400

      Commit message:


	  
		
 Add 'coord_sig' to globalVariables in mock data generation functions
 
    
  
    

      Package: splicelogic

      Commit: cd0834b71bdfb74904c0deb2bf2fae7e56375a5f

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-09-03 21:55:17 -0400

      Commit message:


	  
		
 lowercase functions find_atss and find_ates
 
    
  
    

      Package: splicelogic

      Commit: a1b5afed7f099009fbac1328db505029b0b46471

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-09-03 21:31:17 -0400

      Commit message:


	  
		
 update documentation
 
    
  
    

      Package: splicelogic

      Commit: b76726731744ee32f08360dcddabfe728a276cbc

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-09-03 21:29:36 -0400

      Commit message:


	  
		
 Add functions for alternative transcription start and end site detection with tests
 
    
  
    

      Package: splicelogic

      Commit: c5d76e542805cde079361068ccc2830f5ebe4846

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-09-03 21:20:50 -0400

      Commit message:


	  
		
 Add functions for alternative transcription start and end site detection
 
    
  
    

      Package: splicelogic

      Commit: ea74b27d9d516af98941aa0f0f8bb09ea39baf5d

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-09-03 14:48:16 -0400

      Commit message:


	  
		
 allow a3ss and a5ss to happen in same exon and avoid misslabeling in first and last exons
 
    
  
    

      Package: splicelogic

      Commit: 13f259a9eaaf4dde27098a2d61db82d04a1eeb97

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-08-31 16:35:03 -0400

      Commit message:


	  
		
 Add strand argument to create_mock_data documentation and examples
 
    
  
    

      Package: splicelogic

      Commit: ded70e04a2ec68c5843b7b49f11cded4ea6ca7d3

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-08-31 16:34:36 -0400

      Commit message:


	  
		
 support & tests for minus-strand data handling in event detection functions and mock data generation
 
    
  
    

      Package: splicelogic

      Commit: 95da67951f7343d4569e631154d173925c043748

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-08-31 16:25:06 -0400

      Commit message:


	  
		
 Add support for strand-specific a5ss/a3ss detection in find_alt_ss and corresponding tests
 
    
  
    

      Package: splicelogic

      Commit: 3b91fd3c880316cdd6bef5ec824fecf35a78db3a

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-08-27 16:47:45 -0400

      Commit message:


	  
		
 remove gene_id column for visibility
 
    
  
    

      Package: splicelogic

      Commit: 0ba1f8cddb72c4e4a1f4fe4028640c14dd539cbe

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-08-27 16:44:06 -0400

      Commit message:


	  
		
 Clarify documentation on upstream DTU methods in vignette
 
    
  
    

      Package: splicelogic

      Commit: 028938c48a99e2b8aba5eeae4ef9911a4a9bbf7d

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-08-27 16:33:12 -0400

      Commit message:


	  
		
 Enhance documentation for `find_*()` functions in vignette
 
    
  
    

      Package: splicelogic

      Commit: 30444b66c4158a1fd6f91c01cd96363b102d47bc

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-08-27 16:22:05 -0400

      Commit message:


	  
		
 Update mock data generation script and files for exon_id
 
    
  
    

      Package: splicelogic

      Commit: 5dc7c080aa24ac66a6cf871ffe3aecf98b36ade9

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

      Date: 2026-08-26 13:56:58 -0400

      Commit message:


	  
		
 fix the bug
 
    
  
    

      Package: splicelogic

      Commit: b04e42bd0dabccd6e384187f77034944a162b70b

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

      Date: 2026-08-26 13:31:08 -0400

      Commit message:


	  
		
 one more tweak
 
    
  
    

      Package: splicelogic

      Commit: 4948fe1b50796f3d2cf3a748c1e3b409a3328945

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

      Date: 2026-08-26 13:20:29 -0400

      Commit message:


	  
		
 some vignette tweaks
 
    
  
    

      Package: splicelogic

      Commit: f0c12e7109c04df3b17af46ea32bc951d113f321

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

      Date: 2026-08-26 12:11:08 -0400

      Commit message:


	  
		
 tweak to the README
 
    
  
    

      Package: splicelogic

      Commit: e92abf0c08daa93a2da0e18cf6977aabf25ed5fc

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-08-21 17:24:46 -0400

      Commit message:


	  
		
 Update installation instructions
 
    
  
    

      Package: splicelogic

      Commit: dba60f4b6ef6bff6764a12b7ccc4e4a3240326a4

      Author:  Beatriz Campillo <beatrizcampillo29@gmail.com> 

      Date: 2026-08-21 17:20:43 -0400

      Commit message:


	  
		
 Update README title for clarity 
    
  
    

      Package: splicelogic

      Commit: 66336cb1f052b5843babf699ae819cd7501620bf

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-08-21 17:18:48 -0400

      Commit message:


	  
		
 fix library(splicelogic) call
 
    
  
    

      Package: splicelogic

      Commit: 6a21745dbbbb1504abb2f8ef26388f19365e0ff6

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-08-21 17:11:30 -0400

      Commit message:


	  
		
 Update README to clarify splicelogic functionality for transcript sets
 
    
  
    

      Package: splicelogic

      Commit: 9a8e22ef7a82941e7a8d4b88a5f21ca1f1fedf2e

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-08-21 17:08:00 -0400

      Commit message:


	  
		
 Big reorganization and include example for transcript sets
 
    
  
    

      Package: splicelogic

      Commit: ba05881b0b4001b799a6d4594a385a068592ff66

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-08-21 17:01:17 -0400

      Commit message:


	  
		
 comment fix
 
    
  
    

      Package: splicelogic

      Commit: e4d0fe8207a5f0327b13167e24cb30d872eb719c

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-08-21 16:46:36 -0400

      Commit message:


	  
		
 Add mock data generation script and corresponding exon files
 
    
  
    

      Package: splicelogic

      Commit: cd746588c7e6c505d6123aebe064dc38cae4c721

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-08-20 16:09:32 -0400

      Commit message:


	  
		
 Add test for find_mxe to ignore overlapping middle exon as MX candidate
 
    
  
    

      Package: splicelogic

      Commit: 328178ef785a742a5e4ea04c24f5c5b833c26f03

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-08-20 16:09:17 -0400

      Commit message:


	  
		
 Fix: improve filtering logic for mxe to avoid FP
 
    
  
    

      Package: splicelogic

      Commit: d2f50d2826b0c752740660ef0c64cd9ddcdb3394

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-08-10 15:01:00 -0400

      Commit message:


	  
		
 Add tests for exon_rank validation in preprocess function
 
    
  
    

      Package: splicelogic

      Commit: 8e24c5c057f1f8cb9142d277d54b3a486a0a8678

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-08-10 14:54:47 -0400

      Commit message:


	  
		
 Add cds_mock_data and test for skipped exon detection in cds
 
    
  
    

      Package: splicelogic

      Commit: 784a5a411ebd0d9ebfc4f71104dce7a27cb8dace

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-08-10 14:52:43 -0400

      Commit message:


	  
		
 Fix:  check_exon_rank function to ensure consecutive exon ranks within transcripts in input
 
    
  
    

      Package: splicelogic

      Commit: cb4769ea24bdce6954d34123af07f730da4342d3

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-08-07 10:25:12 -0500

      Commit message:


	  
		
 Fix: update internal flag calculation to correctly handle exon ranks not starting at 1
 
    
  
    

      Package: splicelogic

      Commit: 2c0f9bf996a709bb92abbbe968bdda9e27321151

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

      Date: 2026-07-28 15:04:44 -0400

      Commit message:


	  
		
 adding sim_event column for sim event generators
 
    
  
    

      Package: splicelogic

      Commit: b9ae62f270dc46cd6482df90e455aaf9a6179573

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-07-28 11:58:18 -0400

      Commit message:


	  
		
 Fix: count isoforms not exons when selecting candidates by splitting positive exons by transcript; add testing
 
    
  
    

      Package: splicelogic

      Commit: b8e0f54931162106cd09431e797ac9db89e5c191

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-07-27 17:41:57 -0400

      Commit message:


	  
		
 Fix: count_overlaps() by renaming seqnames to gene_id for accurate gene-specific overlap counting
 
    
  
    

      Package: splicelogic

      Commit: f257e4cf36cefd2991f9b321870a315d471f8337

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

      Date: 2026-07-27 13:04:09 -0400

      Commit message:


	  
		
 fixing the per gene event in generate_se
 
    
  
    

      Package: splicelogic

      Commit: ab22ca47e35aeb030b15902a887e060591c4d125

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

      Date: 2026-07-27 12:10:35 -0400

      Commit message:


	  
		
 per-gene coordinate offset now scales with n_exons_per_tx
 
    
  
    

      Package: splicelogic

      Commit: a24951b26bd4b076657422951774f8127d5b7177

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

      Date: 2026-07-27 11:56:47 -0400

      Commit message:


	  
		
 supressing some select() messages
 
    
  
    

      Package: splicelogic

      Commit: 1ebe730ed7e54affaf96bb5c80fa2f4a7fe2f03f

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-07-27 11:36:34 -0400

      Commit message:


	  
		
 Add alias functions
 
    
  
    

      Package: splicelogic

      Commit: 4bf370c0fbf4401946238cd1ee02a4511d79b9b6

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

      Date: 2026-05-19 17:55:25 -0400

      Commit message:


	  
		
 suppress msg
 
    
  
    

      Package: splicelogic

      Commit: 0f87d488db71ea33251d9f786731f2be20aa72c6

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

      Date: 2026-05-19 17:43:30 -0400

      Commit message:


	  
		
 fix pipe
 
    
  
    

      Package: splicelogic

      Commit: 401821432a62badb4fab6163e8bb2289a3597eca

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

      Date: 2026-05-19 17:43:21 -0400

      Commit message:


	  
		
 fix pipe
 
    
  
    

      Package: splicelogic

      Commit: 3a75b309a9bae20d45074f7832f684443d4e3a25

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

      Date: 2026-05-19 12:47:42 -0400

      Commit message:


	  
		
 updating docs for get_seq
 
    
  
    

      Package: splicelogic

      Commit: 57a21a0460746c4056c05521f8476fd4b5367187

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

      Date: 2026-05-19 09:51:12 -0400

      Commit message:


	  
		
 fix back
 
    
  
    

      Package: splicelogic

      Commit: 5931f89c6a779085ab4d0dbecf2afe088d4bd523

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

      Date: 2026-05-19 09:44:11 -0400

      Commit message:


	  
		
 Merge branch 'devel' of github.com:thelovelab/splicelogic into devel
 
    
  
    

      Package: splicelogic

      Commit: 5044fdc58ba7432a7a59328a44d304e16840a2ac

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

      Date: 2026-05-19 09:44:10 -0400

      Commit message:


	  
		
 small vignette tweaks
 
    
  
    

      Package: splicelogic

      Commit: 6f63ec20d84d765ce0f9140d7f78a8fa813b5156

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-05-19 09:25:58 -0400

      Commit message:


	  
		
 add get_seq() reference
 
    
  
    

      Package: splicelogic

      Commit: 9f8118bef9d1e54a0cd3ddad38dbbfe54ae5ecfe

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-05-18 22:53:29 -0400

      Commit message:


	  
		
 remove check from examples in get_seq documentation
 
    
  
    

      Package: splicelogic

      Commit: 0075a49906ed274720ce5041839976fc0bfdb603

      Author:  beamimc <beatrizcampillo29@gmail.com> 

      Date: 2026-05-18 22:51:16 -0400

      Commit message:


	  
		
 add get_seq function to extract sequences from GRanges
 
    
  
    

      Package: splicelogic

      Commit: c6d723cbfc329cf9832cccc721c14deb88afb902

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

      Date: 2026-05-18 17:18:47 -0400

      Commit message:


	  
		
 some tweaks to the vignette text
 
    
  
    

      Package: SAIGEgds

      Commit: 12a60aa0fd7fcff3041fd8aa5845df028bdf4162

      Author:  Xiuwen Zheng <zhengxwen@gmail.com> 

      Date: 2026-09-04 13:59:39 -0500

      Commit message:


	  
		
 new survial analysis
 
    
  
    

      Package: scpdata

      Commit: f42b85c6bd52be8e9aed352d000c10549d0cd3cb

      Author:  Laurent Gatto <laurent.gatto@uclouvain.be> 

      Date: 2026-09-04 13:46:05 +0000

      Commit message:


	  
		
 Merge pull request #40 from leopoldguyot/master

Add zenodo path for wu2026 
    
  
    

      Package: scpdata

      Commit: 725c98fe87f4e47abcdf7b38534cdca502c6c1ae

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-09-03 17:42:26 +0200

      Commit message:


	  
		
 update data location
 
    
  
    

      Package: scpdata

      Commit: 57c0a9e5df9bbdf64b60a2d5f34338187563b741

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-09-03 17:38:26 +0200

      Commit message:


	  
		
 add data to zenodo
 
    
  
    

      Package: scpdata

      Commit: 9fdd0ae45c0650b0402ea32787145435fe97f3e3

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-09-03 15:31:46 +0200

      Commit message:


	  
		
 Update version and NEWS + fix make-data table
 
    
  
    

      Package: scpdata

      Commit: 1dee3215410ed2bc7ea1aac53015c68e89269a53

      Author:  Léopold Guyot <leopold.guyot13@gmail.com> 

      Date: 2026-09-03 15:25:43 +0200

      Commit message:


	  
		
 Merge branch 'master' into master 
    
  
    

      Package: scpdata

      Commit: 44b5d73969044f7410f821a6d7772bf1f39b3816

      Author:  Léopold Guyot <leopold.guyot13@gmail.com> 

      Date: 2026-04-27 15:58:29 +0200

      Commit message:


	  
		
 Merge branch 'UCLouvain-CBIO:master' into master
 
    
  
    

      Package: scpdata

      Commit: 3578e0d9de4959a29b8541f11c0e9eabed59b5a8

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-04-27 15:58:11 +0200

      Commit message:


	  
		
 change data path to zenodo
 
    
  
    

      Package: BiocCheck

      Commit: d12d0480ea16c2391709df6d010b2c6326d932ad

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

      Date: 2026-09-04 12:03:48 -0400

      Commit message:


	  
		
 Add BiocType as acceptable Description field
 
    
  
    

      Package: BiocCheck

      Commit: ca5c23e019dd695b7a5e29286f593a0e9b13639a

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

      Date: 2026-07-27 11:07:54 -0400

      Commit message:


	  
		
 version bump 1.49.30
 
    
  
    

      Package: BiocCheck

      Commit: d19ace18a62d0f9b2f536eeaa0cdc489cdb3df7c

      Author:  Jeroen Ooms <jeroenooms@gmail.com> 

      Date: 2026-07-27 10:20:06 +0200

      Commit message:


	  
		
 Allow RemoteRef, RemoteUrl, RemoteSha, etc used by R-universe.
 
