fix enrichGO hybrid annotation for unmapped IDs
 

 1.99.1: help pages in Markdown (code font renders), from/to in code font, website in the Spatial Playbook style (cosmo, light navbar), Get started only, more spacing

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FgRx4EtKQgeeWT1qCNkS8S
 

 pkgdown: list SpicyResults-class in the reference index

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FgRx4EtKQgeeWT1qCNkS8S
 

 Core: replace the incomplete beta and gamma functions that followed Numerical Recipes

Numerical Recipes code cannot be redistributed under GPL (Bioconductor self-review,
CODE-14). The regularised incomplete beta is now written from DLMF 8.17.22 and 8.17.4,
evaluated with the fundamental recurrences (DLMF 1.12.5), and takes 1 - x separately.
P-values agree with R's pt() to about 1e-14 (relative) for df up to 500, better than
before. The unused incomplete gamma and pchisq_upper are removed.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FgRx4EtKQgeeWT1qCNkS8S
 

 Vignette and README: abundance-adjusted default, covariate effects, weighted and interactive box plot, example images, callouts; installation from Bioconductor devel; NEWS

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FgRx4EtKQgeeWT1qCNkS8S
 

 Adjusted for abundance and covariates by default

The main test of spicy() is now the design test with the condition indicators, the
centred log share of the counted type (adjustAbundance = TRUE, replacing
availability) and the centred covariates; the unadjusted test is kept in the
unadjusted_* columns and each adjustment's effect is reported (_effect,
_p_value). Core: design_tests() (several contrasts of one fit, per-unit
influences, Hartung-Knapp), per-image weights, abundance-adjusted survival.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FgRx4EtKQgeeWT1qCNkS8S
 </pre>
    </div>
  
    

      Package: spicyR

      Commit: 4936ab8aba680134e70198e15f037e466d4c252d

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

      Date: 2026-10-02 21:52:12 +1000

      Commit message:


	  
		
 Docs: second-round review fixes (installation from GitHub, consistent wording, supported data, box-plot notes, adjusted result, run time, old-test note, badges); CITATION without duplicate DOI

R CMD check: OK. BiocCheck: 0 errors, 0 warnings. 54 tests pass.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FgRx4EtKQgeeWT1qCNkS8S
 
    
  
    

      Package: spicyR

      Commit: 226acb8c9aafe4776a045ac31149b74dad143c67

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

      Date: 2026-10-02 21:36:14 +1000

      Commit message:


	  
		
 Docs revised after biologist, bioinformatician, statistician and technologist reviews

README: runnable quick start on METABRIC, column conventions, installation from GitHub until release, migration
note, descriptive alt text. Vignette: random labelling and label clustering described correctly, hedged claims,
cell-type labels decoded, why the pair was chosen, column dictionary, consistent numbers across sections,
abundance section with the pair's adjusted result and the power caveat, max-T flagged as new, survival and
Hartung-Knapp wording, 5-shuffle check at p < 0.05 and 0.01, reporting and citation, R/Python name table.
Code: SpatialExperiment coordinates used automatically; bind() names the pair's column; plot labels; spicy()
help states the direction and defaults. R CMD check: OK. BiocCheck: 0 errors, 0 warnings.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FgRx4EtKQgeeWT1qCNkS8S
 
    
  
    

      Package: spicyR

      Commit: 33892f9d0a4bdac8255a0cca6235760f392f6d69

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

      Date: 2026-10-02 20:16:13 +1000

      Commit message:


	  
		
 README and vignette rewritten for users (draft for review): one running METABRIC example, question first, method details last; overview figure

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FgRx4EtKQgeeWT1qCNkS8S
 
    
  
    

      Package: spicyR

      Commit: 3024663b7f3aa4af4fbafdc1ac4b58fa74e32fb9

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

      Date: 2026-10-02 19:49:12 +1000

      Commit message:


	  
		
 signifPlot(): with fdr = TRUE the size legend reads -log10 adjusted p-value (it said -log10 p-value); survival bubbles get a size label

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FgRx4EtKQgeeWT1qCNkS8S
 
    
  
    

      Package: spicyR

      Commit: 1f422a6f92da31478595e723d31f6b5f66a99361

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

      Date: 2026-10-02 19:16:06 +1000

      Commit message:


	  
		
 Remove spicy_glm() and its R implementation (Ellis): spicy() is the interface

spicy_glm.R, excess.R, frailty.R, moderated.R and diagnostics.R are removed with their tests; the cell
method runs on the C++ statistics module, which the plain-R reference tests in test-cell.R cover.
enumerate_pairs() moves to cell.R; limma leaves Suggests.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FgRx4EtKQgeeWT1qCNkS8S
 
    
  
    

      Package: spicyR

      Commit: 904e803eb7f0b91643822da57a80affabe97c8eb

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

      Date: 2026-10-02 18:20:55 +1000

      Commit message:


	  
		
 README for spicyR 2.0

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FgRx4EtKQgeeWT1qCNkS8S
 
    
  
    

      Package: spicyR

      Commit: 58a474eac942bbb2b96572314299b8857629807d

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

      Date: 2026-10-02 18:15:58 +1000

      Commit message:


	  
		
 Vignettes and site: spicyR Cell on METABRIC and Schurch 2020; the original test in its own vignette; pkgdown for /dev; NEWS for 2.0

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FgRx4EtKQgeeWT1qCNkS8S
 
    
  
    

      Package: spicyR

      Commit: 2cb4a91a4bdf814423f89d684aa175a95a4e9c02

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

      Date: 2026-10-02 18:15:49 +1000

      Commit message:


	  
		
 Bioconductor checks: portable Makevars, missing covariates, show() for the cell method, image-method from/to recycling

- Makevars without GNU make extensions; object files kept out of the tarball
- covariates: images (or survival patients) with a missing covariate leave only the covariate model
- show(): a summary for the cell method (pairs, units, BH calls raw and at equal availability)
- spicyBoxPlot(): the cell types in the axis label; NaN shown as NA in results
- image method: a single from is recycled over several to (failed in the weight fit in 1.x); test added
- CITATION in ASCII; Description rewritten for version 2; R >= 4.5; dplyr in Suggests (vignette)
R CMD check: Status OK. BiocCheck: 0 errors. 340 tests pass.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FgRx4EtKQgeeWT1qCNkS8S
 
    
  
    

      Package: spicyR

      Commit: e8714f1eff8a653c68b487a205c7e92d9e231ed6

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

      Date: 2026-10-02 17:29:57 +1000

      Commit message:


	  
		
 Qualify stats::relevel and stats::pchisq; import stats::density in plotImage()

Clears the R CMD check "no visible global function" NOTE.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FgRx4EtKQgeeWT1qCNkS8S
 
    
  
    

      Package: spicyR

      Commit: b00718fecb79a0ddd8200775559da25c46c3a476

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

      Date: 2026-10-02 17:28:01 +1000

      Commit message:


	  
		
 Survival: no hazard ratio when tau2 is near 0 (every patient shrunk to the mean); C-locale sorting of images and levels, as the Python twin

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FgRx4EtKQgeeWT1qCNkS8S
 
    
  
    

      Package: spicyR

      Commit: 0c8483b8b6f338ee5d4fadc780a196eb9bdc90d7

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

      Date: 2026-10-02 17:25:01 +1000

      Commit message:


	  
		
 DESCRIPTION: Imports down to base R packages, Rcpp, ggplot2, S4Vectors and survival

Bioconductor container classes and model packages move to Suggests; regenerated
NAMESPACE and man pages.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FgRx4EtKQgeeWT1qCNkS8S
 
    
  
    

      Package: spicyR

      Commit: 733774b7fe646d01240159b865064b9a614587fe

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

      Date: 2026-10-02 17:25:01 +1000

      Commit message:


	  
		
 Plots in plain ggplot2: drop ggforce, ggh4x, ggnewscale, ggthemes, pheatmap and scales

- signifPlot(type = "bubble"): half discs drawn with geom_polygon; Kontextual contexts
  as facet_grid panels labelled in the strip, with a band in the context colour.
- signifPlot(type = "heatmap") now returns a ggplot (geom_tile) instead of a pheatmap.
- signifPlot() plots every cell type in the tested pairs (from and to) by default, and
  shows cell-method excesses on their own scale.
- spicyBoxPlot(): for method = "cell" the y axis is the excess and the title
  " cells around  cells"; "L Function" for the image method.
- plotImage() and imageCrossPlot() without dplyr, tidyr, scales or building a
  SpatialExperiment.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FgRx4EtKQgeeWT1qCNkS8S
 </pre>
    </div>
  
    

      Package: spicyR

      Commit: e8ceeb477f83ba976e39462a82c0e4ebca04788f

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

      Date: 2026-10-02 17:25:01 +1000

      Commit message:


	  
		
 Base R in place of dplyr, tidyr, tibble, magrittr, rlang, cli, lifecycle, BiocParallel, ClassifyR and simpleSeg

- .format_data(), getCellSummary() and helpers in base R; same columns, order and
  return types (getCellSummary(bind = FALSE) is still a SplitDataFrameList).
- Image method: parallel::mclapply / lapply in place of bplapply; cores, nCores and
  BPPARAM still accepted (BiocParallel params become a worker count via bpnworkers).
- Deprecated arguments warn through an internal .deprecate_warn() and now reach the
  calling function even when spicy() passes the new argument at its default.
- colTest(type = "survival") uses the package's C++ Cox fit (Efron ties, Wald test)
  in place of ClassifyR::colCoxTests(); same output.
- Suggested packages (SummarizedExperiment, SpatialExperiment, lmerTest, scam, coxme,
  spatstat, concaveman) are loaded only on the paths that need them, with an
  informative error if missing.
- Outputs checked identical to the previous version (spicy image lm/mixed/survival,
  weightsByPair, sigma and concave windows, colTest, convPairs, topPairs, bind).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FgRx4EtKQgeeWT1qCNkS8S
 
    
  
    

      Package: spicyR

      Commit: 335fe64734ebdea6b98b16560c7c7dad9c6725c3

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

      Date: 2026-10-02 16:49:08 +1000

      Commit message:


	  
		
 Pair direction follows the spatial-statistics convention (from = centre, to = counted); tests for the cell method

tests/testthat/test-cell.R checks the C++ core against a plain-R reference written from the Supplementary
(every pair, label clustering on and off, CR2 and HK; 1e-8), the direction, the design path against the
closed form, covariates against the dense definitions, Cox against survival::coxph, the survival score
test, max-T against an exact integral, more than two conditions, and topPairs/bind/spicyBoxPlot/signifPlot.
The legacy test pins method = "image". 339 tests pass.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FgRx4EtKQgeeWT1qCNkS8S
 
    
  
    

      Package: spicyR

      Commit: 0ab29d410171cebb6164ef7dceac6c690ed346f8

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

      Date: 2026-10-02 16:31:06 +1000

      Commit message:


	  
		
 spicy(): spicyR Cell by default (method = "cell"), the original test as method = "image"

The cell method runs on the C++ statistics module: two or more conditions (levels against the reference),
covariates, the availability-adjusted difference reported beside the raw one, k nearest neighbours,
several radii (max-T or Cauchy) and survival outcomes (score test and hazard ratio). Results are
SpicyResults objects that topPairs(), signifPlot(), spicyBoxPlot() and bind() read for both methods.
On diabetesData (two stages, label clustering off) it matches spicy_glm to 3e-9, about 4x faster.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FgRx4EtKQgeeWT1qCNkS8S
 
    
  
    

      Package: spicyR

      Commit: 4b711b819ef533e51df559107f1281b7fd56de6e

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

      Date: 2026-10-02 16:25:05 +1000

      Commit message:


	  
		
 C++ statistics module: excess GEE, design GEE, availability, Cox, survival tests, Cauchy and max-T

src/core gains stats.hpp with distributions.cpp, excess.cpp, design.cpp, survival.cpp and multiradius.cpp
(plain C++17 + Eigen, shared with the Python twin), R bindings in stats_bindings.cpp and the R driver in
R/cell.R. Checked against R:
- excess pipeline (counts, label clustering, Paule-Mandel, CR2, HK) vs the plain-R reference: 1e-12, 64 pairs
- design GEE vs the excess_design.R prototype: 6e-10 (patient-level, tau2 estimated), 2e-14 (image-level)
- availability adjustment vs adjust_cov.R: 9e-15
- Cox (Efron) vs survival::coxph: beta 4e-16, martingale residuals 9e-16, null model 4e-16
- Student t: 4e-13 relative; normal quantile exact; max-T tail vs exact integrals: 1e-5 relative at p = 2e-5
The label-clustering five-pair rule now subtracts the self-count for self-pairs (Supplementary rule).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FgRx4EtKQgeeWT1qCNkS8S
 
    
  
    

      Package: spicyR

      Commit: 42ba6d757023f93a48749d756c8765a4966774c8

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

      Date: 2026-10-02 15:49:55 +1000

      Commit message:


	  
		
 spicyR 2 (1.99.0): merge the spicyglm C++ core and R front end into spicyR

The C++17 core (src/core, Eigen) is now part of spicyR and will be shared verbatim with the Python twin.
spicy_glm() and its internals move into R/, its tests into tests/testthat (test-glm-*). The separate
spicyglm/ subpackage is removed. Sadiq Dohadwalla and Elijah Willie join as authors.
All 298 tests pass.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FgRx4EtKQgeeWT1qCNkS8S
 
    
  
    

      Package: spicyR

      Commit: ddaa60fe832fe50bcc084598ece1921524057ee0

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

      Date: 2026-10-02 15:42:03 +1000

      Commit message:


	  
		
 Merge remote-tracking branch 'origin/cpp-edge' into spicyR2
 
    
  
    

      Package: spicyR

      Commit: acf87e743ed71dc5ed9680cb02db43ba7570f304

      Author:  Ellis Patrick <ellis.patrick@192.168.20.250> 

      Date: 2026-10-01 08:58:32 +1000

      Commit message:


	  
		
 spicyglm: default to the excess effect with CR2 variance

- spicy_glm() now defaults to effect = "excess", variance = "cr2" (the calibrated
  analysis); the ratio-only designs (sigma, parent, test = "moderated") fall back
  to effect = "ratio" when effect is not given.
- Documentation updated; Hartung-Knapp noted as anti-conservative for rare types.
- Excess composition helpers and their tests.
- Ratio and Hartung-Knapp tests now request those settings explicitly; new test
  for the defaults and the fallback. 52 tests, 286 expectations pass.