    
  
    

      Package: spammR

      Commit: 6a00912bf80a805a7ae7479870a722c1b7e303d3

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

      Date: 2026-09-04 08:54:58 -0700

      Commit message:


	  
		
 bumping version
 
    
  
    

      Package: ramr

      Commit: 6be608986bda9d0f39f48f3610ba0200ae9f5769

      Author:  Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no> 

      Date: 2026-09-04 16:53:24 +0200

      Commit message:


	  
		
 correct measure.vars
 
    
  
    

      Package: ramr

      Commit: 93026620b156d9bce60834a6adc5d318ef37bec3

      Author:  Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no> 

      Date: 2026-09-04 16:44:17 +0200

      Commit message:


	  
		
 mcols to S4Vectors
 
    
  
    

      Package: ramr

      Commit: 8c7fb8f577344439a98054f0f327586a2b81002f

      Author:  Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no> 

      Date: 2026-09-04 16:24:09 +0200

      Commit message:


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

      Package: ramr

      Commit: 28a33b2ed0f227a6709d4403f8feeedb573cd27b

      Author:  Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no> 

      Date: 2026-09-04 16:20:57 +0200

      Commit message:


	  
		
 non-ASCII fix
 
    
  
    

      Package: ramr

      Commit: e949322cd76e8c906a2ac295a86aa30aa3e0f6e5

      Author:  Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no> 

      Date: 2026-09-04 16:19:05 +0200

      Commit message:


	  
		
 fresh flow
 
    
  
    

      Package: exploreSE

      Commit: e15d7f5711b8437f37d434b29281e07043605672

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

      Date: 2026-09-04 11:16:54 +0200

      Commit message:


	  
		
 buf fix in .de_results
 
    
  
    

      Package: exploreSE

      Commit: 48c7d194fc4a3efcc5c36e838b09cc7407196823

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

      Date: 2026-09-04 11:10:50 +0200

      Commit message:


	  
		
 excluded NS from the hitlist
 
    
  
    

      Package: OmniAgeR

      Commit: 21c6cec316fffeeb4ffd22257e8282e8443a7a1e

      Author:  Zhaozhen Du <duzhaozhen@inspur.com> 

      Date: 2026-09-04 17:09:39 +0800

      Commit message:


	  
		
 Address Bioconductor review comments
 
    
  
    

      Package: alabaster.mae

      Commit: 32fd9aad7dfa676c8b28d386b69978cc8a494401

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

      Date: 2026-09-04 19:04:42 +1000

      Commit message:


	  
		
 Officially deprecate the stageObject(), loadObject() methods.

Almost everyone should already be using saveObject and loadObject anyway.
 
    
  
    

      Package: OmniAgeRData

      Commit: f5c64ca486ab428571f06c75c6857cedb31f5263

      Author:  Zhaozhen Du <duzhaozhen@inspur.com> 

      Date: 2026-09-04 16:54:10 +0800

      Commit message:


	  
		
 Fix value documentation for clock resources
 
    
  
    

      Package: alabaster.files

      Commit: c1b99b888836f6ece95eb792f78eea844e5b5600

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

      Date: 2026-09-04 18:51:26 +1000

      Commit message:


	  
		
 Added NEWS, updated LICENSE, fixed doclinks and roxygen warnings.
 
    
  
    

      Package: alabaster.files

      Commit: 8d5c2c111ff41ad86e8533ea11a3137432c927bb

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

      Date: 2026-09-04 18:36:11 +1000

      Commit message:


	  
		
 Officially deprecate the stageObject(), loadObject() methods.

Almost everyone should already be using saveObject and loadObject anyway.
We also deprecated the various Wrapper classes in favor of FileReference.
 
    
  
    

      Package: canceR

      Commit: 92939cd570eb107c6ea9b74b2df3c79effbbee8c

      Author:  kmezhoud <kmezhoud@gmail.com> 

      Date: 2026-09-04 09:31:04 +0100

      Commit message:


	  
		
 add pandoc dependency and omit warning caused by @usage tag
 
    
  
    

      Package: alabaster.bumpy

      Commit: bf0a372898af6a40e026bb6e6ea6ee3d0eb24cf8

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

      Date: 2026-09-04 18:08:49 +1000

      Commit message:


	  
		
 Fixed license, added NEWS.
 
    
  
    

      Package: alabaster.bumpy

      Commit: 41522ed6718e831e7c92bafb5c27e7aff821b272

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

      Date: 2026-09-04 18:02:32 +1000

      Commit message:


	  
		
 Officially deprecate the stageObject(), loadObject() methods.

Almost everyone should already be using saveObject and loadObject anyway.
 
    
  
    

      Package: OmniAgeRData

      Commit: 11f63325fb520fa9923c05b4d696a902a803c593

      Author:  Zhaozhen Du <duzhaozhen@inspur.com> 

      Date: 2026-09-04 15:37:53 +0800

      Commit message:


	  
		
 Add resource licensing information and update documentation
 
    
  
    

      Package: alabaster.matrix

      Commit: b1ca9185cdfe42bd0fb08cf7e4244118dbe1b886

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

      Date: 2026-09-04 16:19:00 +1000

      Commit message:


	  
		
 Fleshed out NEWS with the latest changes.
 
    
  
    

      Package: alabaster.matrix

      Commit: 35c2056594c30b172a237e0ce9dbfa8e007b6407

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

      Date: 2026-09-04 16:10:47 +1000

      Commit message:


	  
		
 Officially deprecated functions associated with stageObject/loadObject.

Almost everyone should already be using saveObject and readObject anyway.
 
    
  
    

      Package: alabaster.base

      Commit: e63144a8f66516989b797494b2d51eda37ce854c

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

      Date: 2026-09-04 16:04:23 +1000

      Commit message:


	  
		
 Updated NEWS with the deprecation notice.
 
    
  
    

      Package: alabaster.base

      Commit: 64d4495c070a3f12cb2e26b35de0996170321922

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

      Date: 2026-09-04 14:02:44 +1000

      Commit message:


	  
		
 Officially deprecate all functions for stageObject/loadObject.

We want to push folks to saveObject/readObject, though hopefully they're
already there, given that we've soft-deprecated stage/load for a long time.
 
    
  
    

      Package: edgeR

      Commit: 4a090edefd1379ec471ea81cb84fee50a30c3505

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

      Date: 2026-09-04 15:30:39 +1000

      Commit message:


	  
		
 edgeR 4.99.3
- New argument `impute.eff.len` for catchSalmon() and catchSalmonWithGencode().
- Moderated gene lengths from catchSalmonWithGencode() are now moderated more strongly towards gene average.
- All catch functions store matrix of effective lengths, now called `effective.length`.
- Annotation columns from catch functions now called AveEffLen, Max2MinEffLen instead of AveTxLength, Max2MinTxLength.
- Bug fix to catchRSEM() to store sample-specific tx lengths. Previously just storing those for first sample.
- Expanded help for catch functions.
 
    
  
    

      Package: QFeatures

      Commit: c4b3bb93ec0b824a52d2f20ea05d5b15a26d7c52

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-09-03 20:29:47 +0200

      Commit message:


	  
		
 add pkgdown topic
 
    
  
    

      Package: QFeatures

      Commit: 05a7fffbb96a52b4020910785736b07a840b539c

      Author:  Laurent Gatto <laurent.gatto@uclouvain.be> 

      Date: 2026-09-03 15:44:16 +0000

      Commit message:


	  
		
 Merge pull request #263 from leopoldguyot/aggregateSamples

Implementation of aggregateSamples 
    
  
    

      Package: QFeatures

      Commit: 053108deed33feedd4a1bd96abcbfcc60f6949d2

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-09-03 17:17:51 +0200

      Commit message:


	  
		
 add ORCID
 
    
  
    

      Package: QFeatures

      Commit: 3f15be698ea763fe134e7f18a9014e3587782666

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-08-27 16:48:20 +0200

      Commit message:


	  
		
 replace moreFUN by fixed aggsd and aggcounts extra assays
 
    
  
    

      Package: QFeatures

      Commit: ed02bdf51f14182e2339dc8c6931a397147c80c5

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-08-19 16:45:06 +0200

      Commit message:


	  
		
 add extra parameters for setAs
 
    
  
    

      Package: QFeatures

      Commit: 1cb5eae9f670bf9a03284b474b0e275a9599ecb7

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-08-19 11:56:49 +0200

      Commit message:


	  
		
 assay into set QFeatures-class.R
 
    
  
    

      Package: QFeatures

      Commit: 26e85fe48758876e4b568fd22120c1d89db91162

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-08-19 11:06:20 +0200

      Commit message:


	  
		
 rename assay into set in aggregate tests
 
    
  
    

      Package: QFeatures

      Commit: fe939d0b12e44e55c037925a4a22500d65cbb698

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-08-19 10:28:15 +0200

      Commit message:


	  
		
 rename assay by set in QFeatures-aggregation.R
 
    
  
    

      Package: QFeatures

      Commit: 22643f908682b99ceda7c8d14a0f391475d5ad8e

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-07-29 15:15:29 +0200

      Commit message:


	  
		
 add NEWS + update outdated condition
 
    
  
    

      Package: QFeatures

      Commit: 79a7e4bc4aaa65c0c65949ba2d02737059caf68d

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-07-29 14:46:48 +0200

      Commit message:


	  
		
 colData joining handled by addAssay, argument forwarding, drop factor + tests and docs
 
    
  
    

      Package: QFeatures

      Commit: 9b35df2522b1cb24984f8a7fa4f928f392d4b8b3

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-07-28 16:25:35 +0200

      Commit message:


	  
		
 add tests for aggregateSamples + styling
 
    
  
    

      Package: QFeatures

      Commit: 62a2eb799f0636ac77ce9ccf45323df54128c3fb

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-07-28 13:07:02 +0200

      Commit message:


	  
		
 enforce i and name of length one
 
    
  
    

      Package: QFeatures

      Commit: 8fe9d57679ba19e9551a99e72d9fdbada75b7c2e

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-06-29 17:13:34 +0200

      Commit message:


	  
		
 first implementation of aggregateSample
 
    
  
    

      Package: spammR

      Commit: 0b17c8af18ef96b4987a08af8d95c281b5c9da3a

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

      Date: 2026-09-03 11:57:06 -0700

      Commit message:


	  
		
 updated to address build issues
 
    
  
    

      Package: spammR

      Commit: 108eb55f1411a76ba8d7caff475cdf8e67bf7d71

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

      Date: 2026-09-03 11:03:26 -0700

      Commit message:


	  
		
 updated documentation
 
    
  
    

      Package: spammR

      Commit: bce77ccc76ecb490e07d57a3cec363b1996722a6

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

      Date: 2026-09-03 10:22:05 -0700

      Commit message:


	  
		
 moved to DT::datatable

Per recommendation from Vince Carey, updated vignettes
 
    
  
    

      Package: exploreSE

      Commit: 16e225f2af495f7c542231f519acd8044f3e1fb7

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

      Date: 2026-09-03 16:45:46 +0200

      Commit message:


	  
		
 added split table
 
    
  
    

      Package: exploreSE

      Commit: f88954b0529d15b61a689496252f8322259144f6

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

      Date: 2026-08-24 13:54:36 +0200

      Commit message:


	  
		
  readme update
 
    
  
    

      Package: exploreSE

      Commit: 8b9700aa5ccaf127bacdf6e24352105967614891

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

      Date: 2026-08-21 11:47:18 +0200

      Commit message:


	  
		
 updated readme
 
    
  
    

      Package: exploreSE

      Commit: 5f433744b4b16416fdc63a71c9cdd43407ec225b

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

      Date: 2026-08-21 11:18:01 +0200

      Commit message:


	  
		
 readme update
 
    
  
    

      Package: exploreSE

      Commit: ad413cab9e0d3634dc34452ed92f368b4749a732

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

      Date: 2026-08-21 11:12:33 +0200

      Commit message:


	  
		
 another readme update
 
    
  
    

      Package: exploreSE

      Commit: a1c9083de90f9f4a19bb945bd5fa2845ba8b21d6

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

      Date: 2026-08-21 11:01:57 +0200

      Commit message:


	  
		
 rereredo of readme
 
    
  
    

      Package: exploreSE

      Commit: b9c45c25f6ca6e04d123c24ea39a8c8ec29d0975

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

      Date: 2026-08-21 10:51:33 +0200

      Commit message:


	  
		
 reredo readme
 
    
  
    

      Package: exploreSE

      Commit: 22d9c4297261ad1d11c925411074921dd4b79276

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

      Date: 2026-08-21 10:22:59 +0200

      Commit message:


	  
		
 updated readme again
 
    
  
    

      Package: exploreSE

      Commit: d5a865c5c22c972d0b93163eefd44ee2328fd30f

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

      Date: 2026-08-21 10:11:02 +0200

      Commit message:


	  
		
 updated readme
 
    
  
    

      Package: lcmsPlot

      Commit: 5c62d07fcdb6d63e1309a440f54a93e6eb57ae3c

      Author:  Ossama Edbali <ossedb@gmail.com> 

      Date: 2026-09-03 14:32:15 +0100

      Commit message:


	  
		
 feat(spectra): add mz_breaks_n option for m/z axis breaks

Expose the number of pretty breaks on the spectrum m/z axis as an
lp_spectra() option instead of a hardcoded value of 20, and bump the
package version. Also renames the internal .cd_node_col helper to
first_matching_column and trims stale xcms cross-references from a
few man pages.
 