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

      Package: spicyR

      Commit: 4ae9b7c2f505b6e74131b5ecc376651bd831457e

      Author:  Ellis Patrick <ellis.patrick@192.168.20.250> 

      Date: 2026-09-28 22:30:01 +1000

      Commit message:


	  
		
 spicyglm: one-pass label-clustering sums per REF type; own-tau2 moderation

- hac_phi_sums_ref: the HAC sums and their random-labelling expectation for one
  REF type and every non-self TARGET in a single neighbour pass per image,
  algebraically identical to the per-pair sums (tested); label clustering is
  about 4x faster (radius excess 1.6 s -> 0.4 s on a 64-pair dataset)
- excess moderation evaluates each pair's model variance at its own tau2

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

      Package: spicyR

      Commit: 6acc3b25b0da7f2143ea6fcc0ac3e0f699157d0c

      Author:  Ellis Patrick <ellis.patrick@192.168.20.250> 

      Date: 2026-09-28 22:13:18 +1000

      Commit message:


	  
		
 spicyglm: frailty GEE, moderated test, excess effect, label-clustering fix

- frailty = TRUE: random-labelling within-image variance, image/subject
  frailty GEE with closed-form CR2 and Satterthwaite df; moderate = TRUE
- test = "moderated": image-level moderated test; Kontextual and
  inhomogeneous designs
- effect = "excess": extra REF neighbours per TARGET cell beyond random
  labelling (additive K / kNN), frailty GEE + CR2, optional moderation;
  new kNN out-degree squared totals in C++
- label clustering: HAC estimate now divided by its own expectation under
  random labelling (previously by phi, biased upward for common REF types)
- tests for all of the above (182 passing)

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

      Package: spicyR

      Commit: 9330b902d279e3bb00c59bb98ef6644c0e465a6e

      Author:  ecool50 <ewillie0004@gmail.com> 

      Date: 2026-09-25 12:26:43 +1000

      Commit message:


	  
		
 Add getPairwiseProp() with a C++ core, and spicy()'s weightZThreshold

getPairwiseProp() is Sadiq's fixed-k observed/expected proportion ratio
from the gee branch (0e51a4d), with the same arguments and output. Its
per-image work now runs in src/pairwiseProp.cpp over threads, using a
neighbour search that reproduces spatstat.geom::nnwhich(), ties included.
It matches the R version to 1e-13 on diabetesData and a 1.2M-cell cohort.

weightZThreshold is carried over from gee (1d4b195) so the weights can be
fitted for a small-scale statistic such as this ratio.
 
    
  
    

      Package: spicyR

      Commit: 29213e9fc152da460c31084689c788bab3d6c63a

      Author:  ecool50 <ewillie0004@gmail.com> 

      Date: 2026-09-23 17:33:29 +1000

      Commit message:


	  
		
 Re-time the benchmarks with both-direction binomial, on gee at 40260c4

The published table predated two changes: binomial fitted one direction per
unordered pair, and the R timings came from gee at b591b17. Everything is
re-timed in one pass on the same machine, against gee at 40260c4, with a fresh
timings.csv so no configuration carried over.

Fitting both directions roughly doubles R's binomial time (1.7x to 2.1x) but
costs spicyglm only 1.1x to 1.2x, because the k-nearest-neighbour index is
built once and shared across directions while only the fits are duplicated.
Binomial speed-ups therefore rose: 61x to 94x at 250k cells, 68x to 109x at
1M, and 279x to 485x on Schurch. Poisson is direction-invariant and its
timings are unchanged (0.96x to 1.17x, within run-to-run spread).

R at 4 cores now passes the 6 GB memory limit from 250k cells for binomial,
where the earlier run reached 250k, so the 4-worker comparison covers less
ground than before.

Figures regenerated from the new timings.csv.
 
    
  
    

      Package: spicyR

      Commit: 2338893432a334cdcf45f189edf91d74090f8742

      Author:  Sadiq Dohadwalla <sadiqdohad@gmail.com> 

      Date: 2026-09-23 14:35:41 +1000

      Commit message:


	  
		
 Damp the tight binomial refit and record the Schurch rerun

tests/r_reference/run_spicyglm.R replaces gee's binomial Firth fit with a
tighter-tolerance brglm2 refit (epsilon 1e-14, maxit 1000) for validation,
but it did not carry over gee's slowit = 0.1 (08d07d9). With brglm2's
undamped default step, 10 of the 809 fitted binomial pairs on Schurch 2020
diverged in the refit (coefficients near 1e15) although gee's own fit
converges. On two of them, gee's fit agrees with spicyglm to about 1e-5
and the damped tight refit to 1e-6. The refit now uses slowit = 0.1.
Regenerating the committed binomial fixtures with it reproduces them to
6e-12, so they are unchanged.

README: the Schurch comparison has been rerun against gee@40260c4. All
four runs match R to 1e-7, with no flipped references and no excluded
non-converged pairs:
- poisson with diagnostics: 419/419 fitted, 16/16 skipped, all five
  diagnostic tables match
- binomial, ordered pairs: 809/809 fitted, 32/32 skipped
- naive poisson: 429/429, 6/6
- naive binomial: 829/829, 12/12
n_jobs = 4 output is identical to n_jobs = 1 throughout. The two
b591b17 differences are kept as history under their fixing commits.
 
    
  
    

      Package: spicyR

      Commit: 25681def1438b7cb4d608629c4ca0376ce30e945

      Author:  Sadiq Dohadwalla <sadiqdohad@gmail.com> 

      Date: 2026-09-23 12:16:16 +1000

      Commit message:


	  
		
 Add a ref argument to choose the reference condition

Mirrors spicyR's spicyGLM(ref =) from gee@d9f8b6f. ref is the last
argument of spicy_glm() in both front ends (ref=None in Python, ref = NULL
in R), so existing calls are unaffected. When ref is given, it must be one of
the condition levels present (otherwise an error listing them, worded as in
gee) and is moved to the front of the level order. Without it, the
reference is the first level as before (category/factor order, otherwise
sorted). Every use of the condition order goes through that one level
vector (condition_ref/condition_comp, the image-to-group coding, skip
messages, diagnostics group labels), so no other code changes.

Swapping the reference is exact. Both families fit one coefficient per
condition independently, so coef_ref and coef_comp swap, the log effect
is negated, and the CR2 variance and Satterthwaite df of the contrast,
and so the p-value, are unchanged. The patient diagnostics (l_i,
influence_i, delta_i) are unchanged too: delta_i is the leave-one-out
shift in the patient's own group coefficient, not in the log ratio.

Verification:
- Against gee's spicyGLM(ref =) on tests/r_reference/cells.csv, for
  ref = "healthy" and "tumour": the same pairs and reference labels.
  Poisson log effects are identical and p-values within 2e-14. Binomial
  is within 3e-5, the same for both refs; that gap is gee's default
  brglm2 tolerance, which the fixtures tighten.
- R and Python agree with ref = "tumour" to 5e-16 (poisson and binomial).
- New tests (tests/test_ref.py, R testthat), for both families: ref set to
  the default level is a no-op; the other level swaps the coefficients,
  negates the effect and keeps p; ref overrides factor/category order; an
  invalid ref errors. Python only: diagnostics are unchanged under a swap.
- pytest 71 passed, R testthat 52 passed.

README: the "Differences from the R implementation" note that spicyglm
lacked ref= is removed, and the Use examples show ref.
 
    
  
    

      Package: spicyR

      Commit: e4cdd09b91a43a957e2f74fb39aedaa062256426

      Author:  Sadiq Dohadwalla <sadiqdohad@gmail.com> 

      Date: 2026-09-23 11:55:05 +1000

      Commit message:


	  
		
 Fit both directions for binomial cell-type pairs

The fixed-k binomial effect is directional: A->B models how many of each A
cell's k nearest neighbours are B, against the background B proportion,
and B->A is a different model. Nearest-neighbour membership is not
symmetric, so the directed edge totals differ, and the logit link keeps
the offset inside expit(beta + logit(p0)), so the score equations differ
for beta != 0 even when the totals agree. On simulated data the two
directions gave log odds ratios of -0.789 and -0.451. Poisson stays
direction-invariant: within-r counts and the offset total are symmetric,
and the log link reduces the estimate and CR2 to those totals (logRR, SE,
df and p identical, checked against clubSandwich).

Both front ends fitted one direction per unordered pair for both
families. For family = "binomial", _pairs() (Python) and
enumerate_pairs() (R) now return every ordered pair in from x to, where
an omitted side means all cell types: n^2 pairs including self-pairs.
Poisson and the single from/to case are unchanged. This matches spicyR's
spicyGLM() from gee@129b248. BH now adjusts over all n^2 binomial tests,
so p_adj changes even where the per-pair fit does not.

Fixtures: run_spicyglm.R enumerates ordered pairs for binomial, and the
three binomial cases (results_ and skipped_) were regenerated with
make_fixtures.R against gee@129b248: 16 fitted plus 9 skipped (every
pair with "Rare") out of 25. The 10 previously fitted directions are
unchanged (max |diff| 0 in the log odds ratio, 1e-16 in the p-value).
The Poisson and diagnostic fixtures were left untouched: regenerating
them against 129b248 reproduces the committed files to 1e-14 relative.

Verification:
- Before/after on the fixture cells, both front ends: Poisson output
  identical, binomial goes from 10 to 16 rows with the old rows
  unchanged exactly, and from = "Tcell", to = c("Tumour", "Bcell") now
  fits exactly those two pairs (previously all 6 unordered pairs).
- R and Python agree on all 16 binomial pairs to 6e-16.
- pytest: 64 passed (adds tests/test_pairs.py). R testthat: 38 passed
  (adds poisson invariance, ordered pairs, both directions matching
  single-pair fits, and from x to).

README: documents which pairs are fitted and why, notes that the 1.22M-cell
R/Python agreement check predates this change, and flags that the binomial
benchmark rows timed one direction in both implementations.
 
    
  
    

      Package: spicyR

      Commit: 45d035c514cd34ad14cca39e87945ff40ff19aa4

      Author:  Sadiq Dohadwalla <sadiqdohad@gmail.com> 

      Date: 2026-09-23 11:54:53 +1000

      Commit message:


	  
		
 README: mark the reference-condition and brglm2 differences as fixed in gee

The "Differences from the R implementation" section described spicyR's
gee branch at b591b17, which the Schurch comparison and benchmarks were run
against. Both R-side differences listed there have since been fixed:

- Reference condition: d9f8b6f factors the condition once on the full
  dataset, so every pair uses the first level (as spicyglm does). It also
  adds a ref= argument, which spicyglm does not have yet.
- Non-converged binomial fits: 08d07d9 damps brglm2's step (slowit = 0.1),
  so R reaches the same Jeffreys-penalised maximum that spicyglm finds by
  root-finding.

States which commit the comparison was run against and that it has not
been rerun since the fixes. The numbers themselves are unchanged.
 
    
  
    

      Package: spicyR

      Commit: 5d1098b0aa3d3923391c1b9047e5d51c82606515

      Author:  ecool50 <ewillie0004@gmail.com> 

      Date: 2026-09-23 09:55:10 +1000

      Commit message:


	  
		
 Port the diagnostics to the R front end

Completes parity with the Python front end. The bindings now marshal the
PairDiagnostics and CR2Result vectors the core already computes, and
R/diagnostics.R ports python/spicyglm/diagnostics.py: the per-pair summary,
the patient and image tables, the within-pair percentile ranks and the
cross-pair flagging with Wilson intervals.

Checked against the Python front end on 1.22M cells across 185 images, 55
pairs, comparing every column after aligning on keys:

  pair           55 rows x  8 cols   7.1e-15
  patient      8378 rows x 22 cols   3.7e-09  (5.0e-14 relative; S_g ~ 7e4)
  image        8378 rows x 19 cols   2.9e-11  (7.0e-13 relative)
  cross pair    185 rows x 15 cols   1.1e-16
  cross image   185 rows x 16 cols   4.4e-16

Rows of cross_pair whose Wilson lower bound is mathematically zero can come
out in a different order: the bound is a difference of two algebraically equal
terms, which R rounds to 0 and Python to 1.2e-17, and that noise reorders
ties. The values themselves agree to 5.6e-17.
 
    
  
    

      Package: spicyR

      Commit: 1735210083f7ddbd84517ccbf0ad3f6e20e712e1

      Author:  ecool50 <ewillie0004@gmail.com> 

      Date: 2026-09-23 09:38:59 +1000

      Commit message:


	  
		
 Add an R front end for the spicyGLM core, beside the Python one

rpkg/ is an R package that reaches the same C++17 core through Rcpp, so the
two front ends cannot drift apart numerically. The core is not duplicated:
rpkg/src/core_*.cpp are one-line stubs including cpp/src/*.cpp, and
rpkg/src/Makevars puts cpp/include on the include path, so both builds compile
the same four translation units.

- src/bindings.cpp mirrors the pybind11 bindings, holding the cell index in an
  external pointer across the per-pair calls.
- R/spicy_glm.R ports python/spicyglm/api.py: pair enumeration, the boundary
  and missing-condition skip rules, and the result table.

Poisson and Binomial, Firth and MLE, cr2_method "fast" and "naive". Checked
against the Python front end on 1.22M cells across 185 images: all 55 pairs at
10 cell types and all 231 at 21 agree to 6e-17 in the log effect and 7e-16 in
the p-value, for both families.

compute_diagnostics is not ported. The core computes the diagnostics but the R
side does not yet assemble them, so the argument is absent rather than
accepted and ignored.
 
    
  
    

      Package: spicyR

      Commit: c2d65d2701ee9454576252d2f827b381fd8c6afd

      Author:  ecool50 <ewillie0004@gmail.com> 

      Date: 2026-09-21 13:33:00 +1000

      Commit message:


	  
		
 Move spicy()'s spatial statistic, weights and models into C++

Ports the per-image inhomogeneous L statistic, the border edge correction,
the random-intercept mixed model and the monotone spline weight fit to an
R-free C++ core, keeping the R functions as a thin layer on top. On
diabetesData, spicy(condition = "stage", subject = "case") drops from about
120 s to 0.75 s on one core and 0.37 s across ten threads.