    
  
    

      Package: PostChicago

      Commit: 865ba5936f89143aca8c1571d2789df12f9ac7b8

      Author:  Angelika Feldmann <angelika.feldmann@dkfz-heidelberg.de> 

      Date: 2026-09-03 14:22:08 +0200

      Commit message:


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

      Package: PostChicago

      Commit: 326117225007e3cd1ffac4f6de623403a33eec13

      Author:  Angelika Feldmann <angelika.feldmann@dkfz-heidelberg.de> 

      Date: 2026-09-03 13:31:03 +0200

      Commit message:


	  
		
 Add files via upload 
    
  
    

      Package: PostChicago

      Commit: dd0175858b82691482f660004794194fa656413c

      Author:  Angelika Feldmann <angifeldmann@gmail.com> 

      Date: 2026-09-03 13:30:41 +0200

      Commit message:


	  
		
 Delete NAMESPACE 
    
  
    

      Package: PostChicago

      Commit: 0f1f93a2db7f8231d6fdfd98088b44d66d1e28cd

      Author:  Angelika Feldmann <angelika.feldmann@dkfz-heidelberg.de> 

      Date: 2026-09-03 13:26:28 +0200

      Commit message:


	  
		
 Add files via upload 
    
  
    

      Package: PostChicago

      Commit: ca928509dd971fdb9e223d3e285ca8beb48e7f47

      Author:  Angelika Feldmann <angelika.feldmann@dkfz-heidelberg.de> 

      Date: 2026-09-03 13:25:37 +0200

      Commit message:


	  
		
 Add files via upload 
    
  
    

      Package: PostChicago

      Commit: ed66d3ae6c63d7fc43022ada000b73cd63d5f2e3

      Author:  Angelika Feldmann <angelika.feldmann@dkfz-heidelberg.de> 

      Date: 2026-09-03 13:25:16 +0200

      Commit message:


	  
		
 Add files via upload 
    
  
    

      Package: PostChicago

      Commit: 10a61dd39e30249d0c118002b87e128e4d1959d4

      Author:  Angelika Feldmann <angifeldmann@gmail.com> 

      Date: 2026-09-03 13:23:09 +0200

      Commit message:


	  
		
 Delete NAMESPACE 
    
  
    

      Package: PostChicago

      Commit: 0c153ea536647372a229fa1d5425409d9f45d61f

      Author:  Angelika Feldmann <angifeldmann@gmail.com> 

      Date: 2026-09-03 13:22:59 +0200

      Commit message:


	  
		
 Delete DESCRIPTION 
    
  
    

      Package: PostChicago

      Commit: 8851f1eb7185b1c0af3465117d7f2b761caf44a8

      Author:  Angelika Feldmann <angifeldmann@gmail.com> 

      Date: 2026-09-03 13:22:45 +0200

      Commit message:


	  
		
 Delete vignettes directory 
    
  
    

      Package: PostChicago

      Commit: 22219d3e94406115164784976e3859b781d021f3

      Author:  Angelika Feldmann <angifeldmann@gmail.com> 

      Date: 2026-09-03 13:22:27 +0200

      Commit message:


	  
		
 Delete man directory 
    
  
    

      Package: PostChicago

      Commit: 2811ab66ed7e55ebd03993cc5344ca2d9612e500

      Author:  Angelika Feldmann <angifeldmann@gmail.com> 

      Date: 2026-09-03 13:22:01 +0200

      Commit message:


	  
		
 Delete inst/extdata directory 
    
  
    

      Package: PostChicago

      Commit: dfafa60b7e9452e0a84e582f98179c227b78d76d

      Author:  Angelika Feldmann <angifeldmann@gmail.com> 

      Date: 2026-09-03 13:21:47 +0200

      Commit message:


	  
		
 Delete R directory 
    
  
    

      Package: miRSM

      Commit: 702e8e3321cb2f57ac98777403afe230ccdd373d

      Author:  zhangjunpeng411 <zhangjunpeng_411@yahoo.com> 

      Date: 2026-09-03 20:07:05 +0800

      Commit message:


	  
		
 Update
 
    
  
    

      Package: miRSM

      Commit: c6462ef0f06da4879b1aba6cf7ae3f7f3356285d

      Author:  zhangjunpeng411 <zhangjunpeng_411@yahoo.com> 

      Date: 2026-07-23 16:56:54 +0800

      Commit message:


	  
		
 update
 
    
  
    

      Package: miRspongeR

      Commit: 58ede134f2904ab6b8a28077cc9d6b2e54fe3a26

      Author:  zhangjunpeng411 <zhangjunpeng_411@yahoo.com> 

      Date: 2026-09-03 19:52:45 +0800

      Commit message:


	  
		
 UPDATE
 
    
  
    

      Package: miRspongeR

      Commit: ebb69e02fe0d5d5f41c23e1ca544dd1ea0b57c60

      Author:  zhangjunpeng411 <zhangjunpeng_411@yahoo.com> 

      Date: 2026-07-23 15:41:37 +0800

      Commit message:


	  
		
 Update
 
    
  
    

      Package: ontoProc2

      Commit: f18431d2289961758a944899d775883e825f002b

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

      Date: 2026-09-03 07:08:21 -0400

      Commit message:


	  
		
 add ggraph/graphlayouts alternatives to onto_plot2 (Rgraphviz-free)

Introduces onto_plot2_sugiyama and onto_plot2_stress as ggplot2-based
alternatives using igraph + ggraph + graphlayouts. All visual constants
are collected in onto_plot2_params() so callers can tune appearance
without touching individual arguments. Bumps version to 0.99.32.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 
    
  
    

      Package: cosmosR

      Commit: b2ed195738479c4ad204cace37fd11ae2fd02bb8

      Author:  Aurelien Dugourd <dugourd@ebi.ac.uk> 

      Date: 2026-09-03 10:31:50 +0100

      Commit message:


	  
		
 fix: remove legacy DoRothEA dependency
 
    
  
    

      Package: spatialFDA

      Commit: 1b1c9d6f6dbf61535d3ff1a4118cc0011e03dc58

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

      Date: 2026-09-03 10:00:13 +0200

      Commit message:


	  
		
 option to apply link inverse to intercept
 
    
  
    

      Package: cosmosR

      Commit: 0cb316a7d6b5d472d1a5db12562e1f6cf8d072f7

      Author:  Aurelien Dugourd <dugourd@ebi.ac.uk> 

      Date: 2026-09-03 09:36:57 +0100

      Commit message:


	  
		
 chore: synchronize Bioconductor devel and GitHub master
 
    
  
    

      Package: cosmosR

      Commit: 78af5e12c9ec2bdcc71e887669c89e74c9f9c263

      Author:  Aurelien Dugourd <dugourd@fwytr7kc7t.windows.ebi.ac.uk> 

      Date: 2026-07-28 14:44:38 +0100

      Commit message:


	  
		
 docs: bundle MOON semantic guides
 
    
  
    

      Package: cosmosR

      Commit: 5e9d5552f249a67309802e0ac2e7be03cb55468f

      Author:  Aurelien Dugourd <dugourd@fwytr7kc7t.windows.ebi.ac.uk> 

      Date: 2026-07-28 13:03:48 +0100

      Commit message:


	  
		
 docs: make MOON skill portable
 
    
  
    

      Package: cosmosR

      Commit: 6d8acf8a7e11cb3a5211c17fa80c7995838a59ce

      Author:  Aurelien Dugourd <dugourd@fwytr7kc7t.windows.ebi.ac.uk> 

      Date: 2026-07-28 11:44:06 +0100

      Commit message:


	  
		
 docs: add COSMOS MOON pipeline skill
 
    
  
    

      Package: cosmosR

      Commit: 3744609402b643afe283dcf35c23069477c6fb97

      Author:  Aurelien Dugourd <dugourd@fwytr7kc7t.windows.ebi.ac.uk> 

      Date: 2026-06-04 16:30:48 +0100

      Commit message:


	  
		
 test push
 
    
  
    

      Package: cosmosR

      Commit: f260369477b4a7910692406cf2e82234d4160a14

      Author:  Aurelien Dugourd <dugourd@ebi.ac.uk> 

      Date: 2026-06-04 11:34:08 +0100

      Commit message:


	  
		
 Add MOON data-to-PKN mapping vignette
 
    
  
    

      Package: cosmosR

      Commit: 469f0fe223652f2613787a3ef116704a31d14558

      Author:  Aurelien Dugourd <dugourd@ebi.ac.uk> 

      Date: 2026-06-04 10:47:32 +0100

      Commit message:


	  
		
 Add perturbation and timepoint MOON guidance
 
    
  
    

      Package: cosmosR

      Commit: 1860432cd9b1dc78ea99fd4bf5ab84b299ebd3fb

      Author:  Aurelien Dugourd <dugourd@ebi.ac.uk> 

      Date: 2026-06-04 09:20:06 +0100

      Commit message:


	  
		
 Refine DNA lesion propagation guidance
 
    
  
    

      Package: cosmosR

      Commit: 84a2f512fdd462c1fbbdca6ed2d51de8d9c0ffd8

      Author:  Aurelien Dugourd <dugourd@ebi.ac.uk> 

      Date: 2026-06-03 17:06:08 +0100

      Commit message:


	  
		
 Add agent-facing MOON workflow guidance
 
    
  
    

      Package: cellNexus

      Commit: 9fb8d97e6a7e4e44223b9df798d050c7254ccebb

      Author:  Mengyuan Shen <129487421+myushen@users.noreply.github.com> 

      Date: 2026-09-03 14:42:57 +1000

      Commit message:


	  
		
 Merge pull request #156 from myushen/bioccheck_dependency

remove cellxgene.census dependency in suggest 
    
  
    

      Package: cellNexus

      Commit: a5f9e79c577884ee361b726586f72d70378a814a

      Author:  myushen <mengyuan.shen@outlook.com> 

      Date: 2026-09-03 14:19:16 +1000

      Commit message:


	  
		
 remove cellxgene.census dependency in suggest
 
    
  
    

      Package: cellNexus

      Commit: fa590e1ff88b9cb58a461a16bc6715892dab3d98

      Author:  Mengyuan Shen <129487421+myushen@users.noreply.github.com> 

      Date: 2026-08-25 14:01:29 +1000

      Commit message:


	  
		
 Merge pull request #151 from myushen/guard_file_download_corruption

Guard file download corruption 
    
  
    

      Package: cellNexus

      Commit: fbe84ad7af6b366d6777e4f33aa9a7410151c414

      Author:  Mengyuan Shen <mengyuan.shen@outlook.com> 

      Date: 2026-08-13 14:21:22 +1000

      Commit message:


	  
		
 NEWS
 
    
  
    

      Package: cellNexus

      Commit: 8c37e3215600c724402333fda5b1ce484763cf5a

      Author:  Mengyuan Shen <mengyuan.shen@outlook.com> 

      Date: 2026-08-13 13:46:07 +1000

      Commit message:


	  
		
 limit server-side parallel connections to 500 per batch
 
    
  
    

      Package: cellNexus

      Commit: 719dec949956a01448c437f08babe21de96e0c7e

      Author:  Mengyuan Shen <mengyuan.shen@outlook.com> 

      Date: 2026-08-13 11:51:03 +1000

      Commit message:


	  
		
 resolve half-download/corrupted files, resume download
 
    
  
    

      Package: cellNexus

      Commit: d49432f6579b0209f786e9cfc0ba0434d7f69088

      Author:  Mengyuan Shen <129487421+myushen@users.noreply.github.com> 

      Date: 2026-08-07 15:58:44 +1000

      Commit message:


	  
		
 Merge pull request #148 from myushen/add_download_only_argument

add download_only argument to get_* functions 
    
  
    

      Package: cellNexus

      Commit: 980a356c86b114b153f0b3dabb31479e9e44dd89

      Author:  Mengyuan Shen <mengyuan.shen@outlook.com> 

      Date: 2026-08-07 15:32:23 +1000

      Commit message:


	  
		
 add download_only argument to get_* functions
 
    
  
    

      Package: jazzPanda

      Commit: 8517a1854dd69c5ee389d181b3bb47b7cab75492

      Author:  Melody <Melody-Jin@outlook.com> 

      Date: 2026-09-03 12:28:28 +1000

      Commit message:


	  
		
 add preprint/workflowr link
 
    
  
    

      Package: DuckDBGRanges

      Commit: 86c1be7bda3c12a7e4c65c51b567dae60204328f

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

      Date: 2026-09-02 21:24:56 -0400

      Commit message:


	  
		
 docs: cleaned up the prose in the results section of the benchmarking vignette
 
    
  
    

      Package: tidyprint

      Commit: dccb01abb0a143257e10d91a802e3a2f02414f87

      Author:  Chen Zhan <chen.zhan@adelaide.edu.au> 

      Date: 2026-09-03 10:43:48 +0930

      Commit message:


	  
		
 Transfer maintainer role to Stefano Mangiola in DESCRIPTION

Chen Zhan remains author; Stefano Mangiola is now maintainer (cre).
 
    
  
    

      Package: tidyprint

      Commit: 4bfafe52910a208f4524f80f3e69872f9e02bbe3

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-08-21 16:31:47 +0930

      Commit message:


	  
		
 Merge pull request #33 from tidyomics/fix-option-overrides-cache-once-per-session

Fix option overrides cache once per session 
    
  
    

      Package: tidyprint

      Commit: 44fef534f86d0b94f8fe658f399d9e2f633c97a7

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-08-21 15:55:18 +0930

      Commit message:


	  
		
 Update NEWS for tidyprint 1.1.1 release

Updated version number to 1.1.1 and added bug fixes. 
    
  
    

      Package: tidyprint

      Commit: 4a37bfc131e69d511a14090a71170169106ff817

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-08-21 15:54:56 +0930

      Commit message:


	  
		
 Change version to 1.1.1 and update description

Updated version number and modified description text. 
    
  
    

      Package: tidyprint

      Commit: b33d6efa8c594383ba4be63a49d55415b1bd58c7

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-08-21 13:34:10 +0930

      Commit message:


	  
		
 Update README.md to reflect changes in tidyprint messages and R version

- Removed outdated warnings related to package versions.
- Improved formatting of messages for clarity.
- Updated R version and platform information in the sessionInfo section.
 
    
  
    

      Package: tidyprint

      Commit: 9fc9cabf840875f2fb57bfcfc4eba46ef8c053d0

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-08-21 13:32:03 +0930

      Commit message:


	  
		
 Update tidyprint to version 1.2.0

- Fixed a subsetting bug in `print.SummarizedExperiment()` for 7-sample pasilla-shaped inputs when assay data is a `data.frame`.
- Added a regression test to ensure `show()` does not produce out-of-bounds errors.
 
    
  
    

      Package: tidyprint

      Commit: db22be3629a6f47fe076560977c57da16f894701

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-08-21 13:31:02 +0930

      Commit message:


	  
		
 Merge branch 'fix-option-overrides-cache-once-per-session' of https://github.com/tidyomics/tidyprint into fix-option-overrides-cache-once-per-session
 
    
  
    

      Package: tidyprint

      Commit: 81172f3647f8eb864b556ab338888d7cbe938523

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-08-21 13:28:01 +0930

      Commit message:


	  
		
 Update tidyprint with enhancements to message frequency control

- Introduced frequency control for messages in `tidy_message()`, allowing messages to be displayed once per R session.
- Updated `tidy_print_enabled()` to show the option-vs-cache mismatch warning only once per session.
- Added tests to verify the new message frequency functionality.
 
    
  
    

      Package: tidyprint

      Commit: 85d1c3f2b39d099dd28d161b2f9bdbbeb3d47045

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-08-21 13:28:01 +0930

      Commit message:


	  
		
 Update tidyprint with enhancements to message frequency control

- Introduced frequency control for messages in `tidy_message()`, allowing messages to be displayed once per R session.
- Updated `tidy_print_enabled()` to show the option-vs-cache mismatch warning only once per session.
- Added tests to verify the new message frequency functionality.
 