- src/inhomL.cpp: per-image L statistic over a search grid and distance
  bins, with edge-weighted sums.
- src/borderEdge.cpp: disc-window intersection areas matching spatstat's
  128-gon, via a one-edge cap shortcut or Green's theorem for convex
  windows and Sutherland-Hodgman otherwise.
- src/pairwise.cpp: getPairwiseCpp() handles every image in a single call
  over std::threads, used for square and convex windows without sigma;
  sigma and concave windows keep the per-image R path.
- src/lmerRI.cpp: REML random-intercept fit with an exact Hessian and
  Satterthwaite degrees of freedom, falling back to lmerTest for odd cases.
- src/scamMono.cpp: the calcWeights() monotone fit, following scam's own
  optimiser path because the inner problem has several local optima; falls
  back to scam if the C++ fit fails.
- src/spicyCore.h: the shared cores the threads use, which touch no R
  objects.

Drops the data.table dependency, which the old inhomL() needed.

Checked against devel: 97% of pair statistics agree to 1e-6 and all to
3e-3, weights to 3e-7 and p-values to 1e-4, with no change to any FDR call
and identical topPairs() ordering. The residual differences come from cells
lying exactly on a convex window's edge and from lme4 stopping its
optimiser early.
 
    
  
    

      Package: spicyR

      Commit: 5daf9ea75d19fb46dcec1ff24504e7ae853272fa

      Author:  ecool50 <ewillie0004@gmail.com> 

      Date: 2026-09-21 13:09:12 +1000

      Commit message:


	  
		
 Add the C++/Python port of spicyGLM under spicyglm/

A standalone reimplementation of spicyGLM's pairwise machinery: an Eigen
C++ core exposed to Python through pybind11, with the public API in
python/spicyglm/.

Covers Poisson and binomial families, Firth and MLE estimators, cr2_method
"fast" and "naive", and the diagnostics. Not ported: the clubSandwich
backend and the concave window.

Validated against the R implementation on the Schurch 2020 data, where
every pair agrees to 1e-7 apart from R's non-converged binomial fits, and
by the fixtures under tests/r_reference/ generated by make_fixtures.R.
 
    
  
    

      Package: spicyR

      Commit: 64675c3eadc689267f6116017396a02717386ff3

      Author:  Shreya Rajesh Rao <shreyar@maths.usyd.edu.au> 

      Date: 2026-02-25 09:13:11 +1100

      Commit message:


	  
		
 removed redundant warning #77
 
    
  
    

      Package: spicyR

      Commit: 844d597a30ceb370d96f05c73044312cd31051a2

      Author:  Farhan Ameen <fame2827@uni.sydney.edu.au> 

      Date: 2025-10-08 17:04:19 +1100

      Commit message:


	  
		
 uncommented the Kontextual survBubble code
 
    
  
    

      Package: spicyR

      Commit: 4c8c1dac6e0cc5ba6a335893307b8b4171c938b1

      Author:  Shreya Rao <shreya.rao@wimr.org.au> 

      Date: 2025-09-29 19:38:06 +1000

      Commit message:


	  
		
 Fix legend flip in half-circle glyph. Fixes #73
 
    
  
    

      Package: SynExtend

      Commit: 30a8d95e401f70909c4071bf1d11d95758779860

      Author:  npcooley <npcooley@gmail.com> 

      Date: 2026-10-02 17:45:01 -0400

      Commit message:


	  
		
 colocalization detection
 
    
  
    

      Package: MACSr

      Commit: 1b6c4f7cd943f81c07b84631ba77aa33e8920e74

      Author:  qhu <huqmail@gmail.com> 

      Date: 2026-10-02 15:55:16 -0400

      Commit message:


	  
		
 Use bundled data in vignette to fix build error, version bump 1.21.2

The vignette downloaded EH4558/EH4563 from ExperimentHub. On the
nebbiolo2 builder, callpeak failed with 'IndexError: list index out
of range', which macs3 raises when the input is not a BED file. The
same files ship in inst/extdata, so the vignette now reads them with
system.file().
 
    
  
    

      Package: MACSr

      Commit: 2c3176ffe8f013e04f7472fa345d4fe733ebae93

      Author:  qhu <huqmail@gmail.com> 

      Date: 2026-10-02 15:55:08 -0400

      Commit message:


	  
		
 Merge Bioconductor devel

# Conflicts:
#	DESCRIPTION
#	NEWS
 
    
  
    

      Package: MACSr

      Commit: 88dbe984ad2a72c24ea64b2383a194905a5fe204

      Author:  philippadoherty <philippa.doherty@roswellpark.org> 

      Date: 2024-09-20 15:33:17 -0400

      Commit message:


	  
		
 fix pileup warning, version bump 1.13.2
 
    
  
    

      Package: MACSr

      Commit: ac4682be83ca91c6c4582cdca95c00791118836f

      Author:  Tao Liu (τν) <vladimir.liu@gmail.com> 

      Date: 2024-09-19 13:34:29 -0400

      Commit message:


	  
		
 Merge pull request #20 from macs3-project/macs3/3.0.2

Macs3/3.0.2 - test without large files 
    
  
    

      Package: MACSr

      Commit: fdcdecb2a544edb44ee6bcd3a9bc95e82415609d

      Author:  philippadoherty <philippa.doherty@roswellpark.org> 

      Date: 2024-09-19 13:10:38 -0400

      Commit message:


	  
		
 rm large test files
 
    
  
    

      Package: MACSr

      Commit: d4de287c28dde5829530b83a34cd017fa8d43866

      Author:  philippadoherty <philippa.doherty@roswellpark.org> 

      Date: 2024-09-19 12:48:06 -0400

      Commit message:


	  
		
 test w/o callvar
 
    
  
    

      Package: MACSr

      Commit: d877f458c0e1767c2f27b944d804a768f6e230cc

      Author:  philippadoherty <philippa.doherty@roswellpark.org> 

      Date: 2024-09-19 12:33:22 -0400

      Commit message:


	  
		
 test without static files
 
    
  
    

      Package: MACSr

      Commit: 9b450ae61183d63058ebaff81ad97a9ca39dec3f

      Author:  Tao Liu (τν) <vladimir.liu@gmail.com> 

      Date: 2024-09-18 23:40:38 -0400

      Commit message:


	  
		
 Merge pull request #19 from macs3-project/macs3/3.0.2

Macs3/3.0.2 
    
  
    

      Package: MACSr

      Commit: 483032f0c9411a99f45bda245dccc65f8ff460d3

      Author:  philippadoherty <philippa.doherty@roswellpark.org> 

      Date: 2024-09-18 17:05:56 -0400

      Commit message:


	  
		
 add author, rebuild site
 
    
  
    

      Package: MACSr

      Commit: 92e793a6c634daa6a13cb84adc1169cf439f4a3e

      Author:  philippadoherty <philippa.doherty@roswellpark.org> 

      Date: 2024-09-16 11:07:35 -0400

      Commit message:


	  
		
 clean up docs
 
    
  
    

      Package: MACSr

      Commit: d098906eb59c22a2b7c92eed70459b1b8944e7e9

      Author:  philippadoherty <philippa.doherty@roswellpark.org> 

      Date: 2024-09-13 14:08:46 -0400

      Commit message:


	  
		
 update html files from pkgdown::buildsite()
 
    
  
    

      Package: MACSr

      Commit: 3dfb0144f5cabdab09458c06ac93c2880ec16e97

      Author:  philippadoherty <philippa.doherty@roswellpark.org> 

      Date: 2024-09-13 14:06:29 -0400

      Commit message:


	  
		
 update .Rd files from devtools:document()
 
    
  
    

      Package: MACSr

      Commit: 1196fab88f79f4a6ffed02ba9c0a6b2cfc1dcd38

      Author:  philippadoherty <philippa.doherty@roswellpark.org> 

      Date: 2024-09-13 13:59:30 -0400

      Commit message:


	  
		
 add testing data
 
    
  
    

      Package: MACSr

      Commit: f2130a926c32d1ea322448b2fece98232f2fff0b

      Author:  philippadoherty <philippa.doherty@roswellpark.org> 

      Date: 2024-09-13 13:51:44 -0400

      Commit message:


	  
		
 update all R commands, add tests for expect_no_error
 
    
  
    

      Package: MACSr

      Commit: 4d8951e978bdf1f626861ce7c7d4c2b618c0817d

      Author:  philippadoherty <philippa.doherty@roswellpark.org> 

      Date: 2024-09-11 16:10:07 -0400

      Commit message:


	  
		
 update hmmratac
 
    
  
    

      Package: MACSr

      Commit: 2839dfb37eb50f6a63a4e179fd84e3af74a11140

      Author:  philippadoherty <philippa.doherty@roswellpark.org> 

      Date: 2024-09-10 18:26:42 -0400

      Commit message:


	  
		
 test 3.0.2
 
    
  
    

      Package: MACSr

      Commit: 2c884dcaa9439148772e51e3760f70d9eaca8751

      Author:  philippadoherty <philippa.doherty@roswellpark.org> 

      Date: 2024-09-10 18:15:16 -0400

      Commit message:


	  
		
 revert r version
 
    
  
    

      Package: MACSr

      Commit: 4b5cbd08d65556cf0eb68336aea57ec9c8fd15f7

      Author:  philippadoherty <philippa.doherty@roswellpark.org> 

      Date: 2024-09-10 17:50:42 -0400

      Commit message:


	  
		
 test workflow
 
    
  
    

      Package: MACSr

      Commit: 0afbf53e9ba39a810d79950ee5caf8a5a4b515ec

      Author:  philippadoherty <philippa.doherty@roswellpark.org> 

      Date: 2024-09-10 16:54:57 -0400

      Commit message:


	  
		
 test with R >4.1, <4.4, py >=3.9
 
    
  
    

      Package: DEP

      Commit: c83f65987ca9787619c998ef654c07a110e2ec1a

      Author:  DijkJel <116422590+DijkJel@users.noreply.github.com> 

      Date: 2026-08-21 14:21:23 +0200

      Commit message:


	  
		
 fixed version
 
    
  
    

      Package: DEP

      Commit: 9b915ff6468fe45c8a65ef623ccd4e6f12a7bd62

      Author:  DijkJel <116422590+DijkJel@users.noreply.github.com> 

      Date: 2026-08-21 14:12:38 +0200

      Commit message:


	  
		
 typo fix
 
    
  
    

      Package: DEP

      Commit: 5a189d83c153a566d3d69506df1aaee003336176

      Author:  DijkJel <116422590+DijkJel@users.noreply.github.com> 

      Date: 2026-08-21 13:35:44 +0200

      Commit message:


	  
		
 add new maintainer
 
    
  
    

      Package: DEP

      Commit: 3540b40d02f069ec905a700125cc82f9bde350a3

      Author:  DijkJel <116422590+DijkJel@users.noreply.github.com> 

      Date: 2026-08-21 13:24:45 +0200

      Commit message:


	  
		
 updated version in description
 
    
  
    

      Package: DEP

      Commit: fc8fc58057c7683d4369d6b361c0f71f8e44aa7d

      Author:  DijkJel <116422590+DijkJel@users.noreply.github.com> 

      Date: 2026-08-21 13:07:53 +0200

      Commit message:


	  
		
 citation fixed
 
    
  
    

      Package: DEP

      Commit: 4d57cb3ecdb3b09b784c6996199f31c6795cc924

      Author:  DijkJel <116422590+DijkJel@users.noreply.github.com> 

      Date: 2026-08-21 11:38:12 +0200

      Commit message:


	  
		
 add project to .gitignore
 
    
  
    

      Package: DEP

      Commit: e1e9094e3e2c7197a217879a7927f04e6db450d1

      Author:  DijkJel <116422590+DijkJel@users.noreply.github.com> 

      Date: 2026-08-10 14:13:40 +0200

      Commit message:


	  
		
 no check, biocCheck errors
 
    
  
    

      Package: DEP

      Commit: e49d9d43b3ad33ad873276dab8a339bbfe58f172

      Author:  DijkJel <116422590+DijkJel@users.noreply.github.com> 

      Date: 2026-08-05 15:46:29 +0200

      Commit message:


	  
		
 update .Rbuildignore
 
    
  
    

      Package: DEP

      Commit: c698d50d13692e37d6e463cceb9a8dcb7a51ddcc

      Author:  DijkJel <116422590+DijkJel@users.noreply.github.com> 

      Date: 2026-08-05 15:20:45 +0200

      Commit message:


	  
		
 Merge branch 'RELEASE_3_9' of https://github.com/MVlab-hub/DEP into RELEASE_3_9
 
    
  
    

      Package: DEP

      Commit: 6dd3585681aab9b8caf5314ecb9e8e4100ea43f4

      Author:  DijkJel <116422590+DijkJel@users.noreply.github.com> 

      Date: 2026-08-05 15:20:10 +0200

      Commit message:


	  
		
 bug fixes after cloning
 
    
  
    

      Package: DEP

      Commit: b2bf3752444f9925b5e3b5b726ef7f35edc02dac

      Author:  MVlab-hub <protechrobioMV@gmail.com> 

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

      Commit message:


	  
		
 Add R-universe testing workflow 
    
  
    

      Package: DEP

      Commit: 7bd6eedcf7ab1c6607c4c1b117447b3bd0b8024d

      Author:  Arne Smits <arne.smits@embl.de> 

      Date: 2019-08-06 20:14:37 +0200

      Commit message:


	  
		
 bug fix: plot_heatmap with plot = FALSE.
 
    
  
    

      Package: seahtrue

      Commit: 981999f90a3392986be819bba847864d2f4dd3ee

      Author:  vcjdeboer <vcjdeboer@gmail.com> 

      Date: 2026-10-02 16:49:33 +0200

      Commit message:


	  
		
 fix: point BugReports to the GitHub issue tracker (1.7.2)

The previous URL (vcjdeboer.github.io/seahtrue/issues) returned 404, so the
Issue Tracking link on the Bioconductor landing page was broken.