    
  
    

      Package: NanoStringNCTools

      Commit: 61ba4660a16cc74b77cc21ec5bad0aea68f096a0

      Author:  Maddy Griswold <mgriswold@nanostring.com> 

      Date: 2026-09-02 15:40:27 -0600

      Commit message:


	  
		
 verison
 
    
  
    

      Package: NanoStringNCTools

      Commit: 2ff510a6a8e164f3eb1d84600e860f85181913a9

      Author:  Maddy Griswold <40255151+maddygriz@users.noreply.github.com> 

      Date: 2026-09-02 15:27:34 -0600

      Commit message:


	  
		
 Merge pull request #43 from Nanostring-Biostats/bioc_build_fail

Bioc build failure  
    
  
    

      Package: NanoStringNCTools

      Commit: d42cf6ad70843e35dfa79d701c322a283521eaf4

      Author:  Maddy Griswold <mgriswold@nanostring.com> 

      Date: 2026-09-02 17:33:53 +0000

      Commit message:


	  
		
 fix build failure
 
    
  
    

      Package: PCAtools

      Commit: 6da9b6856906507f734fcccfe85f341a3ed381f0

      Author:  Jared Andrews <jared.andrews07@gmail.com> 

      Date: 2026-09-02 13:37:30 -0500

      Commit message:


	  
		
 NEWS update
 
    
  
    

      Package: GenomicRanges

      Commit: 44c311c711b9a5a5d6db070a8f3210819e4bc9de

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

      Date: 2026-09-02 11:22:01 -0700

      Commit message:


	  
		
 typo
 
    
  
    

      Package: IFAA

      Commit: 2c1c8be60d4278cefcb1aaff91afb9257364a35f

      Author:  Mingkai Chen <chenm1@ufl.edu> 

      Date: 2026-09-02 13:33:59 -0400

      Commit message:


	  
		
 Bump version to 1.15.1
 
    
  
    

      Package: IFAA

      Commit: ecdbeb6533e0286b5e0f8763125a3732bbd6c2fa

      Author:  Mingkai Chen <chenm1@ufl.edu> 

      Date: 2026-09-02 13:29:21 -0400

      Commit message:


	  
		
 Use HTML output for package vignette
 
    
  
    

      Package: signeR

      Commit: 292bfbd9049c1fec973702f3672c10653dbf2508

      Author:  Renan Valieris <renan.valieris@accamargo.org.br> 

      Date: 2026-09-02 14:06:05 -0300

      Commit message:


	  
		
 fix seqinfo subset error
 
    
  
    

      Package: geyser

      Commit: 7d8ece929adc8723d980e4519ebea66fd8f47137

      Author:  davemcg <mcgaughey@gmail.com> 

      Date: 2026-09-02 12:55:56 -0400

      Commit message:


	  
		
 match devel
 
    
  
    

      Package: geyser

      Commit: 152b7f035619f496a5d16ce060988ce6c985c767

      Author:  davemcg <mcgaughey@gmail.com> 

      Date: 2026-09-02 12:53:03 -0400

      Commit message:


	  
		
 Add pandoc to system req
 
    
  
    

      Package: geyser

      Commit: 2d8114a8942f37e8e6964e242a58557f7f90cf01

      Author:  davemcg <mcgaughey@gmail.com> 

      Date: 2026-04-07 15:44:43 -0400

      Commit message:


	  
		
 x y axis label fix
 
    
  
    

      Package: geyser

      Commit: 489b36d2cfba5c5598bfeab780ede13dedc7f5d2

      Author:  davemcg <mcgaughey@gmail.com> 

      Date: 2026-04-07 11:33:24 -0400

      Commit message:


	  
		
 news update
 
    
  
    

      Package: geyser

      Commit: d1592aed7bfefed3f3914c6b635162a21a1ddacd

      Author:  davemcg <mcgaughey@gmail.com> 

      Date: 2026-04-07 11:32:15 -0400

      Commit message:


	  
		
 checkbox toggles added, readme updated with custom config options explanation
 
    
  
    

      Package: geyser

      Commit: f9973160367ff91cffbaed38d4c990fff84a369e

      Author:  davemcg <mcgaughey@gmail.com> 

      Date: 2026-04-06 15:34:07 -0400

      Commit message:


	  
		
 increment version
 
    
  
    

      Package: geyser

      Commit: 6b5d33ce01871a58a8ea93e718d902d1f90ad261

      Author:  davemcg <mcgaughey@gmail.com> 

      Date: 2026-04-06 14:37:19 -0400

      Commit message:


	  
		
 fix news version numbers that got shifted with bioc release
 
    
  
    

      Package: cigarillo

      Commit: 5add90b609ca0ffa6e22d9d98a2ee1ca32fd902c

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

      Date: 2026-09-01 17:44:59 -0700

      Commit message:


	  
		
 add missing package anchor to Rd \link{} target
 
    
  
    

      Package: GenomicRanges

      Commit: 6248364b20a9a1becdc1e50bd7ff7609ff2e4705

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

      Date: 2026-09-01 17:16:24 -0700

      Commit message:


	  
		
 add missing package anchors to Rd \link{} targets
 
    
  
    

      Package: GenomicRanges

      Commit: 6738af10b90f6c63ac29a1173d73b23ad17b7464

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

      Date: 2026-09-01 16:26:16 -0700

      Commit message:


	  
		
 fix unit tests
 
    
  
    

      Package: BioCor

      Commit: 058cb4cf3ed9d3bd8aa81a6cc95c198ed1405088

      Author:  Lluís <lluis.revilla@gmail.com> 

      Date: 2026-09-01 22:50:54 +0200

      Commit message:


	  
		
 Fix problems with names
 
    
  
    

      Package: BioCor

      Commit: fd2cb0e10580e0633036e0cdb88dc316d762b356

      Author:  Lluís <lluis.revilla@gmail.com> 

      Date: 2026-09-01 22:50:33 +0200

      Commit message:


	  
		
 Increase code coverage by switching to GSC
 
    
  
    

      Package: BioCor

      Commit: 81820e3552387ea536ed478d73c151960448bffe

      Author:  Lluís <lluis.revilla@gmail.com> 

      Date: 2026-09-01 22:08:35 +0200

      Commit message:


	  
		
 Fix seed
 
    
  
    

      Package: BioCor

      Commit: 3ffac8aac6670bac584c1a5ae01811e537473952

      Author:  Lluís <lluis.revilla@gmail.com> 

      Date: 2026-09-01 22:08:24 +0200

      Commit message:


	  
		
 Fix indentation for 4 spaces as Bioconductor requires
 
    
  
    

      Package: BioCor

      Commit: f6e3dfb2d2a363f926b1fb566680226ada1f3e12

      Author:  Lluís <lluis.revilla@gmail.com> 

      Date: 2026-09-01 21:54:12 +0200

      Commit message:


	  
		
 Upgrade acording to BiocCheck
 
    
  
    

      Package: Biostrings

      Commit: 7dc83a0cbbde5708995945a9794b3728e67f25fc

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

      Date: 2026-09-01 12:00:42 -0700

      Commit message:


	  
		
 Fix unit tests.

Also fix regression in as.data.frame.XStringViews() introduced at
commit 3dab5d9.
 
    
  
    

      Package: CNVRanger

      Commit: b58eb43709bcd75df1547d289039c66f9d5abc8a

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

      Date: 2026-05-14 14:24:15 -0400

      Commit message:


	  
		
 Add CITATION.cff (#51) 
    
  
    

      Package: edgeR

      Commit: 61de2f486eebbf9332efabb11c0c80b72e334111

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

      Date: 2026-08-30 18:23:24 +1000

      Commit message:


	  
		
 edgeR 4.99.0

- The genewise C kernels (GLM fitting, deviances, CPM, quasi-likelihood adjustment, exact test,
diffSplice, etc.) are now parallelized with OpenMP. The number of threads is controlled by a new `
nthreads` argument on the affected functions, or globally via `options(edgeR.nthreads=)`, and defaults
to 1 (serial) so results are unchanged by default.

- The C backend for diffSplice() now exploits the bordered block-diagonal ( arrowhead) structure of the
splice design matrix, fitting the genewise null models in time linear, rather than cubic, in the number
of exons per gene. Results are unchanged. diffSplice() also gains `maxit` and `tol` arguments
controlling the genewise GLM fits.

- voomLmFit() has been removed from edgeR and is now provided by the limma package.

- New functions binQLFit() and binQLFTest() to fit quasi-binomial generalized linear models, to estimate
bias-adjusted deviances, and to test hypotheses. These functions are closely analogous to glmQLFit() and
glmQLFTest() but for paired counts and differential proportion analyses instead of regular counts and
differential abundance analyses.

- New functions binFit(), mBinOneWay(), and mBinIWLS() to fit binomial generalized models.

- New class DGEBin to store quasi-binomial generalized linear model fits.

- New function readBismark2PC() to read Bismark output into an edgeR PCList object.

- New class PCList to store paired counts, for example methylated and unmethylated reads, for the same
genomic regions.

- New argument `parent.dir` for catchSalmon(), catchSalmonWithGencode(), catchKallisto(),
catchOarfish(), and catchRSEM(), to more easily read all the samples available in a specified output
directory. New argument `sample.dirs` for catchSalmon(), catchSalmonWithGencode(), and catchKallisto(),
that replaces ` paths` and allows individual samples to be specified.

- New argument `offset.prior` for cpm(), rpkm(), catchSalmon(), and catchSalmonWithGencode() to allow
the offset matrix to be specified relative to the log(library sizes).

- sampleWeights() now accepts a DGEGLM fitted model object from glmQLFit() instead of a matrix of
adjusted unit deviances.

- Revision of all the Rd help files to add DOIs, to fix typos, and to standardize formating and American
spellings.
 
    
  
    

      Package: DOSE

      Commit: df6e838da2ef9c853f80be086ca343f96cbb7ad3

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-08-30 15:46:18 +0800

      Commit message:


	  
		
 update
 
    
  
    

      Package: DuckDBGRanges

      Commit: 9983bb13db331b5f1616d048b37e91512af23a49

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

      Date: 2026-08-29 22:56:20 -0700

      Commit message:


	  
		
 fix: restore checkDuckDBGRanges() for GenomicRanges >= 1.65.2

GenomicRanges 1.65.2 rewrote as.data.frame.GenomicRanges(): it used
to default row.names to names(x) when not supplied, and now hardcodes
row.names = NULL internally (an explicit row.names argument is
silently discarded too), putting names(x) in a new "names" column
instead.

checkDuckDBGRanges()'s own df <- as.data.frame(expected) reference
assumed the old convention, so its row names stopped matching
as.data.frame(object)'s, which still carries real names as row names
via DuckDBDataFrame's own conversion. Not a DuckDBGRanges bug: verified
by installing the exact upstream commit and confirming
as.data.frame,DuckDBGRanges-method itself is unaffected.
 
    
  
    

      Package: limma

      Commit: 57a8de7296ad733ac25d3e3c01de3fdddcd0a9ae

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

      Date: 2026-08-30 10:48:25 +1000

      Commit message:


	  
		
 Add new files for limma 3.99.0.
 
    
  
    

      Package: limma

      Commit: 8f72e4736e4cee7f10b8345088d8328c689e186e

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

      Date: 2026-08-30 10:47:07 +1000

      Commit message:


	  
		
 30 Oct 2026: limma 3.99.0

- voomLmFit() transferred to limma from the edgeR package.
  Previously, voomLmFit() needed to call edgeR::glmFit() in order to
  identify exact zero fitted values, but voomLmFit() now calls a
  new limma C routine `poisfit` for the same purpose, removing the
  dependence on edgeR.

- For the purpose of estimating sample weights, voomLmFit() calls
  arrayWeights() with `method="reml"` if there is no loss of df due to
  exact zero fitted values and `method="genebygene"` otherwise.

- The voomLmFit help page has been expanded, while the voom and
  voomWithQualityWeights help pages now have preambles that point
  users to voomLmFit.

- voomLmFit() now gives priority to `offset` over `offset.prior` or
  `lib.size` and no longer forces the rows of `offset.prior` to add
  to zero.

- New argument `contrasts` for voomLmFit(), lmFit(), lm.series() and
  gls.series(), which converts coefficient estimates and standard
  deviations into contrast estimates and standard deviations. This
  argument provides the  same functionality as calling `contrasts.fit`
  on the output object, but with exact rather than approximate
  standard deviations.

- New argument `nthreads` for voomLmFit(), lmFit(), lm.series(),
  gls.series(), duplicateCorrelation(), .arrayWeightsPrWtsREML(), and
  arrayWeights() to enable OpenMP parallelization of genewise fits.

- C code backends for lm.series() and gls.series().

- C code backend for duplicateCorrelation(). duplicateCorrelation()
  previously called statmod::mixedModel2() to estimate genewise
  correlations, but this functionality is now absorbed into the C
  code. The new code is able to evaluate the genewise SVDs needed by
  mixedModel2() more efficiently than was possible for the univariate
  R function, resulting in substantial speed and memory improvements.

- C code backend for .arrayWeightsPrWtsREML(), which is called by
  arrayWeights() when `method="reml"` and prior weights
  are set.

- The C code for weightedLowess() is not new but has been
  revised to fit in with the new C code elsewhere.

- All the Rd pages have been checked for typos and inconsistent
  formating, especially regarding the reference lists. Reference URLs
  converted to DOIs where possible and some new DOIs added. Author
  lists converted to compact PubMed style without unnecessary
  punctuation. A few instances of British spellings converted to
  American spellings.

- Replace old statsci.org/smyth/pubs preprint URLs with
  gksmyth.github.io/pubs URLs in 05Normalization.Rd and in User's
  Guide.

- Fix documentation link in 06linearmodels.Rd.

- Expand changelog.txt entries for limma 1.0 and earlier.

- Add test files dupcor.R, gls-series-c.R, lmfit-contrasts.R,
  lm-series-c.R, and voomlmfit-contrasts.R.

- All package files now use Unix format line-endings.

- Update author order in DESCRIPTION.
 
    
  
    

      Package: BioCor

      Commit: e1b232499b067226ddd70255bb854214b67fb174

      Author:  Lluís <lluis.revilla@gmail.com> 

      Date: 2026-08-29 12:58:02 +0200

      Commit message:


	  
		
 Fix DESCRIPTION
 
    
  
    

      Package: BioCor

      Commit: f07961f3753047b127745eb5a6e30f8bcb588872

      Author:  Lluís <lluis.revilla@gmail.com> 

      Date: 2026-08-29 12:57:23 +0200

      Commit message:


	  
		
 Upgrade cff
 
    
  
    

      Package: BioCor

      Commit: ac77cee02064312437dd0a12c719509e88fbee60

      Author:  Lluís <lluis.revilla@gmail.com> 

      Date: 2026-08-29 12:53:43 +0200

      Commit message:


	  
		
 Version bump to propagate changes
 
    
  
    

      Package: BioCor

      Commit: d8f4130a40b0de328e14331c9cf06bf8b37f6876

      Author:  Lluís <lluis.revilla@gmail.com> 

      Date: 2026-08-29 12:53:16 +0200

      Commit message:


	  
		
 Update documentation
 
    
  
    

      Package: BioCor

      Commit: 07b7084920f9fc39f37a791db928df81fe9a242d

      Author:  Lluís <lluis.revilla@gmail.com> 

      Date: 2026-08-29 12:39:16 +0200

      Commit message:


	  
		
 Update style
 
    
  
    

      Package: BioCor

      Commit: 6d5e44f87435ca0938a1e06f900a4a8e8ad1c78a

      Author:  Lluís <lluis.revilla@gmail.com> 

      Date: 2026-08-29 12:38:34 +0200

      Commit message:


	  
		
 Fix lintr logical issue
 
    
  
    

      Package: ontoProc2

      Commit: ab2304ef1e401ce463190cbd395fff2fbbb4b768

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

      Date: 2026-08-28 23:06:41 -0400

      Commit message:


	  
		
 remove references to aws throughout
 
    
  
    

      Package: BatchQC

      Commit: e38a3459350dff7d2f41c0d27ea78c132db15401

      Author:  technophilic03 <leng@bu.edu> 

      Date: 2026-08-28 14:44:33 -0400

      Commit message:


	  
		
 Bump version umber to 2.9.2 for devel
 
    
  
    

      Package: BatchQC

      Commit: 01a30073ecc1dc3e2f708fc2ee20be758573a607

      Author:  Jessica <102758461+jessmcc22@users.noreply.github.com> 

      Date: 2026-08-25 14:45:35 -0600

      Commit message:


	  
		
 Merge pull request #144 from jessmcc22/devel

Updated descriptions 
    
  
    

      Package: BatchQC

      Commit: d07b5b55b9d57b79dcaf2b9b9f617bbcc92eefe7

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2026-08-25 16:40:53 -0400

      Commit message:


	  
		
 Merge branch 'devel' of https://github.com/jessmcc22/BatchQC into devel
 
    
  
    

      Package: BatchQC

      Commit: f2ab523559e05818d84dce8eb68df21023826fae

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2026-08-25 15:52:04 -0400

      Commit message:


	  
		
 Updated some descriptions to better support manuscript and provide info to users.
 
    
  
    

      Package: BatchQC

      Commit: 3346f533ff2ac23eab94980df56eafce944e7cf2

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2026-08-25 15:52:04 -0400

      Commit message:


	  
		
 Updated some descriptions to better support manuscript and provide info to users.
 
    
  
    

      Package: BatchQC

      Commit: 3793afca5df726ed28dfa7bd2b2c536d0a72feca

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2026-08-19 14:41:37 -0400

      Commit message:


	  
		
 Updated version to match Description file (even is for release branches)
 
    
  
    

      Package: BatchQC

      Commit: e300047e9d4fb1c108a6ea713159c00ff2772862

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2026-08-19 14:40:55 -0400

      Commit message:


	  
		
 Merge branch 'devel' of https://github.com/jessmcc22/BatchQC into devel
 
    
  
    

      Package: BatchQC

      Commit: 96c1724e4386db46dd132a1e48d9cfed323c6dd6

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2026-08-19 14:39:38 -0400

      Commit message:


	  
		
 Added additional details about the method functionality to the function descriptions and in the vignette.
 
    
  
    

      Package: scRNAseqApp

      Commit: f851c9c88bc453c2ef33adf1e224c8a760a90f56

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

      Date: 2026-08-28 14:08:11 -0400

      Commit message:


	  
		
 Get IP from request string but not session.
 
    
  
    

      Package: MultiAssayExperiment

      Commit: a1764de323ff619f63ecba160e588c7beed73be2

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

      Date: 2026-08-28 13:58:04 -0400

      Commit message:


	  
		
 version bump 1.39.1
 
    
  
    

      Package: MultiAssayExperiment

      Commit: e981f5e2862d218de6805faa06323973ec253913

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

      Date: 2026-08-28 13:57:10 -0400

      Commit message:


	  
		
 use updateObject::updatePackageObjects to update miniACC
 
    
  
    

      Package: MultiAssayExperiment

      Commit: cfe45dec646dea08f389efcedfb18befb138885f

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

      Date: 2026-08-28 13:35:06 -0400

      Commit message:


	  
		
 roxygen2 fixes package docs
 
    
  
    

      Package: MultiAssayExperiment

      Commit: 5f3f14b436d5bc0518692cd3965870023aae6aa0

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

      Date: 2026-08-28 13:34:36 -0400

      Commit message:


	  
		
 NAMESPACE line updates from roxygen2 v8
 
    
  
    

      Package: MultiAssayExperiment

      Commit: b1fcd2d684f53d6493047056384430c3b5f836f2

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

      Date: 2026-08-28 13:34:04 -0400

      Commit message:


	  
		
 add coerce method to docs
 
    
  
    

      Package: MultiAssayExperiment

      Commit: 062eb8fbc6eaf6b88012a18a6f2858c32f65e5a6

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

      Date: 2026-08-28 13:33:25 -0400

      Commit message:


	  
		
 update ref links in Rd docs
 
    
  
    

      Package: MultiAssayExperiment

      Commit: de9d681201b98855cbd7c61f748ab2c8af220f86

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

      Date: 2026-08-28 13:32:32 -0400

      Commit message:


	  
		
 add multi-line @aliases for roxygen
 
    
  
    

      Package: MultiAssayExperiment

      Commit: f14d285f62c59d93380a374bd1c3a9d44fb45e6d

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

      Date: 2026-08-28 13:34:13 -0400

      Commit message:


	  
		
 use roxygen2 v8
 
    
  
    

      Package: MultiAssayExperiment

      Commit: 82663ca8903ff18198c43a7942bdd5a19b44c88c

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

      Date: 2026-04-16 18:50:00 +0000

      Commit message:


	  
		
 Add CITATION.cff 
    
  
    

      Package: S4Vectors

      Commit: 79e0c50e8ca44ed621de69ca63b3e744c53f5d6e

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

      Date: 2026-08-28 09:23:56 -0700

      Commit message:


	  
		
 Small tweaks to as.data.frame() methods for Vector and Rle objects.

Also remove a bunch of uneeded coercion methods from Rle to various base
types (they're redundant with the same methods defined for Vector objects).
 
    
  
    

      Package: scrapper

      Commit: 224ce0f797369612000a3650ef61264c2866d2e7

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

      Date: 2026-08-28 22:24:05 +1000

      Commit message:


	  
		
 Optionally filter for high-quality cells in each quick*Qc.se() function.

Also report the unfiltered SE in analyze.se(), just in case users want to
examine the entire distribution of QC metrics prior to any filtering.
 
    
  
    

      Package: MsBackendMetaboLights

      Commit: c33fad99e6bc48c5bb9fd5ef7814e0e32393eed3

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

      Date: 2026-08-28 14:21:39 +0200

      Commit message:


	  
		
 Merge pull request #25 from rformassspectrometry/jomain

refactor: reduce need to load BiocFileCache for offline use 
    
  
    

      Package: MsBackendMetaboLights

      Commit: e3564b3d802422f9e953116a68b50e2847a5bb13

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

      Date: 2026-08-28 13:00:15 +0200

      Commit message:


	  
		
 refactor: reduce need to load BiocFileCache for offline use
 
    
  
    

      Package: terapadog

      Commit: 1a7aef14a891ecca87e779080e518ffefdd21f62

      Author:  gionmattia <gionmattia@gmail.com> 

      Date: 2026-08-28 13:16:28 +0100

      Commit message:


	  
		
 added_ranks
 
    
  
    

      Package: betterChromVAR

      Commit: 0341160ba7e994ad6755cbba92d6f644efebeb3a

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

      Date: 2026-08-28 13:55:26 +0200

      Commit message:


	  
		
 fixed typo in citation
 
    
  
    

      Package: betterChromVAR

      Commit: 24a6eee3450ef6d0ca11d5e8d787c9a0f61e6139

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

      Date: 2026-08-28 13:44:01 +0200

      Commit message:


	  
		
 changed paper url to point direct to biorxiv
 
    
  
    

      Package: betterChromVAR

      Commit: 7ff55e0660f4c164855c5ca176c4c65389c7fc30

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

      Date: 2026-08-28 13:41:11 +0200

      Commit message:


	  
		
 Merge branch 'devel' of github.com:plger/betterChromVAR into devel
 
    
  
    

      Package: betterChromVAR

      Commit: d34d3b7c8bfd8e2ec83d37105ff227e4ab1ece98

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

      Date: 2026-08-28 13:40:53 +0200

      Commit message:


	  
		
 added references to the preprint
 
    
  
    

      Package: betterChromVAR

      Commit: d7916f7fbe6138323e667edfca72957d7ffe0956

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

      Date: 2026-08-21 14:45:36 +0200

      Commit message:


	  
		
 Split BiocManager install calls for clarity 
    
  
    

      Package: betterChromVAR

      Commit: 649881272514ddf03d34e5eff3860bce8102ed3f

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

      Date: 2026-08-21 14:33:20 +0200

      Commit message:


	  
		
 Add Biobase to BiocManager install list 
    
  
    

      Package: betterChromVAR

      Commit: 9abd6bb633c66287af26228c50336a11ca14ff43

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

      Date: 2026-08-21 14:17:56 +0200

      Commit message:


	  
		
 Change check pkg installation to BiocManager 
    
  
    

      Package: OSCA.multisample

      Commit: 6984d54a2143230e7d2bfe835d1e1379f3632754

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2026-08-28 08:58:34 +0100

      Commit message:


	  
		
 Merge pull request #20 from OSCA-source/stripped

Stripped out all content and replaced with redirects to scrapbook. 
    
  
    

      Package: OSCA.multisample

      Commit: 1fc1562368a1c0b2b9530269cd38dea607005531

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

      Date: 2026-08-28 16:04:09 +1000

      Commit message:


	  
		
 Removed unnecessary GHA.
 
    
  
    

      Package: OSCA.multisample

      Commit: 386ef6f9b10500cb49e2838e1311ee81f78a1ae5

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

      Date: 2026-08-28 15:59:48 +1000

      Commit message:


	  
		
 Replaced all chapters with redirects to scrapbook.
 
    
  
    

      Package: SingleR

      Commit: f550f73f67c2b8e0a234f05039c6166ba44ab104

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

      Date: 2026-08-28 14:25:08 +1000

      Commit message:


	  
		
 Updated C++ bindings for find_classic_markers.
 
    
  
    

      Package: assorthead

      Commit: caf3a73117c673b9f613bec040c4927c76f37fee

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

      Date: 2026-08-28 14:26:32 +1000

      Commit message:


	  
		
 Update the version of singler_classic_markers.
 
    
  
    

      Package: DuckDBDataFrame

      Commit: 1b797dfe5b363d0154fabf624a3af9b97868a69f

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

      Date: 2026-08-27 16:07:28 -0700

      Commit message:


	  
		
 fix: reverted the previous fix
 
    
  
    

      Package: VDJdive

      Commit: 819f671011374f336f7597c9f70a6fa9a8d6e1fc

      Author:  Kelly Street <street.kelly@gmail.com> 

      Date: 2026-08-27 15:28:28 -0700

      Commit message:


	  
		
 removed compiled artifacts
 
    
  
    

      Package: DuckDBDataFrame

      Commit: e0324474831ec2a28395954e658a19de518a80bc

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

      Date: 2026-08-27 14:32:13 -0700

      Commit message:


	  
		
 fix: the previous fix
 
    
  
    

      Package: DuckDBDataFrame

      Commit: b05e881461dce0f08dec627ed338406398435cd4

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

      Date: 2026-08-27 14:13:14 -0700

      Commit message:


	  
		
 fix: dim-table partition pruning used positional indexing on keycol values (0.99.26)

.filter_tblconn()'s dimtbl[set, , drop = FALSE] indexed a dimension table
by a keycol's raw stored values, but a numeric index in R is always
positional (row number), not a value lookup. This was silently wrong
whenever a key's value differs from its row position in the dim table --
exactly the shape a DuckDBTable/DuckDBArray shard (a subset of a larger
dataset's keys) takes, which is what dimtbls-based partition pruning
exists to optimize.
 
    
  
    

      Package: scRNAseqApp

      Commit: e512f606db4d8b49a4819b86e1f52753de18599f

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

      Date: 2026-08-27 12:39:23 -0400

      Commit message:


	  
		
 Fix the bug for splash screen.
 
    
  
    

      Package: methodical

      Commit: 92fa1369c1b6b5c34470019a41c298343a2cebce

      Author:  Richard Heery <richardheery@gmail.com> 

      Date: 2026-08-27 17:25:10 +0100

      Commit message:


	  
		
 update
 
    
  
    

      Package: assorthead

      Commit: cfb13bd090130480c7f7543df9a8e4905d3fdbc8

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

      Date: 2026-08-28 02:15:33 +1000

      Commit message:


	  
		
 Updated the vendored version of knncolle.
 
    
  
    

      Package: BiocSingular

      Commit: 8544ac52d53b7bb2149fed8268a99484a606c18e

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

      Date: 2026-08-28 01:57:31 +1000

      Commit message:


	  
		
 Bumped version and date, re-run roxygen.
 
    
  
    

      Package: BiocSingular

      Commit: 16a8dd7f0a85c0e6df32a472e3e6cb7ec24ebbef

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

      Date: 2026-08-28 01:33:22 +1000

      Commit message:


	  
		
 Replace most of our custom C++ functions with tatami.* utils from beachmat.

Also refactor the compute_scale() implementation to improve work-sharing upon
parallelization, at the cost of some small floating-point differences depending
on the number of threads. This aligns with the policy in the new tatami_stats.

Also switch the edge cases to report NaNs instead of NA_real_. The former is
more appropriate as the statistics are invalid, not missing.
 
    
  
    

      Package: miaViz

      Commit: 33a50dc49f455a62695592fbb4d8d5806dc5bc20

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

      Date: 2026-08-27 18:39:01 +0300

      Commit message:


	  
		
 Update plotAbundance defaults for showing sample grouping (#232) 
    
  
    

      Package: msa

      Commit: c07a1e4fa646df33b5094a1cb30705abf690f524

      Author:  UBod <ulrich@bodenhofer.com> 

      Date: 2026-08-27 17:18:20 +0200

      Commit message:


	  
		
 some updates and corrections; version number bumped to 1.45.6
 
    
  
    

      Package: beachmat

      Commit: c6b2b5b65620ac89ee5058b3ba93b9cb289e7d94

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

      Date: 2026-08-28 01:13:05 +1000

      Commit message:


	  
		
 Docfixes for some soft-deprecated functions.
 