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

      Package: scpdata

      Commit: c7b4837cc5b06be7dcf52ae3bfe224709ae091cd

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-10-02 15:34:18 +0200

      Commit message:


	  
		
 update maintainer
 
    
  
    

      Package: scpdata

      Commit: 27c038958c46437befdf983a3fd1d266e52648e1

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-09-06 10:59:50 +0200

      Commit message:


	  
		
 rebuild all mans
 
    
  
    

      Package: scpdata

      Commit: f070ff5fb5546421d2047cc1bba3099ff54fe0b9

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-09-05 15:37:57 +0200

      Commit message:


	  
		
 increase img size
 
    
  
    

      Package: scpdata

      Commit: a1770fc9d5ba761aaecb8993b5362de09882f44c

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-09-05 15:30:16 +0200

      Commit message:


	  
		
 add padding
 
    
  
    

      Package: scpdata

      Commit: 8e4a1dae78451805ced081f438efe0ff90ac7e7d

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-09-05 14:46:50 +0200

      Commit message:


	  
		
 fix sticker size
 
    
  
    

      Package: scpdata

      Commit: 106389be7fcd3dafb59ece970d4436a12f8d0963

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-09-05 13:58:56 +0200

      Commit message:


	  
		
 use small sticker
 
    
  
    

      Package: scpdata

      Commit: 9a55d867902e3c97d32285bba5e739f1bd1d91ef

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

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

      Commit message:


	  
		
 udapte contib
 
    
  
    

      Package: scpdata

      Commit: aea1b67d545eb6949b46928deba0953236ee7840

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-09-05 13:10:43 +0200

      Commit message:


	  
		
 get sticker to properly show up
 
    
  
    

      Package: scpdata

      Commit: 5feb125f7fa75cf94d248317d98d7df3e21feef7

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-09-05 11:31:49 +0200

      Commit message:


	  
		
 use local sticker on readme
 
    
  
    

      Package: scpdata

      Commit: 35e197fbae094254d9acea344b565e6291692e55

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-09-05 11:29:46 +0200

      Commit message:


	  
		
 update news
 
    
  
    

      Package: scpdata

      Commit: e048312e1e08c32378961dac54bccc4ae00f007b

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-09-05 11:29:03 +0200

      Commit message:


	  
		
 update contributions guidelines
 
    
  
    

      Package: scpdata

      Commit: a5367ee5ef05919fa1a280554a4ddd2747c8d4e9

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-09-05 10:47:20 +0200

      Commit message:


	  
		
 update vignette and pkgdown
 
    
  
    

      Package: MsBackendMetaboLights

      Commit: d23abb7e9fd02342edc6f0c09659065c4c90b0bf

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

      Date: 2026-10-01 16:01:40 +0200

      Commit message:


	  
		
 Merge pull request #30 from rformassspectrometry/phili

fix: keep metadata of previously cached files when syncing data files 
    
  
    

      Package: MsBackendMetaboLights

      Commit: 12558de6a233e15905fb74fd3c7869b827eed03a

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

      Date: 2026-10-01 15:06:09 +0200

      Commit message:


	  
		
 refactor: use rbindFill and parenthesis.
 
    
  
    

      Package: MsBackendMetaboLights

      Commit: 4d5d6f699d0a2b53e6f49f8734c339d12a45457e

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

      Date: 2026-10-01 14:24:23 +0200

      Commit message:


	  
		
 fix: syncing issues
 
    
  
    

      Package: MsBackendMetaboLights

      Commit: 6cfad4f2e531aea60a7dc98bf1b49ee936ad8810

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

      Date: 2026-10-01 14:00:42 +0200

      Commit message:


	  
		
 Merge pull request #28 from rformassspectrometry/phili

fix: Fix assay IDs when syncing assays individually 
    
  
    

      Package: MsBackendMetaboLights

      Commit: f2077b804483c28015d6bf81139a6922e63a363d

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

      Date: 2026-10-01 11:46:41 +0200

      Commit message:


	  
		
 Update check-bioc.yml
 
    
  
    

      Package: MsBackendMetaboLights

      Commit: 770d16c59429f047e22bbab8696bb1ff7095953b

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

      Date: 2026-10-01 11:32:07 +0200

      Commit message:


	  
		
 version bump and news updates
 
    
  
    

      Package: MsBackendMetaboLights

      Commit: 939f75412a07503de0a53840991ae5da33dab088

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

      Date: 2026-10-01 11:27:13 +0200

      Commit message:


	  
		
 fix: fix assay IDs when syncing assays individually
 
    
  
    

      Package: scp

      Commit: 13c7d0b0e09129e2eb3abc11b23b6464c937ab50

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-10-02 15:22:29 +0200

      Commit message:


	  
		
 update maintainer, fix vdiffr
 
    
  
    

      Package: scp

      Commit: aaf537784fc0ecd1f4febbde0e28b7ab064028bf

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

      Date: 2026-10-02 13:17:11 +0000

      Commit message:


	  
		
 Merge pull request #99 from leopoldguyot/fix_bioccheck

remove expect_warning for nipals failed convergence + regexp update 
    
  
    

      Package: scp

      Commit: 6b6a55adad244245e54c3d21919951a71ee76a93

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

      Date: 2026-09-16 14:32:05 +0200

      Commit message:


	  
		
 proper defunct + fix NOTE
 
    
  
    

      Package: scp

      Commit: 86e49bfa41d2edf94e36176d0018041925f9db33

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

      Date: 2026-09-16 13:07:41 +0200

      Commit message:


	  
		
 skip test that depends on QFeatures warning message
 
    
  
    

      Package: scp

      Commit: c58253f96282cd69b1701b9fdc15e9cd475ddbaf

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

      Date: 2026-09-16 11:41:51 +0200

      Commit message:


	  
		
 update snapshots based on gha artifact
 
    
  
    

      Package: scp

      Commit: 78e617b150745911fb2a32331cedcf6fe5d59395

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

      Date: 2026-09-16 11:14:27 +0200

      Commit message:


	  
		
 add ggrepel reproducible params
 
    
  
    

      Package: scp

      Commit: 43a6eda82de373873f34bb1e09611cad8bb220c4

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

      Date: 2026-09-16 10:23:15 +0200

      Commit message:


	  
		
 add diffr snapshots
 
    
  
    

      Package: scp

      Commit: a747a487f644d5fadd7887747d12c926b799e0dd

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

      Date: 2026-09-15 15:11:17 +0200

      Commit message:


	  
		
 remove expect_warning for nipals failed convergence + regexp update
 
    
  
    

      Package: gDRimport

      Commit: baef2cd4bd8a9504a7f5779373ee5ab417b1911e

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

      Date: 2026-10-02 14:52:28 +0200

      Commit message:


	  
		
 Merge pull request #126 from gdrplatform/GDR-3652

refactor: move CoreGx and PharmacoGx from Imports to Suggests 
    
  
    

      Package: gDRimport

      Commit: dff226b48562302d7fff528b54749db61f89665a

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

      Date: 2026-10-02 12:08:22 +0200

      Commit message:


	  
		
 chore: reword the NEWS entry to start with a known imperative verb
 
    
  
    

      Package: gDRimport

      Commit: c7120acba0f783daa9b1962dde954cd27aaa5d34

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

      Date: 2026-10-02 08:33:02 +0200

      Commit message:


	  
		
 refactor: move CoreGx and PharmacoGx from Imports to Suggests

Those two carry 37 further dependencies and are needed only by the
PharmacoSet conversion functions. Dropping them from the hard dependency
set takes the recursive closure of the gDR stack from 235 packages to 185
when WGCNA moves too, which matters in environments that build every
package from source.

Neither package was in NAMESPACE and both were called only through `::`,
so the change is guards rather than a refactor. The three exported entry
points now fail with a message naming the missing package; tests skip and
the two vignettes render without evaluating when the packages are absent.
 
    
  
    

      Package: gDRtestData

      Commit: 3bf1f759d2c229ce00f1240d59eaf32506dac6cf

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

      Date: 2026-10-02 14:07:58 +0200

      Commit message:


	  
		
 Merge pull request #83 from gdrplatform/GDR-3490

feat: add annotations for gCSI Sotorasib workshop dataset 
    
  
    

      Package: gDRtestData

      Commit: 34f38da3e4fac5804e632d3ab03262ebd90ae3f9

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

      Date: 2026-10-01 23:00:42 +0200

      Commit message:


	  
		
 Merge remote-tracking branch 'origin/main' into GDR-3490

# Conflicts:
#	DESCRIPTION
#	NEWS.md
 
    
  
    

      Package: gDRtestData

      Commit: 85c17751c6c83dad5c050d8db32f036aeb9508db

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

      Date: 2026-10-01 22:59:57 +0200

      Commit message:


	  
		
 fix: use the two parental cell lines and add sotorasib for the workshop dataset
 
    
  
    

      Package: gDRtestData

      Commit: 4fa91976511dba237119cb3e03d9cd384425b368

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

      Date: 2026-09-09 13:00:56 +0200

      Commit message:


	  
		
 fix: remove internal compound codes from drug annotations
 
    
  
    

      Package: gDRtestData

      Commit: 9d9688d4e5a7b068f72064c4dd605d4511d85353

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

      Date: 2026-09-09 00:34:33 +0200

      Commit message:


	  
		
 feat: add annotations for gCSI Sotorasib workshop dataset
 
    
  
    

      Package: MsDataHub

      Commit: 06190cef8cc3f46dc5facb6b93c5c2c25029ae55

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

      Date: 2026-10-02 11:44:54 +0000

      Commit message:


	  
		
 Merge pull request #24 from rformassspectrometry/jomain

feat: add faahKO test files 
    
  
    

      Package: MsDataHub

      Commit: 1fbab4ab8fa7c017f26ff4bc17053e764efcc8d1

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

      Date: 2026-10-02 10:22:07 +0200

      Commit message:


	  
		
 Fix documentation
 
    
  
    

      Package: MsDataHub

      Commit: 0ea49ec0a3d4f2e62d9ca9d55e094d2b40bc4c85

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

      Date: 2026-10-02 09:46:33 +0200

      Commit message:


	  
		
 Update vignette
 
    
  
    

      Package: MsDataHub

      Commit: d68be73f3329cc4ad3699180875cc125b3be5acd

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

      Date: 2026-10-02 09:39:43 +0200

      Commit message:


	  
		
 fic: faahKO function calls correct functions
 
    
  
    

      Package: MsDataHub

      Commit: f4c5843308c98e1f5ed0e380663b4005c71dfa99

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

      Date: 2026-10-02 08:22:41 +0200

      Commit message:


	  
		
 feat: add faahKO test files
 
    
  
    

      Package: mia

      Commit: b78e622540b093a74a13170dc108a5a3373b661f

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2026-10-02 18:05:30 +0800

      Commit message:


	  
		
 Initialise applyByModule (#825)

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

      Package: GSVA

      Commit: 1d70cc065a26f4aa5122372724b3267a9029487b

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

      Date: 2026-10-02 11:48:00 +0200

      Commit message:


	  
		
 Fixes in the GHA workflow. Among them, setting has_RUnit: false to spare one of the three times that unit tests are run in the workflow, reducing the time to execute it
 
    
  
    

      Package: TDbasedUFEadv

      Commit: fae3717912b0bd18b9d6a9cc0afe6bb8b4873de9

      Author:  Y-h. Taguchi <tag@granular.com> 

      Date: 2026-10-02 18:33:02 +0900

      Commit message:


	  
		
 Replace removed enrichDGN example with HDO enrichment
 
    
  
    

      Package: methylSig

      Commit: 0a9c0243b3eed40c4788ee3014cf4b2346c066a9

      Author:  Raymond Cavalcante <626455+rcavalcante@users.noreply.github.com> 

      Date: 2026-10-02 03:22:55 -0600

      Commit message:


	  
		
 Merge pull request #69 from sartorlab/news-1.26.0

Roll the 1.25.z NEWS sections into 1.26.0 
    
  
    

      Package: methylSig

      Commit: 492006ccf4b17ce880e7752e593be9c26bbb51c4

      Author:  Raymond Cavalcante <rcavalca@umich.edu> 

      Date: 2026-10-02 03:21:50 -0600

      Commit message:


	  
		
 Roll the 1.25.z NEWS sections into 1.26.0

Collect the 1.25.1 to 1.25.12 entries under one CHANGES IN VERSION 1.26.0
section, the version of the next Bioconductor release, with one sub-section
per category. Add 1.24.1 to 1.24.4 sections for the fixes backported to
RELEASE_3_23, and note them in the 1.26.0 entries.

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

      Package: annotatr

      Commit: 4567918a24fffbc2bbf78c0cb73fc82b444bca1c

      Author:  Raymond Cavalcante <626455+rcavalcante@users.noreply.github.com> 

      Date: 2026-10-02 03:19:56 -0600

      Commit message:


	  
		
 Merge pull request #88 from rcavalcante/news-backports

Add the 1.38.1 to 1.38.3 backports to NEWS 
    
  
    

      Package: annotatr

      Commit: 0c3e063a4ed6a5a3d961eaeeb828a3eadadac4ea

      Author:  Raymond Cavalcante <rcavalca@umich.edu> 

      Date: 2026-10-02 03:16:55 -0600

      Commit message:


	  
		
 Add the 1.38.1 to 1.38.3 backports to NEWS

Copy the three sections from RELEASE_3_23, and note in the matching
1.40.0 entries which release version each fix was backported to.