    
  
    

      Package: beachmat

      Commit: e5192e337743d9efa3f9fba91d10635fb3a722ea

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

      Date: 2026-08-28 01:00:06 +1000

      Commit message:


	  
		
 Added the tatami.variances() function for quick dimwise variances.
 
    
  
    

      Package: scRNAseqApp

      Commit: 9dec50101b96f552c68e16cbab2fd7fcd16889e9

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

      Date: 2026-08-27 11:01:01 -0400

      Commit message:


	  
		
 Fix a bug for splash screen
 
    
  
    

      Package: scuttle

      Commit: d3476eb0833aaa38cd59b2db3c941c38fc64677b

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

      Date: 2026-08-28 00:25:15 +1000

      Commit message:


	  
		
 Updated bindings to the new C++ functions.
 
    
  
    

      Package: scpdata

      Commit: c2d8a7629773cde959000522e18f1f6995f8261c

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-08-27 12:58:23 +0200

      Commit message:


	  
		
 add missing leduc2025 man page
 
    
  
    

      Package: geneslator

      Commit: e9b59c133ff48f0d4a2d72b5b3a2862e81f5e314

      Author:  GMicale <gmgmicky@gmail.com> 

      Date: 2026-08-27 12:58:32 +0200

      Commit message:


	  
		
 Fixed query for KEGG pathways
 
    
  
    

      Package: geneslator

      Commit: 9524d78e37e75d405e431b1fedf85996be491b65

      Author:  GMicale <gmgmicky@gmail.com> 

      Date: 2026-08-27 12:38:57 +0200

      Commit message:


	  
		
 Fixed query for keytypes
 
    
  
    

      Package: OSCA.basic

      Commit: 7311fc4071852124485659738a1df71e621ae7b7

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2026-08-27 11:19:07 +0100

      Commit message:


	  
		
 Merge pull request #21 from OSCA-source/stripped

Replace all content with redirects to scrapbook chapters. 
    
  
    

      Package: OSCA.basic

      Commit: a9d404c3bce32dafd881cdc43158e0de565f2aa7

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

      Date: 2026-08-24 23:35:16 +1000

      Commit message:


	  
		
 Replace all content with redirects to scrapper chapters.
 
    
  
    

      Package: MetaboDynamics

      Commit: 067faf9d5333f249b9049a357612ed1be18af989

      Author:  Katja Danielzik <katja.danielzik@uni-due.de> 

      Date: 2026-08-27 11:46:59 +0200

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: MetaboDynamics

      Commit: 05e7b2151146ff2cef1fc2591a943e3d9baabba2

      Author:  Katja Danielzik <katja.danielzik@uni-due.de> 

      Date: 2026-08-27 11:46:23 +0200

      Commit message:


	  
		
 corrected vignette title
 
    
  
    

      Package: scrapbook

      Commit: a1fc037fa7451af8afb35e15f87a8b79a9f76d40

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

      Date: 2026-08-27 19:13:15 +1000

      Commit message:


	  
		
 More streamlined wording of the normalization chapter.
 
    
  
    

      Package: eisaR

      Commit: 4d658f04bd930761d190d0e8a8d02f14d0da6bc2

      Author:  Michael Stadler <stadler.michael@gmail.com> 

      Date: 2026-08-27 09:38:41 +0200

      Commit message:


	  
		
 Merge pull request #44 from fmicompbio/test-r-devel

Adapt to upcoming changes in rbinom in R devel 
    
  
    

      Package: eisaR

      Commit: 77cbce1a657307453daedba857e8d018c73ec8a0

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-08-27 08:35:41 +0200

      Commit message:


	  
		
 Disable running of devel GHA workflow
 
    
  
    

      Package: eisaR

      Commit: 2879a2a3b2d51697344cc100e38b0917e44271cd

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-08-27 07:16:18 +0200

      Commit message:


	  
		
 Suppress warnings instead of expecting them (to avoid failing in release R)
 
    
  
    

      Package: eisaR

      Commit: e07a3f29e55a8c10d2049b932b19e89cbfc690ad

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-08-27 06:53:04 +0200

      Commit message:


	  
		
 Run devel workflow also on PR to devel
 
    
  
    

      Package: eisaR

      Commit: 3d10f5dd6acedd1a9ee79139b35cdcd0a8cd4cdb

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-08-26 21:55:29 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: eisaR

      Commit: 9bda5e69929f1f340e4aba9e22927cecbf7c09c8

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-08-26 21:55:12 +0200

      Commit message:


	  
		
 Set RNGversion to 4.6 in tests to get consistent values from rmultinom
 
    
  
    

      Package: eisaR

      Commit: 018a8791307c7d91f83ec4130a4938aa65c159d1

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-08-26 21:54:37 +0200

      Commit message:


	  
		
 Only run R-devel checks upon request
 
    
  
    

      Package: eisaR

      Commit: 518bfca442950fc7c7e2973d87f111e346ac9dbb

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-08-26 21:26:50 +0200

      Commit message:


	  
		
 Fix Linux system dependencies installation
 
    
  
    

      Package: eisaR

      Commit: 1e150e6984569105f2c72e5bd87aa02954f3d196

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-08-26 20:43:36 +0200

      Commit message:


	  
		
 Add more configs to GHA matrix
 
    
  
    

      Package: eisaR

      Commit: 2a422f3c07136ce9a27397ce52e3a5b49d36cf73

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-08-26 20:03:54 +0200

      Commit message:


	  
		
 Update setup-r action version
 
    
  
    

      Package: eisaR

      Commit: 93eed55670fb8b71491e80363217ee5fa0d615a6

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-08-26 20:02:26 +0200

      Commit message:


	  
		
 Remove scheduled run
 
    
  
    

      Package: eisaR

      Commit: 1957f797e47996fd4a80b39ddb1eecd8da622c02

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-08-26 17:12:20 +0200

      Commit message:


	  
		
 Add GHA workflow testing on R-devel
 
    
  
    

      Package: scrapbook

      Commit: 4d63d107821318f91bcee9b731535d7207bb04a0

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

      Date: 2026-08-27 16:58:27 +1000

      Commit message:


	  
		
 Bumped version and date.
 
    
  
    

      Package: scrapbook

      Commit: 260b9b4894c823f5dd0abacdd6e2a2eb99c445c8

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

      Date: 2026-08-27 16:47:21 +1000

      Commit message:


	  
		
 Improved explanation of composition biases, plus minor text fixes.
 
    
  
    

      Package: scrapbook

      Commit: bb157ae4eacd85db91b9e4b29626f1626601cea5

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

      Date: 2026-08-27 16:10:58 +1000

      Commit message:


	  
		
 Added a paragraph on dealing with composition biases in DA analyses.
 
    
  
    

      Package: scrapbook

      Commit: f5bf81eb70c833088794e8f9d914cd8c5177863f

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

      Date: 2026-08-27 00:24:55 +1000

      Commit message:


	  
		
 Migrated the ambient contamination section from OSCA.multisample.
 
    
  
    

      Package: DuckDBDataFrame

      Commit: 5eec18f076aa376188ef9879905a9f957b0f2b8d

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

      Date: 2026-08-26 22:52:16 -0700

      Commit message:


	  
		
 feat: add anyNA and is.na methods
 
    
  
    

      Package: AnnotationDbi

      Commit: 00bc715f3ecc0d78d7794257c041d3d463766e11

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

      Date: 2026-08-26 18:54:04 -0700

      Commit message:


	  
		
 spelling
 
    
  
    

      Package: SplicingGraphs

      Commit: 841410fcac751fe3ce3a811b10c63644654007ae

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

      Date: 2026-08-26 18:52:17 -0700

      Commit message:


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

      Package: SplicingGraphs

      Commit: 7063f7a222a2e35275de15930eddaa082d9dd3ef

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

      Date: 2026-08-26 18:51:41 -0700

      Commit message:


	  
		
 spelling
 
    
  
    

      Package: BSgenome

      Commit: da2ce6bcbe3b850db8458bdb0d60bad5fadaea9d

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

      Date: 2026-08-26 18:49:44 -0700

      Commit message:


	  
		
 spelling
 
    
  
    

      Package: GenomicFeatures

      Commit: 406313962cfb98d282a85728b9718f096c317bc5

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

      Date: 2026-08-26 18:49:12 -0700

      Commit message:


	  
		
 spelling
 
    
  
    

      Package: HDF5Array

      Commit: c4132ae2db816faf0a8c93dd7fccb502aad92e5d

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

      Date: 2026-08-26 18:40:22 -0700

      Commit message:


	  
		
 small tweak to long tests
 
    
  
    

      Package: HDF5Array

      Commit: 6d442dc8c9c01f8538fa2ad57e2f29698630a2bb

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

      Date: 2026-08-26 18:38:54 -0700

      Commit message:


	  
		
 tidy NAMESPACE
 
    
  
    

      Package: HDF5Array

      Commit: a73534d9963fcd1d0f5331c66815b17503a79bee

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

      Date: 2026-08-26 18:35:20 -0700

      Commit message:


	  
		
 spelling (again)
 
    
  
    

      Package: HDF5Array

      Commit: 2312b92cbdeff66440f34a44a66c99c54ed0de9e

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

      Date: 2026-08-26 18:32:12 -0700

      Commit message:


	  
		
 Revert "spelling"

This reverts commit 6e071082859536e7a773d1f0c8a11b9e5a47fd78.
 
    
  
    

      Package: HDF5Array

      Commit: 008c9d5ce9eadf6470acf552dc289bb67a4748ad

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

      Date: 2026-08-26 18:31:41 -0700

      Commit message:


	  
		
 Revert "spelling"

This reverts commit 22568f16a608cb968109a42a481ba2626e253510.
 
    
  
    

      Package: HDF5Array

      Commit: 46678ea2217b1ad88cb21f65f759ed7ddef1d3ca

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

      Date: 2026-08-26 18:24:57 -0700

      Commit message:


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

      Package: HDF5Array

      Commit: 22568f16a608cb968109a42a481ba2626e253510

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

      Date: 2026-08-26 18:18:05 -0700

      Commit message:


	  
		
 spelling
 
    
  
    

      Package: HDF5Array

      Commit: 6e071082859536e7a773d1f0c8a11b9e5a47fd78

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

      Date: 2026-08-26 18:18:05 -0700

      Commit message:


	  
		
 spelling
 
    
  
    

      Package: S4Arrays

      Commit: 22cee5bc9e8025ab7a46e82e61a43e82a3379d07

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

      Date: 2026-08-26 18:17:40 -0700

      Commit message:


	  
		
 spelling
 
    
  
    

      Package: updateObject

      Commit: 9be97ff3556fdafe683b0818c1421443e708eca6

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

      Date: 2026-08-26 18:17:14 -0700

      Commit message:


	  
		
 spelling
 
    
  
    

      Package: scRNAseqApp

      Commit: c860b60511c994c173ee3e7b6e7818a42cc508b8

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

      Date: 2026-08-26 21:16:34 -0400

      Commit message:


	  
		
 allow user to close the splash screen.
 
    
  
    

      Package: GenomicRanges

      Commit: b0be93253202832f530135f732a5b8d6d9740a88

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

      Date: 2026-08-26 18:15:26 -0700

      Commit message:


	  
		
 spelling
 
    
  
    

      Package: GenomicAlignments

      Commit: 5ab0e428f28d6632acb2c4534e146cdeeac435c9

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

      Date: 2026-08-26 18:14:21 -0700

      Commit message:


	  
		
 spelling
 
    
  
    

      Package: IRanges

      Commit: 75107e286bf13c8696ea2c3962ed9cd0c7c50d48

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

      Date: 2026-08-26 18:13:55 -0700

      Commit message:


	  
		
 spelling
 
    
  
    

      Package: S4Vectors

      Commit: e7446f1ce8c2c88773acbbc006d7dfafcb21b625

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

      Date: 2026-08-26 18:07:54 -0700

      Commit message:


	  
		
 spelling
 
    
  
    

      Package: Biostrings

      Commit: e9c2456e1761818986a9f6fe342566b0e5c8c7a5

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

      Date: 2026-08-26 18:01:28 -0700

      Commit message:


	  
		
 removing github workflows as they keep causing problems
 
    
  
    

      Package: Biostrings

      Commit: 3dab5d92fa32a5a6cb68f265ccd0176681975686

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

      Date: 2026-08-26 17:53:14 -0700

      Commit message:


	  
		
 Biostrings 2.81.7

Refactor as.data.frame.XStringSet() and as.data.frame.XStringViews().

Also revisit show() methods for XString, XStringSet, and MaskedXString
objects.
 
    
  
    

      Package: IRanges

      Commit: e4969215e13dd557714d6a0bc88248dcd6ae4520

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

      Date: 2026-08-26 17:49:11 -0700

      Commit message:


	  
		
 IRanges 2.47.5: Revisit show() method for MaskCollection objects
 
    
  
    

      Package: IRanges

      Commit: 36b34e09b6551cf43328359a51edd61d15f009bb

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

      Date: 2026-08-26 13:50:59 -0700

      Commit message:


	  
		
 more tweaks to as.data.frame.IPosRanges() and as.data.frame.IPos()
 
    
  
    

      Package: GenomicRanges

      Commit: 4b626b5ed07dc043df803c0974aa3e661fc45ff6

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

      Date: 2026-08-26 13:45:33 -0700

      Commit message:


	  
		
 GenomicRanges 1.65.3: More tweaks to as.data.frame.GenomicRanges() and as.data.frame.GPos()
 
    
  
    

      Package: Seqinfo

      Commit: 93f9978435ee2ff778f21368ef7d54492492de2f

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

      Date: 2026-08-26 13:39:39 -0700

      Commit message:


	  
		
 Seqinfo 1.3.2: Another tweak to as.data.frame.Seqinfo()
 
    
  
    

      Package: scRNAseqApp

      Commit: d2cff64852449c260c6d6aa03016f1f969d79ba5

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

      Date: 2026-08-26 16:33:45 -0400

      Commit message:


	  
		
 update splash screen style.
 
    
  
    

      Package: IRanges

      Commit: 41524d507cefefd7657cc15660baf5edd8beed9b

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

      Date: 2026-08-26 13:25:59 -0700

      Commit message:


	  
		
 more tweaks to as.data.frame.IPosRanges() and as.data.frame.IPos()
 
    
  
    

      Package: IRanges

      Commit: 3ea56ddef61e988bcf3bf87d14f0c2440994c462

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

      Date: 2026-08-26 13:17:43 -0700

      Commit message:


	  
		
 IRanges 2.47.4: Fix handling of names and mcols in ranges() method for Views objects
 
    
  
    

      Package: Seqinfo

      Commit: ad77d503ccfafa779e92e483a71350f8ef3d01b4

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

      Date: 2026-08-26 11:12:52 -0700

      Commit message:


	  
		
 one more tweak to as.data.frame.Seqinfo()
 
    
  
    

      Package: IRanges

      Commit: 0233e68b34b31029d97e35caaf841eed1ba54363

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

      Date: 2026-08-26 10:54:50 -0700

      Commit message:


	  
		
 more tweaks to as.data.frame.IPosRanges() and as.data.frame.IPos()
 
    
  
    

      Package: S4Vectors

      Commit: 61ed37f650b7391534e1a9a032335350ce420a93

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

      Date: 2026-08-26 10:51:22 -0700

      Commit message:


	  
		
 another tweak to as.data.frame.DataFrame()
 
    
  
    

      Package: GenomicRanges

      Commit: a6269257dc2a876c6907c857b7f61fba14e55ade

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

      Date: 2026-08-26 10:47:42 -0700

      Commit message:


	  
		
 GenomicRanges 1.65.2: Small tweaks to as.data.frame.GenomicRanges() and as.data.frame.GPos()
 
    
  
    

      Package: DuckDBArray

      Commit: 4aae0acc188206b6e334fca1d9205514f39420ba

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

      Date: 2026-08-26 10:34:14 -0700

      Commit message:


	  
		
 fix: correct integer64 handling in DuckDBArraySeed, fix writeCoordArray() docs (0.99.8)

Bug report on writeCoordArray()/DuckDBArray() surfaced two issues:

- Constructing a DuckDBArray/DuckDBArraySeed/DuckDBMatrix over a genuinely
  BIGINT/HUGEINT-typed value column crashed with "vector: cannot make a
  vector of mode 'integer64'". coltypes() reports "integer64" for such
  columns, and 9 call sites built the seed's structural fill value via
  vector(coltypes(...), 1L), which errors because "integer64" isn't a valid
  vector() mode. Replaced with a shared .coltypeFillVector() helper.

- Fixing that crash surfaced a second, more serious bug: as.matrix() /
  extract_array() on a successfully-constructed integer64-valued
  DuckDBArray silently returned garbage values (e.g. 4.94e-324 instead of
  1) instead of erroring. array() and [<- are class-blind and operate on
  the underlying double storage only, so an integer64-classed datacol value
  (the standard construction path opens its connection with bigint =
  "integer64", see acquireDuckDBConn()) never goes through bit64's
  as.double.integer64() conversion and its raw 64-bit pattern gets copied
  in as-is. rowSums()/rowCounts() were unaffected (SQL-computed, not
  R-side materialized). extract_array(), extract_sparse_array(), and the
  COO fast path (.collectCOO()) now normalize any integer64-classed
  datacol value to plain double at the point it's materialized from the
  database (.dropInteger64()), consistent with how DuckDBArray already
  treats integer64 everywhere else.

- DuckDBArraySeed's fill slot is now "ANY" (was "atomic"), with validity
  enforced via is.atomic() instead of the slot's formal class, so a genuine
  integer64 fill value is accepted without needing a class union that names
  "integer64" -- which triggered a bit64-related warning at install/build
  time, since bit64 registers integer64 via setOldClass() but never calls
  exportClasses(). bit64 is no longer an import of this package.

- writeCoordArray()'s arrowtype/max_dim docs now correctly describe the
  DuckDBArray fast-path method: unlike the ANY method, which infers the
  narrowest type from the data (or from dim(x) for index columns) when
  these are NULL, the DuckDBArray method takes the source's existing
  declared column type as-is, with no data-driven narrowing.

Full test suite: 0 failures. R CMD check: 0 errors, 0 warnings (2
pre-existing, unrelated NOTEs).
 
    
  
    

      Package: S4Vectors

      Commit: d6cc3bb14469380fba2d03698d82615c103d7fc3

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

      Date: 2026-08-26 10:19:38 -0700

      Commit message:


	  
		
 S4Vectors 0.51.9: One more tweak to as.data.frame.DataFrame()
 
    
  
    

      Package: Seqinfo

      Commit: 2c09ad5381b033458636a59b919e6959e37dbfc4

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

      Date: 2026-08-26 09:31:30 -0700

      Commit message:


	  
		
 Seqinfo 1.3.1: Minor tweaks to as.data.frame.Seqinfo()
 
    
  
    

      Package: MOFA2

      Commit: 4a102f2b491ab600738ddf693a70f0baf032ca68

      Author:  Jan Sprengel <janlsprengel@gmail.com> 

      Date: 2026-08-26 15:21:02 +0200

      Commit message:


	  
		
 increment minor version to 1.23.2
 
    
  
    

      Package: MOFA2

      Commit: fd80044229b91e8cedad90160a5b7a3759bc3829

      Author:  Jan Sprengel <janlsprengel@gmail.com> 

      Date: 2026-08-20 15:41:24 +0200

      Commit message:


	  
		
 run_mofa(): relax warning for patch versions ahead
 
    
  
    

      Package: MOFA2

      Commit: 90fbbae10b32e38fafa2a4450eb2e23b9c0a0dd5

      Author:  Jan Sprengel <janlsprengel@gmail.com> 

      Date: 2026-08-26 10:55:48 +0200

      Commit message:


	  
		
 bump mofapy2 version to 0.7.5, reformulate run_mofa() docs
 
    
  
    

      Package: MOFA2

      Commit: eeb3ab8f0383eb268b8900bdeea2194bd705db9e

      Author:  Jan Sprengel <janlsprengel@gmail.com> 

      Date: 2026-08-20 17:03:26 +0200

      Commit message:


	  
		
 increment mofapy2 version to 0.7.4
 
    
  
    

      Package: MOFA2

      Commit: 3c0d58025e6abf506f5347d7d0c11f96639f746a

      Author:  Jan Sprengel <janlsprengel@gmail.com> 

      Date: 2026-07-30 16:23:56 +0200

      Commit message:


	  
		
 update run_mofa() docs to recommend py_require(), pin version in vignettes

pin mofapy2 in examples and vignette calls of py_require
 
    
  
    

      Package: MOFA2

      Commit: 288df7d2c465dbaa926cf18535927111b0c3fd0c

      Author:  Jan Sprengel <janlsprengel@gmail.com> 

      Date: 2026-07-31 11:19:39 +0200

      Commit message:


	  
		
 CI: add Bioconductor GitHub Actions workflow

Also pin Python 3.12.10 (3.12.12 is not resolvable on the windows CI runner), switch to testthat 3rd edition and switch vignettes from basilisk to py_require()
 
    
  
    

      Package: MOFA2

      Commit: 2f3eb9522906baf951ace8da86eb8c0adb9a285a

      Author:  Jan Sprengel <janlsprengel@gmail.com> 

      Date: 2026-07-17 22:14:02 +0200

      Commit message:


	  
		
 implement plot_factor_mean_cor() QC visualiser, adjust QC warning message

implements plot_factor_mean_cor() with multi-group option, bold factor labels. Also the scope of a warning suppression is adjusted.
 
    
  
    

      Package: multipointR

      Commit: 2af89138ec317c161d5d0df885016bf63dd2287b

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

      Date: 2026-08-26 16:28:29 +0200

      Commit message:


	  
		
 Enable elastic net fit for complex models with splines  (#3)

* added option for relaxed enet fit

* add requirement on glmnet for type enet fit

* adjust for the fact that all terms are zero - intercept only model

* updated vignette and various fixes 
    
  
    

      Package: PhyloProfile

      Commit: 5118a80cbccd977895f17fc7a0948c7114106642

      Author:  trvinh <trvinh@gmail.com> 

      Date: 2026-08-26 09:36:57 +0200

      Commit message:


	  
		
 option to ignore invalid/unknown taxa; URL for pseudo taxID
 
    
  
    

      Package: eisaR

      Commit: 3f710e547ad31f80aaa5406e0c03889b9b84d9ff

      Author:  mbstadler <stadler.michael@gmail.com> 

      Date: 2026-08-26 09:26:10 +0200

      Commit message:


	  
		
 bump version to trigger a new R-universe build
 
    
  
    

      Package: gdsfmt

      Commit: 4ec0aeba21824461c200388caa9c3a143dbf94bb

      Author:  Xiuwen Zheng <zhengxwen@gmail.com> 

      Date: 2026-08-26 02:15:52 -0500

      Commit message:


	  
		
 cloud update & export
 
    
  
    

      Package: MsBackendMetaboLights

      Commit: 582814291e7bb4040144cc3a69fb3a37aa7b734e

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

      Date: 2026-08-26 08:08:41 +0200

      Commit message:


	  
		
 Merge pull request #24 from rformassspectrometry/jomain

Add pause to examples 
    
  
    

      Package: MsBackendMetaboLights

      Commit: aa6026ef99c5bf59e1774a6c87ed79feda3d9af4

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

      Date: 2026-08-26 07:47:32 +0200

      Commit message:


	  
		
 Add pause to examples
 
    
  
    

      Package: scrapbook

      Commit: 80cd6b605a39982b31e368fc45bc172ea1287ee1

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

      Date: 2026-08-26 12:45:13 +1000

      Commit message:


	  
		
 Fixed section title for consistency.
 
    
  
    

      Package: scrapbook

      Commit: 7eedf6966f01ba717e66f7e0b4c94c8d5c811208

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

      Date: 2026-08-26 12:40:31 +1000

      Commit message:


	  
		
 Migrated a short nuclei analysis chapter from OSCA.advanced.
 
    
  
    

      Package: IRanges

      Commit: 28c9970cca9bcec8eec020bff6390924b0a0e583

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

      Date: 2026-08-25 17:29:34 -0700

      Commit message:


	  
		
 IRanges 2.47.3: Minor tweaks to as.data.frame.IPosRanges() and as.data.frame.IPos()
 
    
  
    

      Package: S4Vectors

      Commit: e4668d7b6cb34e21de42f251764d4a8d13e31824

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

      Date: 2026-08-25 17:12:56 -0700

      Commit message:


	  
		
 S4Vectors 0.51.8: Various tweaks to as.data.frame.DataFrame()

This fixes issue #138.
 
    
  
    

      Package: DuckDBDataFrame

      Commit: ddcf2f5d57058deaf061d41f07a43ecf7a6958e3

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

      Date: 2026-08-25 16:36:48 -0700

      Commit message:


	  
		
 fix: pair the _INCOMPLETE reader check with the directory-wrap fix
 
    
  
    

      Package: DuckDBGRanges

      Commit: 94ecf2a80b6b4be8cf50dc9cb0f1739ecbd1b91d

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

      Date: 2026-08-25 14:18:11 -0700

      Commit message:


	  
		
 fix: validate narrow()'s start/end/width request as base does

narrow() accepted four requests base refuses, and two of them returned a
range wider than the input. A supplied width fixes whichever side was
left NA, so exactly one of start/end must be NA; "width only" quietly
anchored at the start and supplying all three quietly ignored end. And
narrow() may only shrink a range (base solves with
allow.nonnarrowing = FALSE), so narrow(x, start=5, end=200) on a
101-wide range returned 104-299 instead of erroring. The widen/invert
check is per row, matching base, and costs one aggregate query.

The start/end resolution is factored into .narrow_resolve(), used both
to build the new columns and to build the validation predicate.

Review item R-G3 described this as narrow(width=w) leaving coordinates
unchanged while writing an inconsistent width. That does not reproduce:
.modify_DuckDBGRanges_datacols() recomputes end as start + width - 1
when only the width changes. The missing validation is the real gap.
All solvable forms already matched GenomicRanges and still do.
 
    
  
    

      Package: DuckDBGRanges

      Commit: 8adfde28d7d74dea23d8a6a61f84804f84fbf74e

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

      Date: 2026-08-25 13:54:57 -0700

      Commit message:


	  
		
 fix: correct the remaining element-wise set operations and distance()

punion() and pintersect() share .parallel_set_op(), which paired x[i] with
y[i] using a bare row_number() over DuckDB's undefined scan order (review
item R-G4) and coordinate-sorted its result, so result[i] was not
x[i] combined with y[i]. Pairing now goes through the recorded keycol,
matching the pgap() and psetdiff() rewrites, and the result keeps the
pairing order.

Fixing that surfaced the same defect class as R-G1 in both callers, which
base treats differently and which was not modelled at all: pintersect()
produced a negative width for a non-overlapping pair (unmaterializable)
where base returns a zero-width range, and punion() silently spanned a gap
where base errors unless fill.gap=TRUE. Neither checked seqname or strand
compatibility, so both combined ranges across chromosomes. ignore.strand,
strict.strand, and drop.nohit.ranges were all accepted and ignored.

Separately, distance() returned a number rather than NA for a pair on
different seqnames whenever either strand was '*': the strand OR-chain was
not parenthesized inside the AND, so SQL precedence let any '*' strand make
the pair valid on its own. Same hazard already documented on pgap(); the
existing test never combined a seqname mismatch with a '*' strand.

All three operations are now checked against GenomicRanges with and without
an explicit keycol; each fix was reverted individually to confirm it is
load-bearing.
 
    
  
    

      Package: DuckDBDataFrame

      Commit: adfaf4686e19826e596d1b0ad5d93f0328558a35

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

      Date: 2026-08-25 13:38:00 -0700

      Commit message:


	  
		
 fix: readParquetSchema() leak
 
    
  
    

      Package: DuckDBDataFrame

      Commit: 3b3a38e9cca3093d2e9052ec564e5315d92b8742

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

      Date: 2026-08-25 13:18:42 -0700

      Commit message:


	  
		
 fix: release the parquet file handle before renaming or unlinking

Follow-up to the mmap fix: removing the memory mapping unblocked the
in-place write but not the rename and unlink that splitParquetPart()
performs on its source. ParquetFileReader opens the file and has no
Close() method, so .findFactorColumns() left a handle live until GC, and
Windows refuses to rename or unlink a file that any handle still holds.

It now creates its own ReadableFile, passes that to ParquetFileReader,
and closes it explicitly; the returned Schema stays valid afterwards.
Confirmed by file-descriptor count: the old form leaves one handle open,
the new form leaves none. splitParquetPart() also drops its DuckDB temp
table before touching the source rather than at function exit, and the
"failed to move aside" error now names the Windows cause.
 
    
  
    

      Package: DuckDBDataFrame

      Commit: ad1a3e9bb7b8f3d55710c0ec1da325605bec900b

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

      Date: 2026-08-25 12:01:26 -0700

      Commit message:


	  
		
 fix: unmap parquet reads so in-place rewrites work on Windows

The factor-restoration path reads and rewrites each parquet file in
place, and arrow's default memory-mapped read leaves a mapping open that
Windows refuses to write over, rename, or unlink (error 1224). Staging
the write elsewhere and renaming would not help: replacing a mapped file
is blocked the same way, so the mapping itself has to go.