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

      Package: MetMashR

      Commit: 5deeed2ee416b3720c2438a3393aa6ab723fe829

      Author:  Gavin Rhys Lloyd <grlloyd@users.noreply.github.com> 

      Date: 2026-10-02 10:05:26 +0100

      Commit message:


	  
		
 update pkgdown

- tidying appearance
- clearer documentation
 
    
  
    

      Package: MetMashR

      Commit: a597b5bd11215566c3ffc607e39215eec6ac5db6

      Author:  Gavin Rhys Lloyd <grlloyd@users.noreply.github.com> 

      Date: 2026-10-01 17:24:11 +0100

      Commit message:


	  
		
 fix pkgdown issue

- use default figure path for mms vignette
- prevent covr
- minor text edits
 
    
  
    

      Package: MetMashR

      Commit: 1c8a7bd9e8d6ba7aea5afb5f6a7fc69d2dbe8e71

      Author:  Gavin Rhys Lloyd <grlloyd@users.noreply.github.com> 

      Date: 2026-10-01 16:44:54 +0100

      Commit message:


	  
		
 Chore/feedback (#1)

* add `pubchem_id_exchange` for batch identifier conversion
* add `classyfire_batch_lookup` for batch ClassyFire queries
* add `cts_lite_lookup` for Chemical Translation Service queries
* add `mwb_refmet_lookup` and `mwb_study_source` for Metabolomics Workbench
* add `lipidmaps_database` to import the full LIPID MAPS database
* add `columns` input to `chebi_lookup`
* add `cache_mode` input to `rest_api` lookups and `kegg_lookup`
* add `unique` input to `select_max` and `select_min`
* add case study vignette reimplementing the Metabolites Merging Strategy
* vectorise `mz_match` and `rt_match` interval-overlap matching
* `mspurity_source` is now an `lcms_table`
* fix `vertical_join` matching_columns rename direction
* fix silent type coercion in `database_lookup`
* fix crash when importing an empty `ls_source`
* fix outside-label positioning in bar and pie charts
* fix `BiocFileCache_database` when the cache has duplicate entries
* use environment variable for  GitHub API requests to avoid rate limits 
    
  
    

      Package: GSVA

      Commit: d1dfba27e3a4b0daa5812270bf03e71ff67aebff

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

      Date: 2026-10-02 11:09:01 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: GSVA

      Commit: be8052b360910b48447f4175e3c750925961bd6b

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

      Date: 2026-10-02 11:07:34 +0200

      Commit message:


	  
		
 Merge pull request #278 from rcastelo/277-serialize-gsva-output-using-parquet

Serialize GSVA output using Parquet files 
    
  
    

      Package: GSVA

      Commit: cf83a1baf133865cccc997e205d787b9445fd084

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

      Date: 2026-10-02 10:51:55 +0200

      Commit message:


	  
		
 Added gcs:// and file:// as valid schemes in the error message triggered when the scheme given in the URI to loadParquetGSVA() is not valid
 
    
  
    

      Package: GSVA

      Commit: e23dfa33337571f42ea3c5fac83ce4d229a24e71

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

      Date: 2026-10-02 10:37:20 +0200

      Commit message:


	  
		
 Added safeguard in saveParquetGSVA() when using argument replace=TRUE
 
    
  
    

      Package: GSVA

      Commit: 04969a952529d32a27f25bd2af39064e0a6dd772

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

      Date: 2026-10-01 19:22:06 +0200

      Commit message:


	  
		
 Reduce time in some of the unit tests
 
    
  
    

      Package: GSVA

      Commit: 0a93c6f5ef3b32e6366e5117dff692af68ac0845

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

      Date: 2026-10-01 19:01:04 +0200

      Commit message:


	  
		
 Capping colsPerRowGroup to avoid downstream problems
 
    
  
    

      Package: GSVA

      Commit: 76afbb1f41c109d6a5f4e7832a99255753b5e9a4

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

      Date: 2026-10-01 18:06:13 +0200

      Commit message:


	  
		
 Update .rowgridsize() works now like .colgridsize() to improve reading HDF5-based files
 
    
  
    

      Package: GSVA

      Commit: 80d75816977fa2155dc1cfa2071782d4dcdba9f4

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

      Date: 2026-10-01 17:29:20 +0200

      Commit message:


	  
		
 Updated manual page of saveParquetGSVA() and loadParquetGSVA() to clarify what dependencies should install the user
 
    
  
    

      Package: GSVA

      Commit: c288989ef51fe76abe97a6539d3f9637dc1e87de

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

      Date: 2026-10-01 17:16:58 +0200

      Commit message:


	  
		
 Check that colsPerRowGroup is finite when is not a character string, before being used after calling saveParquetGSVA()
 
    
  
    

      Package: GSVA

      Commit: 17cd110d119272591f61b5900cb2a0c570698058

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

      Date: 2026-10-01 16:56:25 +0200

      Commit message:


	  
		
 Check that main argument in loadParquetGSVA() is a single character string
 
    
  
    

      Package: GSVA

      Commit: 8d55b2534d744be55599fb025158b6773e29c047

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

      Date: 2026-10-01 15:16:40 +0200

      Commit message:


	  
		
 Added duckdb as a backend for lazily loading Parquet files with loadParquetGSVA(). This enables column range access of GSVA ranks stored in Parquet files in HTTPS URLs
 
    
  
    

      Package: GSVA

      Commit: 703bcf6ec271a07cef866bc13d079f7b72f12607

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

      Date: 2026-10-01 09:57:59 +0200

      Commit message:


	  
		
 Updated HPC and cloud storage vignette
 
    
  
    

      Package: GSVA

      Commit: 74a21366f171b69736bf6aefc1edbed1036574bf

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

      Date: 2026-09-30 21:28:09 +0200

      Commit message:


	  
		
 Expanded HPC vignette to illustrate the new functionality on accessing GSVA output stored as Parquet files in the cloud
 
    
  
    

      Package: GSVA

      Commit: 55a0a89d7c6672500dceef17f72a7412c887b0f3

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

      Date: 2026-09-30 20:35:17 +0200

      Commit message:


	  
		
 Merge branch 'devel' into 277-serialize-gsva-output-using-parquet
 
    
  
    

      Package: GSVA

      Commit: 21695638fcb7edf06ee4a27878464c4c792109a8

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

      Date: 2026-09-30 18:50:39 +0200

      Commit message:


	  
		
 Merge branch 'devel' into 277-serialize-gsva-output-using-parquet
Fix R and C code to catch invalid ranks
 
    
  
    

      Package: GSVA

      Commit: 973ef613b452015f71ed83587ad5245b5c4070f9

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

      Date: 2026-09-30 15:23:51 +0200

      Commit message:


	  
		
 Fix to catch a subsetted ranks input that may cause unexpected errors on gsvaColScores()
 
    
  
    

      Package: GSVA

      Commit: 42f9fdea38903af9b771f78d20974f306c0995c4

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

      Date: 2026-09-30 12:39:25 +0200

      Commit message:


	  
		
 loadParquetGSVA() handles gracefully timeouts or credential problems with gs:// or s3:// URIs
 
    
  
    

      Package: GSVA

      Commit: fb0c358e26c23761ab021d11eb96605f1e0c89f2

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

      Date: 2026-09-29 13:20:31 +0200

      Commit message:


	  
		
 Fixed unit test for map-reduced to avoid writing temporary files in the working directory where the test is run
 
    
  
    

      Package: GSVA

      Commit: 2620aebea1d30966fba295795db1c29f40c3d2ef

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

      Date: 2026-09-29 12:59:46 +0200

      Commit message:


	  
		
 Enable saving/loading GSVA scores stored outside an SE, using the save*GSVA/load*GSVA functions
 
    
  
    

      Package: GSVA

      Commit: 37fb8e4de1bca0448e638365d07147720d13d4ce

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

      Date: 2026-09-29 11:51:47 +0200

      Commit message:


	  
		
 Replaced the returnPath (TRUE/FALSE) parameter in gsvaMap() by another one called output=c("object", "HDF5" , "Parquet") that tells gsvaMap() to asks workers to either return an object (default) or paths to HDF5 or Parquet based serialized formats. Unit tests adapted. Since gsvaMap() was created in this development cycle, there is no need to deprecate the previous parameter returnPath
 
    
  
    

      Package: GSVA

      Commit: 9f206f2188d8060bcf7b6ad23c773fffed7829ff

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

      Date: 2026-09-29 10:52:31 +0200

      Commit message:


	  
		
 gsvaReduce() now accepts Parquet file paths. Fixed bug when file paths point to objects saved using HDF5. Added corresponding unit test
 
    
  
    

      Package: GSVA

      Commit: 018b8dfda9e63dbe55353204c6e282c520d88e3e

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

      Date: 2026-09-29 10:04:55 +0200

      Commit message:


	  
		
 gsvaColRanks() and gsvaColScores() now accept Parquet file paths. Added unit tests for loadParquetGSVA() and saveParquetGSVA(). Updated NAMESPACE and documentation
 
    
  
    

      Package: GSVA

      Commit: 5e27f953fadbbc13c9decf835c6621e14c827291

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

      Date: 2026-09-29 09:15:49 +0200

      Commit message:


	  
		
 Added loadParquetGSVA() and saveParquetGSVA() to load and save GSVA row-normalized values and GSVA column ranks into Parquet files. Updated also the function .colgridsize() to align column blocks with chunks to read and write faster HDF5 and Parquet files
 
    
  
    

      Package: GSVA

      Commit: 69fcfc1bb61d72d62c4e0627277bcd7f0414865d

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

      Date: 2026-09-28 15:01:17 +0200

      Commit message:


	  
		
 Added new GsvaParquetSeed class, which wraps Parquet file input into a DelayedMatrix and returns a SVT_SparseMatrix when reading from a Parquet file. Parquet format functionality depends on the arrow package, which is on suggests and only loaded when the user is using the functionality to load or write from/to Parquet files
 
    
  
    

      Package: annotatr

      Commit: 342d6cdd5c9ea6587fd11c09cd170bc83669d501

      Author:  Raymond Cavalcante <626455+rcavalcante@users.noreply.github.com> 

      Date: 2026-10-02 03:08:25 -0600

      Commit message:


	  
		
 Merge pull request #87 from rcavalcante/news-merge-sections

Combine duplicated subsections in the 1.40.0 NEWS 
    
  
    

      Package: annotatr

      Commit: 8776f4a8e2218b6c81a0e9fe2476d5d1108a4c55

      Author:  Raymond Cavalcante <rcavalca@umich.edu> 

      Date: 2026-10-02 03:06:51 -0600

      Commit message:


	  
		
 Combine duplicated subsections in the 1.40.0 NEWS

BUGFIXES and USER-FACING CHANGES each appeared twice. No item text changed.

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

      Package: miaViz

      Commit: 7a584efdf3bfc07fe6fed12fd9e9e1aa75cea4d1

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

      Date: 2026-10-02 08:56:50 +0300

      Commit message:


	  
		
 Revert https://github.com/microbiome/miaViz/pull/233 (#234) 
    
  
    

      Package: miaTime

      Commit: 22b06ec75c8cbbe0d1d7606e3703e814f063092c

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

      Date: 2026-10-02 08:34:54 +0300

      Commit message:


	  
		
 Add HMP_2019_ibdmdb data (#126) 
    
  
    

      Package: gemma.R

      Commit: 95558663d9ddd534bfd882124136ace4a4c14f8c

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2026-10-01 21:28:22 -0700

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: gemma.R

      Commit: e778f60d1dae6ee52b03908c4a7137865801b08c

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2026-10-01 21:26:32 -0700

      Commit message:


	  
		
 spec update
 
    
  
    

      Package: gemma.R

      Commit: 20698f7fefd561b10fbf4138138c8b7c68dfbba2

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2026-10-01 21:25:55 -0700

      Commit message:


	  
		
 code regen and a vignette fix
 
    
  
    

      Package: gemma.R

      Commit: b01569312ea5d8c4b4ca6d2014f3e8aadd416176

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2026-10-01 21:25:25 -0700

      Commit message:


	  
		
 registry fixes
 
    
  
    

      Package: gemma.R

      Commit: f56e770500dd0588bb93dc10ef263b7d7d7c8a22

      Author:  ogan Mancarci <ogan.mancarci@gmail.com> 

      Date: 2026-09-16 20:40:08 -0700

      Commit message:


	  
		
 tolerate 503 responses with retryAfters and continue retrying without the usual 3 times limit
 
    
  
    

      Package: gemma.R

      Commit: 859145eb062df32474e45c2711f8304405536c00

      Author:  Paul Pavlidis <paul@msl.ubc.ca> 

      Date: 2026-08-31 11:25:39 -0700

      Commit message:


	  
		
 read the renamed annotation fields Gemma 2.0 serves

Gemma 2.0 renamed four fields on the annotation value object
(Gemma b5c6747f68, live on gemma2.msl.ubc.ca):

    className -> category        termName -> value
    classUri  -> categoryUri     termUri  -> valueUri

There are no aliases: gemma.msl.ubc.ca (1.32.x) serves only the old
spelling, gemma2.msl.ubc.ca only the new one. Verified by fetching
/datasets/1/annotations from both.

The result reads BOTH. gemmaPath() still defaults to
https://gemma.msl.ubc.ca/rest/v2/ and tests/testthat.R pins
setGemmaPath('prod'), so a Gemma 2 server is reached only by setting
options(gemma.API=...); a hard switch would blank the columns against
the default target and take the suite with it. accessRenamedField()
picks the spelling the payload actually carries, per field, per
response, and can be deleted when gemma.R drops Gemma 1.x.

Released gemma.R is unaffected -- it targets Gemma 1.0, which still
serves the old names.

The package's own columns do not move: class.name, class.URI,
term.name and term.URI keep their names and only change which wire
field they read. Whether gemma.R adopts category/value is a separate
decision for a major version.

processAnnotations, behind get_dataset_annotations, is the only reader
affected. processSearchAnnotations (search_annotations,
get_annotation_children, get_annotation_parents) and
processCharacteristicValueObject (sample.characteristics) already read
category/value on both servers.

Also documented: on a FactorValue row the term field is now the term's
label instead of a composed sentence. GSE2018's disease factor value
reads "acute  disease related to solid organ transplantation" on Gemma
1.0 and "disease related to solid organ transplantation" on Gemma 2.0.
Across 13 datasets every row that differs is a FactorValue; the
ExperimentTag and BioMaterial rows are identical on both servers.
 