Fixed at three sites, not just the one in the traceback.
.restoreFactorColumns() and .findFactorColumns() both read the source
file that splitParquetPart() later renames aside and unlinks, so leaving
either mapped would simply have moved the failure downstream into the
rollback path. .findFactorColumns() switches from open_dataset(), which
cannot opt out of mapping, to ParquetFileReader$create(mmap = FALSE).
writeDuckDBTableParquet()'s sample_df read is unmapped for the same
reason, though it was not implicated here.

The splitParquetPart() half of this is a pre-existing 0.99.22 defect that
only surfaced now because that function had no test coverage until this
release. Adds a test asserting the files stay renameable and removable
after both helpers touch them.
 
    
  
    

      Package: DuckDBGRanges

      Commit: a4634eb0dc514478a326e28fc849d8daea18951b

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

      Date: 2026-08-25 11:54:59 -0700

      Commit message:


	  
		
 fix: correct psetdiff for non-overlapping, covering, and inside pairs

psetdiff() handled only edge-aligned overlaps, as its header comment
conceded. A non-overlapping pair came back wider than x, and a covering
pair came back with negative width, which is not merely wrong but
unmaterializable ("each range must have a non-negative width"). A y
sitting strictly inside x cannot be expressed as one range and base
refuses it; this returned garbage instead.

Three further defects in the same method: seqname and strand
compatibility were ignored, so ranges were subtracted across
chromosomes; ignore.strand was accepted and never used; and the result
was coordinate-sorted by .build_DuckDBGRanges()'s default ordering, so
result[i] was not x[i] minus y[i].

Pairing also moves from a bare row_number() over DuckDB's undefined scan
order to .add_keycol_indices(), matching the pgap() rewrite. That is
review item R-G4, done here because correct pairing is a precondition
for this method being correct at all; punion/pintersect still need it.
 
    
  
    

      Package: flowViz

      Commit: 077ee734b27398a50661e772f281368eeae324d5

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2026-08-25 11:47:51 -0700

      Commit message:


	  
		
 Bump version to 1.77.1
 
    
  
    

      Package: flowViz

      Commit: 065ecc59d52d978d4ee20af3e2bdd77a18985ce9

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2026-08-25 11:47:37 -0700

      Commit message:


	  
		
 Migrate parallel to parallelplot for lattice >= 0.23

lattice 0.23 removed the long-deprecated parallel() function
(replaced by parallelplot() in 0.20). setGeneric("parallel")
therefore fails at install time with:
  must supply a function skeleton for 'parallel'

Rename the generic, methods, exports, and docs to parallelplot.
 
    
  
    

      Package: DuckDBGRanges

      Commit: 5a9784db51058d3c90e4127a2c63e129b67f55ef

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

      Date: 2026-08-25 11:19:18 -0700

      Commit message:


	  
		
 fix: repair the nearest-neighbour family for row-number-keyed objects

Three stacked defects made nearest(), precede(), follow(), and
distanceToNearest() unusable on any DuckDBGRanges without an explicit
keycol, which is the default for a file-backed object. Every existing
test in this family supplies one, so none of it was covered.

.add_keycol_indices() treated the keycols slot as literal key values,
but a row-number-keyed frame stores set_row_number()'s c(NA, -n)
sentinel there; joining against it matched nothing and silently emptied
the result. It now derives the position with row_number()
instead. window_order() is deliberately avoided: dbplyr keeps that
ordering attached and re-emits it after the column has been grouped
away.

.build_nearest_single_result() subscripted with the SQL-derived index
directly, and an integer64 subscript silently yields NA for every
position.

.nearest_ddb() lacked the is.na(subj_idx) guard .distanceToNearest_ddb()
has. DuckDB's greatest() skips NULLs, so a query on a seqname with no
subject scored greatest(NULL, NULL, 0) = 0, won its own min-distance
filter, and produced a hit to a NULL subject.
 </pre>
    </div>
  
    

      Package: scRNAseqApp

      Commit: d89bc02109e271b19c586b4c991307869a421ae3

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

      Date: 2026-08-25 13:57:35 -0400

      Commit message:


	  
		
 adjust a little bit the css.
 
    
  
    

      Package: scRNAseqApp

      Commit: 1e32f964f7f3a58664072f5d40a63f784e8ea98d

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

      Date: 2026-08-25 13:27:20 -0400

      Commit message:


	  
		
 add splash screen.
 
    
  
    

      Package: DuckDBDataFrame

      Commit: cfa12fb3e564aed3178e5968a18a10aa06fbd358

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

      Date: 2026-08-25 09:49:49 -0700

      Commit message:


	  
		
 fix: prevent data loss on two DuckDBTable parquet write paths

splitParquetPart() unlinked the source file before copying the split
parts into place, discarded file.copy()'s return value, and left
overwrite=FALSE. A failed copy destroyed the only copy of the data and
returned without error. The source is now moved aside, the copy is
checked, and any failure rolls the directory back to its original
contents. A read-only target directory previously produced a silent
no-op reported as success; it now errors.

writeDuckDBTableParquet() never consulted @collevels, so its SQL COPY
flattened every factor column to VARCHAR and dropped any level unused in
the data. It now re-applies the recorded levels via the same arrow-side
fixup splitParquetPart() already used, refactored into a shared
.applyFactorLevels() helper, and does so before sample_df is read back
so the caller's schema inference sees the factors too.
 
    
  
    

      Package: maaslin3

      Commit: 4b6855d6a2f8283e1667208ab3c643d71f596426

      Author:  Will Nickols <willanickols@gmail.com> 

      Date: 2026-08-25 08:25:03 -0700

      Commit message:


	  
		
 Fix random effects handling for multiple crossed random intercepts
 
    
  
    

      Package: IFAA

      Commit: 7f243b8d985160cb53bb8c623c6ca91054f893fa

      Author:  Mingkai Chen <chenm1@ufl.edu> 

      Date: 2026-08-10 16:03:22 -0400

      Commit message:


	  
		
 Internalize HDCI routines to restore package build
 
    
  
    

      Package: scRNAseqApp

      Commit: 6f1778ebb777237397264aa6dd17e557109f3fce

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

      Date: 2026-08-25 09:17:59 -0400

      Commit message:


	  
		
 Add gene score vs gene expression modules.
 
    
  
    

      Package: scRNAseqApp

      Commit: d3ad57d7b80bcc406dbf2f0b488b412cb189810c

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

      Date: 2026-08-14 15:32:02 -0400

      Commit message:


	  
		
 fix a typo.
 
    
  
    

      Package: scRNAseqApp

      Commit: 4a473552eba18c3c3082405140ebb686da40bf85

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

      Date: 2026-08-14 13:23:18 -0400

      Commit message:


	  
		
 fix column names for fragments.
 
    
  
    

      Package: cytomapper

      Commit: 2efbbe1b58492660783b898a3c1cbf87676ecb22

      Author:  Lasse Meyer <73339780+lassedochreden@users.noreply.github.com> 

      Date: 2026-08-25 12:29:00 +0200

      Commit message:


	  
		
 Merge pull request #102 from BodenmillerGroup/bioc24_buildfix

Bioc24 fix 
    
  
    

      Package: cytomapper

      Commit: 65bc5a7969825d303d8caa708c88b01a156494b2

      Author:  lassedochreden <lasse.meyer@uzh.ch> 

      Date: 2026-08-25 11:18:24 +0200

      Commit message:


	  
		
 Revert "fix runners for shinytest", "update runners" x2

Reverts 6206c47, 67ec23c, f6bc0d8. Back to the bioc24_buildfix branch
state as of "bioc24 fix" (064205c), before the GitHub Actions
runner/PhantomJS-caching changes.
 
    
  
    

      Package: cytomapper

      Commit: 6206c4746fd06ac28baac39f0892e8530370f1b5

      Author:  lassedochreden <lasse.meyer@uzh.ch> 

      Date: 2026-08-25 10:30:23 +0200

      Commit message:


	  
		
 fix runners for shinytest
 
    
  
    

      Package: cytomapper

      Commit: 67ec23c4b27b6edc84e44f1babb147e4a1138cf8

      Author:  lassedochreden <lasse.meyer@uzh.ch> 

      Date: 2026-08-25 10:06:09 +0200

      Commit message:


	  
		
 update runners
 
    
  
    

      Package: cytomapper

      Commit: f6bc0d89a4b6c34cb0363107430483fdcbb98464

      Author:  lassedochreden <lasse.meyer@uzh.ch> 

      Date: 2026-08-24 17:14:57 +0200

      Commit message:


	  
		
 update runners
 
    
  
    

      Package: cytomapper

      Commit: 064205cfb4f488e62aee5705ef05256194b84a8f

      Author:  lassedochreden <lasse.meyer@uzh.ch> 

      Date: 2026-08-24 16:30:33 +0200

      Commit message:


	  
		
 bioc24 fix
 
    
  
    

      Package: bluster

      Commit: ef34d956f9c1184265beef3fb868bf680ab83d17

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

      Date: 2026-08-25 18:29:59 +1000

      Commit message:


	  
		
 Cleaned up docstring warnings, bumped version and date.
 
    
  
    

      Package: bluster

      Commit: 40b38d0eef9fd2b31b728fcc000d18ce87bacd33

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

      Date: 2026-08-25 16:58:05 +1000

      Commit message:


	  
		
 Switch from scuttle/scran to scrapper for dataset setup.
 
    
  
    

      Package: bluster

      Commit: 4c7e644f89cce76561341ea6ee7ccf92ca05545d

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

      Date: 2026-08-25 16:36:33 +1000

      Commit message:


	  
		
 Migrated explanatory text from OSCA.advanced's cluster redux chapter.

Also switch to scrapper to set up the dataset in the diagnostics.Rmd.
 
    
  
    

      Package: bluster

      Commit: ce7ac0a3deaf212f86c90c9463bcb515b0ebd657

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

      Date: 2026-08-25 15:28:35 +1000

      Commit message:


	  
		
 Tidied up pairwiseRand manpage.
 
    
  
    

      Package: msa

      Commit: 2e9a9e9728455d7c097f7f7f8c9ee66d5429e14f

      Author:  UBod <ulrich@bodenhofer.com> 

      Date: 2026-08-25 10:07:18 +0200

      Commit message:


	  
		
 updated vignette; version number bumped to 1.45.5
 
    
  
    

      Package: MsBackendMetaboLights

      Commit: f49c8bc69d49d62c988a85a5a55389a586950592

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

      Date: 2026-08-25 09:05:17 +0200

      Commit message:


	  
		
 Update README
 
    
  
    

      Package: MsBackendMetaboLights

      Commit: fdfed26db27a8c5b3fb4c9fe4602898c62857eb5

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

      Date: 2026-08-25 08:39:00 +0200

      Commit message:


	  
		
 Fix installation instructions and add 4 second breaks to unit tests
 
    
  
    

      Package: MsBackendMetaboLights

      Commit: 798de387ad331d8e097fbedad942367eb77abf5e

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

      Date: 2026-08-25 08:20:12 +0200

      Commit message:


	  
		
 small updates in NEWS and README
 
    
  
    

      Package: MsBackendMetaboLights

      Commit: bbaddc706e3ee49efd1983e0616578518cc8f164

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

      Date: 2026-08-24 09:01:32 +0200

      Commit message:


	  
		
 Update roxygen version
 
    
  
    

      Package: scrapper

      Commit: 985ad210f9f2b964dcd072ddc4a2bed302d0caef

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

      Date: 2026-08-25 11:27:58 +1000

      Commit message:


	  
		
 Vignette is now a stub that redirects to the book.

No point having a poor man's duplicate of the documentation when we could just
point users to the real deal and save ourselves some build time.
 
    
  
    

      Package: drugTargetInteractions

      Commit: a95ecf0aec40f8aadec98ee09258d4371b359392

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

      Date: 2026-08-24 21:19:29 -0700

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: drugTargetInteractions

      Commit: 93058dc4cc5b0f8350481e46fe2ae40d1b173eea

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

      Date: 2026-08-24 21:16:28 -0700

      Commit message:


	  
		
 Add buildMoaMasterTable(): enumerate the drugs that have a mechanism

assembleMoaTable() shapes whatever queryDrugTargets() was asked for, so
you have to name the drugs going in. There was no way to ask which drugs
have a mechanism at all.

A mechanism belongs to the drug, not to a drug-target edge, and the
difference is not academic. Measured against the real sources: 1,470 of
the Broad Hub's 6,855 drugs with a mechanism name no target gene (21%),
as do 329 of ChEMBL's 5,727 (6%). Roughly two thousand annotated drugs
are therefore unreachable from buildGenomeWideDrugTargetTable(), which is
anchored on genes - "c-Myc inhibitor", "polyamine biosynthesis
inhibitor", "Radiotherapy agent" and so on.

Sweeps the two sources that can be enumerated: ChEMBL's /mechanism is a
pageable collection (7,561 records, ~8 requests) and the Broad Hub is
already local SQLite. The whole table is 14,723 rows over 12,582 drugs
and 3,263 mechanisms in about a minute. Open Targets carries real MOA too
but its GraphQL has no clean enumeration path and its drug annotations
derive largely from ChEMBL, so it stays with queryMoa().

Two data details that would otherwise mislead:

- The Broad Hub packs up to 6 mechanisms into one "a | b" string, for 493
  drugs. Splitting them turns 1,612 apparent mechanisms into 1,294 real
  terms; without it, 318 of the "distinct MOAs" are combinations.
- ChEMBL records "Unknown" as the mechanism for 228 rows. Dropped by
  default as a placeholder; includeUnknown = TRUE keeps them.

Sources are kept side by side, not merged: drug_id is a ChEMBL id on
ChEMBL rows and the Hub's own drug name on Broad rows. They also word
mechanisms at different granularity - ChEMBL names the isoform
("Carbonic anhydrase VII inhibitor") where Broad names the family
("carbonic anhydrase inhibitor") - so only 7 of 3,263 terms are shared
verbatim, and 102 after lower-casing. Documented, since it decides
whether grouping the column across sources means anything.

Every count reconciles against independent raw measurements of both
sources. New .dtiPageAll() for unfiltered collection paging, beside the
existing .dtiBatchGET(). Vignette section 7 gains "A Master Table of
Mechanisms". test-moaTable.R 57 -> 90 with the network on, the Broad half
network-free against a synthetic SQLite.
 
    
  
    

      Package: drugTargetInteractions

      Commit: 05e656c64d1f073c2c0fb29fd6391de68dbd7c0b

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

      Date: 2026-08-24 20:48:20 -0700

      Commit message:


	  
		
 version bump
 
    
  
  


</div>

</div>