    
  
    

      Package: gemma.R

      Commit: 48ca1adcf24e6e048830908ae38cf825fb7631c9

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2026-08-13 18:15:59 -0700

      Commit message:


	  
		
 regen code
 
    
  
    

      Package: gemma.R

      Commit: fe39a18e7d5bd1e678365e2811b1bd232af18645

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2026-08-13 18:15:21 -0700

      Commit message:


	  
		
 fill in missing documentation elements
 
    
  
    

      Package: gemma.R

      Commit: f558c6bfb9f44a81d8559eef50fc6ca53a1e35cc

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2026-08-13 18:15:07 -0700

      Commit message:


	  
		
 annotation file processor
 
    
  
    

      Package: gemma.R

      Commit: 5bd6502d666b0fbc8917ef2304962c9307c88166

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2026-08-13 18:14:53 -0700

      Commit message:


	  
		
 fix link in docs
 
    
  
    

      Package: gemma.R

      Commit: 497bf2e91ba5840b13cf0ce6701290216b97a11c

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2026-08-13 18:14:35 -0700

      Commit message:


	  
		
 platform annotations enpdoint replaces the convenience function for the same purpose
 
    
  
    

      Package: gemma.R

      Commit: cb035b64c92bc8aaddb4a9bf75cc0a610c52ad1f

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2026-08-13 18:13:26 -0700

      Commit message:


	  
		
 spec update
 
    
  
    

      Package: gemma.R

      Commit: 3bb50f68cbff4cd2645ebc2c3b301c91c594c5b0

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2026-08-13 17:12:10 -0700

      Commit message:


	  
		
 codegen skips non-get endpoints
 
    
  
    

      Package: gemma.R

      Commit: cbc14b3ac871347d1f86ae472305f648c9785968

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2026-06-18 15:51:15 -0700

      Commit message:


	  
		
 merge

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

# Conflicts:
#	DESCRIPTION
#	R/convenience.R
#	R/processors.R
 
    
  
    

      Package: gemma.R

      Commit: 5949522260ae3fe5e53b8b8543ac8b0c54bf6d6b

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2026-06-18 15:44:49 -0700

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: gemma.R

      Commit: 8fcfd70ed49a285594cda2210bc84c0dfa754c49

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2026-06-18 15:44:38 -0700

      Commit message:


	  
		
 fix processing of sample names that contain others
 
    
  
    

      Package: gemma.R

      Commit: 1cc7515831b9a6d2fa6096e760687113a2c62285

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2026-05-14 16:00:42 -0700

      Commit message:


	  
		
 allow setting headers with gemma_call
 
    
  
    

      Package: gemma.R

      Commit: 7fef345fa0c40127156a87221810647e26f4d1a8

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2026-03-31 16:04:21 -0700

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: gemma.R

      Commit: 2aa454f5b0ce7ce1f48534bf8fa35bc28cb5a16b

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2026-03-31 16:03:56 -0700

      Commit message:


	  
		
 interaction baselines fix
 
    
  
    

      Package: gemma.R

      Commit: 9aa696c26dfe3e87c2e3023a6c296c80ae8c74fe

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2026-03-09 18:20:45 -0700

      Commit message:


	  
		
 require R 4.1.0
 
    
  
    

      Package: gemma.R

      Commit: 04ae78a716a31c54c39344e22f78767adcecee66

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2026-03-04 15:57:31 -0800

      Commit message:


	  
		
 add "local" to setGemmaPath
 
    
  
    

      Package: gemma.R

      Commit: 1984030766d8dff45af3192283abb5a19ae27480

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2026-01-29 13:22:37 -0800

      Commit message:


	  
		
 remove p vals from plot
 
    
  
    

      Package: gemma.R

      Commit: eed1644f440201a2abea73af7be7354649196fea

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2026-01-29 13:21:14 -0800

      Commit message:


	  
		
 better printability
 
    
  
    

      Package: gemma.R

      Commit: b359f0fc60d8dbe7470d3920c5647ca0e4653fff

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2026-01-29 13:07:03 -0800

      Commit message:


	  
		
 diff exp plotting
 
    
  
    

      Package: gemma.R

      Commit: 69794de464617407ab5314e98863a64e82931503

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2026-01-22 15:38:08 -0800

      Commit message:


	  
		
 expression processor fix for single cell
 
    
  
    

      Package: bambu

      Commit: 0b4151559ab50fadc74623e3a5f3a58d210d705f

      Author:  Chen Ying <chen_ying@a-star.edu.sg> 

      Date: 2026-10-02 11:47:38 +0800

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: bambu

      Commit: ca8a0fb17f0f4ca8c5d9b74deba949790129eae5

      Author:  Chen Ying <chen_ying@a-star.edu.sg> 

      Date: 2026-10-02 11:45:44 +0800

      Commit message:


	  
		
 fix conflict in description version change
 
    
  
    

      Package: bambu

      Commit: 80658dae549d4138e9b81f00694b27724f1ba897

      Author:  Chen Ying <chen_ying@a-star.edu.sg> 

      Date: 2026-10-02 11:42:00 +0800

      Commit message:


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

      Package: bambu

      Commit: c3ba5cf333282b4db909597e9d62bd45112029b0

      Author:  Chen Ying <chen_ying@a-star.edu.sg> 

      Date: 2026-10-02 11:39:38 +0800

      Commit message:


	  
		
 Merge pull request #593 from GoekeLab/devel_pre

update NEWS and release notes in README 
    
  
    

      Package: bambu

      Commit: 00e8ef2c6b5264922d3b9c606ceec33475b5e59c

      Author:  Chen Ying <chen_ying@a-star.edu.sg> 

      Date: 2026-10-02 11:31:49 +0800

      Commit message:


	  
		
 update NEWS and release notes in README
 
    
  
    

      Package: bambu

      Commit: aff3470038fc3cf975362797dda1a881533cc94d

      Author:  Chen Ying <chen_ying@a-star.edu.sg> 

      Date: 2026-10-02 11:21:34 +0800

      Commit message:


	  
		
 Merge pull request #592 from GoekeLab/devel_pre

fix bugs and update contact for devel branch 
    
  
    

      Package: bambu

      Commit: 98217bdc628b50ca6ed1a9d8314b1b8eb4b49371

      Author:  Chen Ying <chen_ying@a-star.edu.sg> 

      Date: 2026-10-02 09:12:45 +0800

      Commit message:


	  
		
 Merge pull request #538 from GoekeLab/update_contact

Bump version to 3.13.2 and update author emails 
    
  
    

      Package: bambu

      Commit: 9ea17856613825ba9007cf44394bf9e17afe2386

      Author:  Chen Ying <chen_ying@a-star.edu.sg> 

      Date: 2026-10-02 09:12:19 +0800

      Commit message:


	  
		
 Merge pull request #588 from GoekeLab/fix_offline_genome_check

Fix bambu requiring internet access when given a local FASTA genome path 
    
  
    

      Package: bambu

      Commit: 6aac1e998776c9a471b1560cb1482f084a85cd22

      Author:  Chen Ying <chen_ying@a-star.edu.sg> 

      Date: 2026-10-01 17:52:44 +0800

      Commit message:


	  
		
 Merge pull request #591 from GoekeLab/plotBambu_fix

temporarily disable plot annotations in vignettes and unit test function 
    
  
    

      Package: bambu

      Commit: 8c36345048c8a03352ca2c45644a005599275520

      Author:  Chen Ying <chen_ying@a-star.edu.sg> 

      Date: 2026-10-01 17:25:56 +0800

      Commit message:


	  
		
 Merge pull request #590 from GoekeLab/devel

update devel_pre with merge commits from devel  
    
  
    

      Package: bambu

      Commit: 216363b37e484fb59cf3fc971ffbe08a3d2edd39

      Author:  Chen Ying <chen_ying@a-star.edu.sg> 

      Date: 2026-10-01 16:25:17 +0800

      Commit message:


	  
		
 temporarily disable the plotBambu for plot annotations in vignettes and unit test functions
 
    
  
    

      Package: bambu

      Commit: 8dbc3193067efef64281e22dd6f629cdf4969cd2

      Author:  jonathangoeke <10560051+jonathangoeke@users.noreply.github.com> 

      Date: 2026-09-02 09:53:26 +0800

      Commit message:


	  
		
 Fix bambu requiring internet access when given a local FASTA genome path

checkInputSequence() unconditionally called BSgenome::available.genomes()
for any character genome argument, including local FASTA file paths -
the documented, common case. That call reaches out to Bioconductor's
package repository over the network, so bambu failed on offline
clusters/containers even when the user supplied a local file (issue #339).

Now the BSgenome lookup is only attempted when the string is not an
existing local file, and is wrapped in tryCatch so a blocked network
call falls through to the existing FASTA-read error path instead of
crashing with a raw Bioconductor/BiocManager error.

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

      Package: bambu

      Commit: 066b92ff222df50b9c74c9eb8ae306d2947ffc8c

      Author:  Ling Min Hao <53725270+lingminhao@users.noreply.github.com> 

      Date: 2026-04-20 16:34:39 +0800

      Commit message:


	  
		
 Merge pull request #575 from GoekeLab/devel_pre

Update bambu pr template 
    
  
    

      Package: bambu

      Commit: a445dcfb60b6778378fe3e831fec255c4ca6b047

      Author:  Ling Min Hao <53725270+lingminhao@users.noreply.github.com> 

      Date: 2026-04-20 16:09:21 +0800

      Commit message:


	  
		
 Merge pull request #574 from GoekeLab/update_bambu_pr_template

Update bambu pr template 
    
  
    

      Package: bambu

      Commit: 48017de0739a39c2dc170c97a0ee029769a713d4

      Author:  lingminhao <lingminhao31@gmail.com> 

      Date: 2026-04-20 15:17:28 +0800

      Commit message:


	  
		
 update bambu pr template
 
    
  
    

      Package: bambu

      Commit: 129559a8de5d002fc313203d1b790d8f1a9464a0

      Author:  lingminhao <lingminhao31@gmail.com> 

      Date: 2026-04-20 14:39:16 +0800

      Commit message:


	  
		
 update bambu pr template
 
    
  
    

      Package: bambu

      Commit: 5967af91300ad4869667e9b29680389c6dca9ac6

      Author:  lingminhao <lingminhao31@gmail.com> 

      Date: 2026-04-20 14:33:27 +0800

      Commit message:


	  
		
 update bambu pr template
 
    
  
    

      Package: bambu

      Commit: b5811e35cffa74f49bf4f151104e2fe66e027566

      Author:  Ling Min Hao <53725270+lingminhao@users.noreply.github.com> 

      Date: 2026-04-15 13:43:14 +0800

      Commit message:


	  
		
 Merge pull request #557 from GoekeLab/devel_pre

add github issue and pull request template to the main repository 
    
  
    

      Package: bambu

      Commit: 554e2f4aa5cc4435087499b3aa1dd454adf32a6b

      Author:  Ling Min Hao <53725270+lingminhao@users.noreply.github.com> 

      Date: 2026-04-15 12:28:48 +0800

      Commit message:


	  
		
 Merge pull request #556 from GoekeLab/github_issuepr_template

add github issue and pull request template to the main repository 
    
  
    

      Package: bambu

      Commit: f3b48bd94ec22d4dd2077072734049e9bf32b9ec

      Author:  lingminhao <lingminhao31@gmail.com> 

      Date: 2026-04-15 12:22:26 +0800

      Commit message:


	  
		
 add github issue and pull request template
 
    
  
    

      Package: bambu

      Commit: caff79a4c9ea935ac0a8f64b026a430e37527e1a

      Author:  Chen Ying <chen_ying@gis.a-star.edu.sg> 

      Date: 2026-02-02 13:17:07 +0800

      Commit message:


	  
		
 Fix email address for Jonathan Goeke

Updated email address for Jonathan Goeke in DESCRIPTION file. 
    
  
    

      Package: bambu

      Commit: f352115dc28250ec55a433f81b3195e8df5a65f2

      Author:  Chen Ying <chen_ying@gis.a-star.edu.sg> 

      Date: 2026-02-02 10:43:32 +0800

      Commit message:


	  
		
 Bump version to 3.13.2 and update author emails

Updated version number and author emails in DESCRIPTION file. 
    
  
    

      Package: bambu

      Commit: 4bcd807b4f51ddceb5c13ea4fcce783fec4bbe4d

      Author:  Chen Ying <chen_ying@gis.a-star.edu.sg> 

      Date: 2026-02-02 10:38:49 +0800

      Commit message:


	  
		
 Merge pull request #537 from GoekeLab/devel

update devel_pre to be updated with devel branch  
    
  
    

      Package: DESeq2

      Commit: 76c5f8523716804dbe0a9500b4b7e216c6af225c

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

      Date: 2026-10-01 19:32:34 -0400

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: DESeq2

      Commit: 66bb31ad3a9f745ce2d2b770038e90a67aa8ee54

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

      Date: 2026-10-01 19:32:20 -0400

      Commit message:


	  
		
 note about fitting
 
    
  
    

      Package: DESeq2

      Commit: c62c60c6ff83fd84ce115cacd1c49827533f85a7

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

      Date: 2026-09-28 13:26:19 -0400

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: MSstatsBioNet

      Commit: a49c8a81d06bda7d70ab6ebd38681b40c26027ab

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2026-10-01 18:18:46 -0400

      Commit message:


	  
		
 refactor(getSubnetworkFromIndra): Remove paper count filter and deprecate correlation filter (#112) 
    
  
    

      Package: scanMiRApp

      Commit: e004e90698e124c2c89e9edcca7bcf66a57e4065

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

      Date: 2026-10-01 20:45:29 +0200

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: MSnbase

      Commit: ce3766d772e335dcf3e5e452af3fc8e87f6cf049

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-10-01 16:31:20 +0200

      Commit message:


	  
		
 fix fun call with |> and keep msdata suggestion until MM14 is in MsDataHub
 
    
  
    

      Package: MSnbase

      Commit: c6bdb5db2a65119e614afbf141f1ae9022d2af27

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-10-01 15:53:33 +0200

      Commit message:


	  
		
 fix error, use MsDataHub
 
    
  
    

      Package: scanMiR

      Commit: daf45602d30dda8e4b664277d6636036250fc7ae

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

      Date: 2026-10-01 14:48:43 +0200

      Commit message:


	  
		
 Merge branch 'devel' of github.com:ETHZ-INS/scanMiR into devel
 
    
  
    

      Package: scanMiR

      Commit: 942ffe3e7d3314cec334ef86562b1f4d9cb3655c

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

      Date: 2026-09-30 20:54:33 +0200

      Commit message:


	  
		
 added missing deps
 
    
  
    

      Package: scanMiR

      Commit: f96738726d4a56878a0ab0768461a2755384498f

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

      Date: 2026-09-30 20:53:56 +0200

      Commit message:


	  
		
 Update BiocCheck installation to include BiocStyle 
    
  
    

      Package: scanMiR

      Commit: 032b0012e3ea64a5d4d29ea148f248c769f28fc4

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

      Date: 2026-09-30 20:49:39 +0200

      Commit message:


	  
		
 Add 'pwalign' to BiocCheck installation 
    
  
    

      Package: scanMiR

      Commit: effb99bb455303266a40203d594cfb8905f86a0e

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

      Date: 2026-09-30 20:46:30 +0200

      Commit message:


	  
		
 Merge branch 'devel' of github.com:ETHZ-INS/scanMiR into devel
 
    
  
    

      Package: scanMiR

      Commit: 2f4dcaec97bfb6f655fc3d1442316541e564f9c1

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

      Date: 2026-09-30 16:23:54 +0200

      Commit message:


	  
		
 Change default branch from master to devel 
    
  
    

      Package: MetaboDynamics

      Commit: 590996ed4acf9dfadd0e463ffeb48c42b2a6ca81

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

      Date: 2026-10-01 14:38:47 +0200

      Commit message:


	  
		
 revision of vignettes
 
    
  
    

      Package: RBedMethyl

      Commit: 493883f6cf20b9520bbe00842b5e5628e9aaa71d

      Author:  vaslem <vaslemonidis@hotmail.com> 

      Date: 2026-10-01 14:11:33 +0200

      Commit message:


	  
		
 bump version to 1.1.2 in DESCRIPTION file
 
    
  
    

      Package: RBedMethyl

      Commit: b14c96afc88d921927341b80ad85cf42f8159c03

      Author:  vaslem <vaslemonidis@hotmail.com> 

      Date: 2026-10-01 14:10:10 +0200

      Commit message:


	  
		
 bump version to 1.2.1 in DESCRIPTION file
 
    
  
    

      Package: RBedMethyl

      Commit: b7d5bad3dd2e7a5c7b7c4c40c7173dbc9b4cdbd6

      Author:  vaslem <vaslemonidis@hotmail.com> 

      Date: 2026-10-01 14:09:19 +0200

      Commit message:


	  
		
 bump version to 1.2.0 in DESCRIPTION file
 
    
  
    

      Package: RBedMethyl

      Commit: 18e2562e34ece7b1f5b8a68375e5c52560db3591

      Author:  vaslem <vaslemonidis@hotmail.com> 

      Date: 2026-10-01 14:06:34 +0200

      Commit message:


	  
		
 Replace DelayedArray with S4Arrays for assay binding in RBedMethyl methods
 
    
  
    

      Package: BiocWorkflowTools

      Commit: 5b9184b916f6450422b3fecbb3da2190f298186c

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-01 12:36:49 +0200

      Commit message:


	  
		
 Add link to deNBI survey
 
    
  
    

      Package: Rarr

      Commit: 89017d7891c470be860c26c6f71c1af4c7d65240

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-30 18:43:27 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: Rarr

      Commit: 0178013f4a3ee44b865deb65aa0194d565c28e98

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-30 11:31:46 +0200

      Commit message:


	  
		
 Place chunks in output as they are read

To avoid keeping all chunks in memory and reduce peak memory usage
 
    
  
    

      Package: Rarr

      Commit: 9e77c190fa07aeb7c886056e4099588a92f8f58f

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-28 17:23:02 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: Rarr

      Commit: eea3f4752064e0126d39d72524734dd969314889

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-28 17:22:46 +0200

      Commit message:


	  
		
 Run devtools::document()
 
    
  
    

      Package: Rarr

      Commit: 29c7bb52fc5ce7ba816d4a3a0c885dce3545ae2c

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-28 10:10:39 +0200

      Commit message:


	  
		
 Merge consecutive mapply and improve comment
 
    
  
    

      Package: Rarr

      Commit: 0d5c3c11a4f5ebc892fe24ce03a159ae8f2de2a1

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-26 20:01:42 +0200

      Commit message:


	  
		
 Use mapply() rather than Map()
 
    
  
    

      Package: Rarr

      Commit: 51114ddaa0ec0c202970ce8870f41ae7a8e57cf6

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-26 18:20:01 +0200

      Commit message:


	  
		
 Improve transposing step
 
    
  
    

      Package: Rarr

      Commit: 387d4c2a7a4534a2cb23203b7846d6ecceaad961

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-26 18:04:24 +0200

      Commit message:


	  
		
 Use better var names
 
    
  
    

      Package: Rarr

      Commit: 770399ba38d69c28cfa7a286232821978d50d84d

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-26 17:19:28 +0200

      Commit message:


	  
		
 Put if/else inside Map loop

So the shortcut can be applied even if a single dimension of the index is compact
 
    
  
    

      Package: Rarr

      Commit: a99da22d0e4ff6853d1351b896270e652fd80758

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-26 16:32:57 +0200

      Commit message:


	  
		
 Avoid unlist()/relist()
 
    
  
    

      Package: NanoporeRNASeq

      Commit: 5994e53262d5c5c0f57dff77778a2e29233d1b91

      Author:  Chen Ying <chen_ying@a-star.edu.sg> 

      Date: 2026-10-01 17:48:47 +0800

      Commit message:


	  
		
 version bump and bug fix
 
    
  
    

      Package: NanoporeRNASeq

      Commit: 52bca07dc04109af6ca407e8622578c7cd873ade

      Author:  Chen Ying <chen_ying@a-star.edu.sg> 

      Date: 2026-10-01 17:44:26 +0800

      Commit message:


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

      Package: NanoporeRNASeq

      Commit: 1129a096bcbcc3e9fc4d3d3b7bf2a2932d58539f

      Author:  Chen Ying <chen_ying@a-star.edu.sg> 

      Date: 2026-10-01 17:23:00 +0800

      Commit message:


	  
		
 Merge pull request #14 from GoekeLab/plotBambu_fix

temporary fix for plotBambu annotation function 
    
  
    

      Package: NanoporeRNASeq

      Commit: 5999126e7063e006f8e0dbb031e9453458458577

      Author:  Chen Ying <chen_ying@a-star.edu.sg> 

      Date: 2026-10-01 16:59:25 +0800

      Commit message:


	  
		
 temporary fix for plotBambu annotation function
 
    
  
    

      Package: miaViz

      Commit: adeebeb33e090bf72d0e8983f8855b4e67d73595

      Author:  YihanLiu4023 <149611140+YihanLiu4023@users.noreply.github.com> 

      Date: 2026-10-01 03:15:43 -0400

      Commit message:


	  
		
 Add multimedia example datasets (se_relative, tse_relative) (#233)

Co-authored-by: YihanLiu4023 <yihan.liu@yale.edu>
Co-authored-by: Leo Lahti <leo.lahti@iki.fi>
Co-authored-by: Tuomas Borman <tvborm@utu.fi> 
    
  
    

      Package: miaViz

      Commit: 89aaf4ed9e83ae2c1bde87880a4f209fc6e25307

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

      Date: 2026-09-21 09:53:25 +0300

      Commit message:


	  
		
 Fix fill parameter handling in plotHistogram (#214)

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

      Package: HiCcompare

      Commit: bec288aceb1a0d00093237e3b545a56713047b87

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

      Date: 2026-09-30 20:34:43 -0400

      Commit message:


	  
		
 Restore GInteractions conversion on Bioconductor 3.24

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

      Package: TDbasedUFE

      Commit: 9b5d24019859461ed24f78626179bed36e739058

      Author:  Y-h. Taguchi <tag@granular.com> 

      Date: 2026-10-01 09:19:49 +0900

      Commit message:


	  
		
 Bundle six-sample QuickStart data and remove tximportData dependency
 
    
  
    

      Package: BiocDuckDB

      Commit: 444d953f66149dedd3802a97a635727f67eedb24

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

      Date: 2026-09-30 15:22:23 -0700

      Commit message:


	  
		
 docs: Document sizing writeCoordArray's grid for large or sparse writes

writeParquet()'s array delegation to writeCoordArray() inherits its default
grid, which budgets partitions from dim(x) alone with no sparsity awareness.
Cross-reference DuckDBArray::writeCoordArray's new density-correction section
(setAutoBlockSize()/setAutoBlockShape()) and its hard ceiling. Add a third
@examples entry and a matching vignette snippet showing those calls made
before writeParquet() on a sparse matrix.
 
    
  
    

      Package: DuckDBArray

      Commit: 8c837cdc4217c70437ec1cd9bf3faf4b351ebd37

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

      Date: 2026-09-30 15:02:38 -0700

      Commit message:


	  
		
 docs: Document partition sizing for large or sparse writeCoordArray writes

The grid = NULL default (defaultAutoGrid(COO_SparseArray(dim(x)))) budgets
partitions from dim(x) alone, with no sparsity awareness, and setAutoBlockShape()
only redistributes that budget across axes rather than correcting it. Document
the density correction via setAutoBlockSize()/setAutoBlockShape("scale"), and
the hard ceiling on block.length (.Machine$integer.max) beyond which no such
tuning can reach a given partition-count target. createDimTables() cross-
references the same section instead of duplicating it. Adds a matching
vignette section with a worked example.
 
    
  
    

      Package: BiocDuckDB

      Commit: 6bdc1c69c5477a7ffe10520e6aacfe5935ec653e

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

      Date: 2026-09-30 14:13:12 -0700

      Commit message:


	  
		
 fix: SingleCellExperiment with no rowRanges silently discarded rowData (0.99.25)

writeParquet,SummarizedExperiment-method chose rowRanges(x) vs rowData(x)
for the features resource using is(x, "RangedSummarizedExperiment")
alone. Every SingleCellExperiment extends RangedSummarizedExperiment by
class definition regardless of whether real ranges were ever provided,
so this was TRUE even for the ordinary case of an SCE built from rowData
only -- rowRanges(x) for such an object is a GRangesList whose every
element has zero rows, so the real rowData was silently discarded in
favor of an empty, meaningless genomic_ranges_list resource. Found via a
downstream project's real single-cell release build, which worked around
it by never constructing an actual SingleCellExperiment object at all.

Fixed to check for a non-empty rowRanges(x) before taking that branch;
the same check now also drives the "ranged_summarized_experiment" vs.
"summarized_experiment" model default, which had the identical bug.
Added a regression test (SingleCellExperiment built from rowData alone)
that fails against the old dispatch check and passes against the fix.
 
    
  
    

      Package: BiocDuckDB

      Commit: d2caca9f24af0edaf5bb831d0938b42cfdd50da0

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

      Date: 2026-09-30 13:46:35 -0700

      Commit message:


	  
		
 docs: Document Assays transpose/naming, link writeStreamingResource (0.99.25)

writeParquet()'s Assays-class method transposes each assay matrix and
reverses indexcols/indexrefs/grid before writing (so a hive-partitioned
assay lands sample-major, __sample__group__=.../__feature__group__=...),
and prefixes each assay's on-disk directory with assay_ while keeping the
Frictionless resource name as the bare assay name -- neither was
documented anywhere outside an inline code comment. Found while a
downstream project ported the write path to a new, non-array streaming
source and had to reverse-engineer both from source to get partition
nesting right. Added a "Assays objects:" paragraph to writeParquet()'s
@details covering both, plus the existing (but previously unwritten)
append=TRUE recipe for streaming a hive-partitioned coordinate array from
a source with no natural in-memory array representation, its one real
restriction (append=TRUE requires length(grid) > 1L for the slab's own
grid), and a note that BiocDuckDB's own writers always pass
existing_data_behavior="error" to arrow::write_dataset, never the
data-losing "delete_matching".

writeStreamingResource() -- an existing, exported, already
thoroughly-documented function for streaming a flat resource from a
callback -- was referenced from nowhere: not writeParquet()'s or
writeDatapackage()'s @seealso, not the vignette. Added the
cross-references and a new "Streaming a flat resource from a cursor"
vignette subsection using it in place of the previous from-memory-only
example.

readParquet()'s "Supported Object Types" section now notes, per model,
which resources carry a __feature__group__/__sample__group__ dimtbl
column (features/samples do; sample_embeddings/feature_embeddings never
do) and the assay's partition nesting order. writeDatapackage()'s @param
model pointed at "the storage-layout vignette" for this table, but the
vignette's storage-layout section never contained one; retargeted that
pointer at this section instead, since it already had the right shape.
 
    
  
    

      Package: GSVA

      Commit: 0dd91717a172251047dba56f0f9d3f2deb4ee90f

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

      Date: 2026-09-30 20:34:03 +0200

      Commit message:


	  
		
 Further fixes in C code to properly handle unexpected NA values
 
    
  
    

      Package: GSVA

      Commit: 0550679acc183126df57cdd4ec3ddcd87feaf7ce

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

      Date: 2026-09-30 18:50:01 +0200

      Commit message:


	  
		
 Check on the C code that ranks are valid
 
    
  
    

      Package: GSVA

      Commit: 6b05e845195835ed91ff4be240ddb9efd07b6d6a

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

      Date: 2026-09-30 15:04:21 +0200

      Commit message:


	  
		
 Fix to catch a subsetted ranks input that may cause unexpected errors on gsvaColScores()
 
    
  
    

      Package: BiocCheck

      Commit: 28c6e9438e005dd6af104f1e89703ac5f3e2ef0f

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

      Date: 2026-09-30 15:18:46 -0400

      Commit message:


	  
		
 Closes #259

 - Tarballs now have appropriate package size and individual file size check
 - Improves message when package size is skipped on open directory indicating limit
 
    
  
    

      Package: scanMiR

      Commit: a9337796f89872a6abbcf0a8714ed04b2d3f0144

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

      Date: 2026-09-30 20:45:32 +0200

      Commit message:


	  
		
 updated docker image
 
    
  
    

      Package: fishpond

      Commit: c706e65af8689c07b25659e6f949c676671305fe

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

      Date: 2026-09-30 14:01:05 -0400

      Commit message:


	  
		
 update re alevin EC
 
    
  
    

      Package: tximeta

      Commit: 9425e9d5b940d5ad6edd2d0023dc2f594b8f095a

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

      Date: 2026-09-28 13:21:05 -0400

      Commit message:


	  
		
 Update for reduced tximportData (1.41.1); fix updateMetadata bugs

tximportData 1.41.1 removed the GENCODE v48 GTF, salmon_gibbs,
kallisto_boot, and 4 of 6 GEUVADIS samples.

- test_mixed_reference.R and vignette: build a dummy GRanges from the
  |-delimited GENCODE transcript names in the oarfish quant files and
  register it with makeLinkedTxpData() instead of makeLinkedTxome(gtf=)
- test_tximeta.R: 2 samples, drop salmon_gibbs/kallisto_boot usage,
  use macrophage for inferential replicate checks
- updateMetadata() now respects its `prefer` argument
- mergeTxpDataIntoRowData() fills new atomic columns with NA rather
  than the string "NA"
- Suggests: tximportData (>= 1.41.1); version 1.31.9

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01YSdKbzoGfPru1WQba1HcXY
 
    
  
    

      Package: geneLenDataBase

      Commit: 93b3ad332c91a1a69ef776265ab819c5adfb1572

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2026-09-30 16:38:02 +0200

      Commit message:


	  
		
 updated news accordingly
 
    
  
    

      Package: geneLenDataBase

      Commit: ff36ebb8cf575a460d1055c44bb4eb59f4d544e3

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2026-09-30 16:37:44 +0200

      Commit message:


	  
		
 correct version bump, 1.49.1

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

# Conflicts:
#	DESCRIPTION
 
    
  
    

      Package: geneLenDataBase

      Commit: ffead84896322cdd76fb4fc8b1b98fe49e10b1f4

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2026-09-30 16:35:31 +0200

      Commit message:


	  
		
 updated date in DESCRIPTION
 
    
  
    

      Package: geneLenDataBase

      Commit: 23c4c8c06e9330bb1a24d7729f5032a5e72fcf5b

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2026-09-30 16:33:44 +0200

      Commit message:


	  
		
 Merge pull request #3 from federicomarini/smaller_data

Smaller data 
    
  
    

      Package: geneLenDataBase

      Commit: dac5c046b402f2b8e59100df3bb0c9b759b8f258

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2026-09-28 17:30:22 +0200

      Commit message:


	  
		
 updated .Rbuildignore
 
    
  
    

      Package: geneLenDataBase

      Commit: fd99ea223475e288a33234621e52e47f20db562e

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2026-09-25 21:05:09 +0200

      Commit message:


	  
		
 updated news for upcoming versions
 
    
  
    

      Package: geneLenDataBase

      Commit: 02f527e80083cfe537f628368589b42f724e815a

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2026-09-25 21:04:58 +0200

      Commit message:


	  
		
 updated dependency on R version to enable serialized objects
 
    
  
    

      Package: geneLenDataBase

      Commit: 1a1f9bf5935063b35bc7f228b25a0a17685109f9

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2026-09-25 21:01:26 +0200

      Commit message:


	  
		
 version bump, 1.45.1
 
    
  
    

      Package: geneLenDataBase

      Commit: 0bfa4774ba0b18c3e99034de338502b5ca7a38d2

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2026-09-25 21:01:13 +0200

      Commit message:


	  
		
 replacing the older RData objects with the smaller (10-15% extra compression achieved) ones
 
    
  
    

      Package: geneLenDataBase

      Commit: c01ab00c6e49e48cc60712cfdc21b47e3bc2cb10

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2026-09-25 20:59:47 +0200

      Commit message:


	  
		
 namespace re-rendered
 
    
  
    

      Package: geneLenDataBase

      Commit: ff79451db8328ff43e579404552b96c57e832305

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2026-09-25 20:59:32 +0200

      Commit message:


	  
		
 updated roxygen version
 
    
  
    

      Package: geneLenDataBase

      Commit: 17ec2f0ddc13697657e874971234d9d453e12914

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2026-09-25 20:59:19 +0200

      Commit message:


	  
		
 resolved indentation for no note to show in roxygen
 
    
  
    

      Package: geneLenDataBase

      Commit: c24523949df72572ff0e561196a35b6dfff51506

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2025-05-02 10:03:31 +0200

      Commit message:


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

      Package: geneLenDataBase

      Commit: ce234e253573b295a4af9ac1f0f41ced02d03dae

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2025-03-07 14:35:57 +0100

      Commit message:


	  
		
 updating GHA to a more recent cache version
 
    
  
    

      Package: geneLenDataBase

      Commit: ebf65d5e43b31b13d17c975424efdf3047424024

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2025-02-07 10:19:37 +0100

      Commit message:


	  
		
 updated roxygen version
 
    
  
    

      Package: geneLenDataBase

      Commit: 394ba62cd5b8f93562743957ad848996541b722c

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2025-02-07 10:19:03 +0100

      Commit message:


	  
		
 updating GHAs
 
    
  
    

      Package: scanMiR

      Commit: f54482a38c8fb9465e4c524b8111b811e8fbff23

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

      Date: 2026-09-30 15:57:53 +0200

      Commit message:


	  
		
 fixed newly-introduced bugs...
 
    
  
    

      Package: exploreSE

      Commit: ac75ff55cf9bceaa362eec54572590f6620bd26c

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

      Date: 2026-09-30 14:34:23 +0200

      Commit message:


	  
		
 movid file selector into coditional panel
 
    
  
    

      Package: DelayedArray

      Commit: 5b7100c1a8a98cc5e0dafc095afad562485ea5fa

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

      Date: 2026-09-29 22:43:24 -0700

      Commit message:


	  
		
 DelayedArray 0.39.8: Minor tweaks to abind() method for DelayedArray objects

Also add coercion methods from ANY to DelayedArray and to DelayedMatrix.
 
    
  
    

      Package: SparseArray

      Commit: 4b7dc31217763d42754205bf3fa3604a594f193a

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

      Date: 2026-09-29 22:39:06 -0700

      Commit message:


	  
		
 SparseArray 1.13.4: Minor tweaks to abind() method for SparseArray objects
 
    
  
    

      Package: S4Arrays

      Commit: e68bb21989319fe7e47b14bc1345616c761053b0

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

      Date: 2026-09-29 22:22:50 -0700

      Commit message:


	  
		
 S4Arrays 1.13.2: Default abind() method now handles heterogeneity

The default abind() method now accepts an heterogeneous mix of objects
like any combination of ordinary arrays, Matrix/sparseMatrix derivatives,
SparseArray derivatives, and DelayedArray derivatives.

As a consequence rbind() and cbind() now also handles heterogeneity.
 
    
  
    

      Package: TDbasedUFEadv

      Commit: e3947a982483a82d6405e49e8b81b8095adc13e7

      Author:  Y-h. Taguchi <tag@granular.com> 

      Date: 2026-09-30 12:24:53 +0900

      Commit message:


	  
		
 Replace RTCGA dependencies and preserve gene names
 
    
  
    

      Package: SeqArray

      Commit: cea9cef8d1f88a716562705d94fc36b10d36dcb9

      Author:  Xiuwen Zheng <zhengxwen@gmail.com> 

      Date: 2026-09-29 20:10:16 -0500

      Commit message:


	  
		
 memory optimized
 
    
  
    

      Package: igvShiny

      Commit: bd7a6a83fd5df571c4bd06b2d94c2b6a97d2f91e

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

      Date: 2026-09-30 01:50:39 +0200

      Commit message:


	  
		
 chore(demo): pin Connect Cloud manifest to 1.9.51 (a61d604) (#194) 
    
  
    

      Package: igvShiny

      Commit: a61d6042031b0e60ac4658e9964a4c3ccd7bf42b

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

      Date: 2026-09-30 01:40:35 +0200

      Commit message:


	  
		
 fix(demo): name chromosome 1 'chr1' in the demo BED and bedGraph tables (#192)

The showcase, two-instances and modules demos built their bed table with
chr = "1" on hg38, so the reference check (#179) warned on the first
three showcase buttons. All eleven showcase track buttons now load
without a reference warning (clicked headless with shinytest2). 
    
  
    

      Package: igvShiny

      Commit: 597fd221d1a66a34eda5ed9e6ba0a2b16a6427d0

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

      Date: 2026-09-30 01:26:33 +0200

      Commit message:


	  
		
 fix(js): manage pending-message queue lifecycle and sanitize error banner (#189) (#190)

* fix(js): manage pending-message queue lifecycle and sanitize error banner (#189)

- Track container generation and lifecycle status (loading, ready, failed)
- Drop queued calls from superseded renders when re-rendering with a new genome
- Drop calls immediately when browser creation fails instead of queueing silently
- Use textContent for genomeName and error message in the error banner
- Add Node.js runtime harness and testthat integration
- Bump version to 1.9.50

* fix(news): use standard imperative verb for gDRstyle linter and assert template escaping

* fix(js): isolate pending renders and queues by widget instance

* refactor(js): drop the unreachable innerHTML fallback of the error banner

Every errorDiv comes from document.createElement, which has
querySelector in browsers and in the Node harness, so the escaped
innerHTML branch never ran. One code path, textContent only. 
    
  
    

      Package: Banksy

      Commit: 9c834cd5d484583c2604a0b8776dc6ac4fb32922

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-09-29 15:24:52 -0700

      Commit message:


	  
		
 rebuild pkgdown site
 
    
  
    

      Package: Banksy

      Commit: 1c7b63e8cecbb1d823b2ed5fe497f710300315ce

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-09-29 15:24:52 -0700

      Commit message:


	  
		
 allow seed to vary lazy pca start
 
    
  
    

      Package: Banksy

      Commit: a6514d38ac82aa975e17c3d3ce44b3c4a1d5c587

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-09-29 14:59:52 -0700

      Commit message:


	  
		
 rebuild pkgdown site
 
    
  
    

      Package: Banksy

      Commit: 2609003691e9c4204ad26764244feabbe3b2922b

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-09-29 14:59:52 -0700

      Commit message:


	  
		
 bump version to 1.9.4
 
    
  
    

      Package: Banksy

      Commit: b8b2a1b289eef7f36a92f1df3945f1eff63e7b99

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-09-29 14:59:52 -0700

      Commit message:


	  
		
 make lazy pca deterministic
 
    
  
    

      Package: Banksy

      Commit: c8324e0a8cda9d9185bc6a87536e3e96c1272647

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-09-29 14:23:49 -0700

      Commit message:


	  
		
 rebuild pkgdown site
 
    
  
    

      Package: Banksy

      Commit: 699cfefacf390c89fcb65999abbaafa8ebc6b4dd

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-09-29 14:23:49 -0700

      Commit message:


	  
		
 bump version to 1.9.3
 
    
  
    

      Package: Banksy

      Commit: c907949b9838dd9233f7924e4124feefd7180654

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-09-29 13:29:17 -0700

      Commit message:


	  
		
 rebuild pkgdown site
 
    
  
    

      Package: Banksy

      Commit: 01ccc8aa8f9ac936f9ed0b76eb39cb50245cdc5c

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-09-29 13:29:17 -0700

      Commit message:


	  
		
 document scaling benchmarks in news
 
    
  
    

      Package: Banksy

      Commit: 25140a06a17a78a3efdad8cb941fb22340b37a82

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-09-29 13:29:17 -0700

      Commit message:


	  
		
 use sessioninfo in vignettes
 
    
  
    

      Package: Banksy

      Commit: 5ffe51f35220fb50901a70ea0b4caa020057fcc4

      Author:  Joseph Lee <joseph.lee@u.nus.edu> 

      Date: 2026-09-28 23:02:33 -0700

      Commit message:


	  
		
 Merge pull request #74 from prabhakarlab/feat-sparse-matmul 
    
  
    

      Package: Banksy

      Commit: f02d0020bafe39d401fbdff5274cb5476f9f9749

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-09-28 22:45:55 -0700

      Commit message:


	  
		
 add regression tests for lazy pca
 
    
  
    

      Package: Banksy

      Commit: ac16ada90120b83ddd6fc7ea59c74ff156a859de

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-09-28 22:45:55 -0700

      Commit message:


	  
		
 support on-disk matrices in ungrouped lazy path
 
    
  
    

      Package: Banksy

      Commit: 504467c733a72fb6bb2f19e5cec6d4c18c27065d

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-09-28 22:45:55 -0700

      Commit message:


	  
		
 guard against empty groups in lazy pca
 
    
  
    

      Package: Banksy

      Commit: 7ad5c50690095c6c7990a3754b4046157c8430ab

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-09-28 22:45:55 -0700

      Commit message:


	  
		
 add openmp work threshold, drop unused csc helpers
 
    
  
    

      Package: Banksy

      Commit: de9c35d90a766263bd54e73cfdc20b57f986a6b4

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-09-28 22:45:55 -0700

      Commit message:


	  
		
 document scale_max as one-sided clipping
 
    
  
    

      Package: Banksy

      Commit: d1b224e51c214a14d92ef0e1cea578e1ec3cbf18

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-09-28 22:45:55 -0700

      Commit message:


	  
		
 check use_agf instead of missing compute_agf
 
    
  
    

      Package: Banksy

      Commit: 5b16e82698bf1d19699f8c8e97f488f9e54d9552

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-09-28 22:45:55 -0700

      Commit message:


	  
		
 fix rings cluster column name in docs
 
    
  
    

      Package: Banksy

      Commit: 4e33f6467ebaa8fca914ebac105e2fdb37b3db41

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-09-28 22:45:55 -0700

      Commit message:


	  
		
 untrack compiled objects and ignore build artifacts
 
    
  
    

      Package: Banksy

      Commit: 9134df94fd92912e372505027a7a3a1248619b16

      Author:  jleechung <joseph.lee@u.nus.edu> 

      Date: 2026-05-29 21:37:48 -0700

      Commit message:


	  
		
 rebuild pkgdown site
 
    
  
    

      Package: Banksy

      Commit: f78168a6dd4c44bf7aa21f869e9d2491cb0545fa

      Author:  jleechung <joseph.lee@u.nus.edu> 

      Date: 2026-05-29 21:37:48 -0700

      Commit message:


	  
		
 bump to 1.9.2, update imports, README and pkgdown nav
 
    
  
    

      Package: Banksy

      Commit: 2b2b56864ce1199185e8c92abc2db1aad1bc542e

      Author:  jleechung <joseph.lee@u.nus.edu> 

      Date: 2026-05-29 21:37:48 -0700

      Commit message:


	  
		
 update vignettes to lazy M0 defaults, refresh figures
 
    
  
    

      Package: Banksy

      Commit: 40fd1fa85c18de092e81381623c31b37f86b113f

      Author:  jleechung <joseph.lee@u.nus.edu> 

      Date: 2026-05-29 21:37:35 -0700

      Commit message:


	  
		
 fix Rd lost braces in computeBanksy docs
 
    
  
    

      Package: Banksy

      Commit: 7e86302591b7af8ccd2860838f41dbff1be1d9e3

      Author:  jleechung <joseph.lee@u.nus.edu> 

      Date: 2026-05-29 21:37:35 -0700

      Commit message:


	  
		
 use lazy M0 defaults in examples and tests
 
    
  
    

      Package: Banksy

      Commit: a8861fe006ad4e139236325455c609438ae5824d

      Author:  jleechung <joseph.lee@u.nus.edu> 

      Date: 2026-05-29 21:37:35 -0700

      Commit message:


	  
		
 fix lazy per-group scaling to keep split-zero genes
 
    
  
    

      Package: Banksy

      Commit: 2965ce780d306bdae616df7a3c727548d3a9bd4e

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-05-28 22:45:14 -0700

      Commit message:


	  
		
 make lazy pca the default in runBanksyPCA, add banksy-matrix vignette
 
    
  
    

      Package: Banksy

      Commit: fa40cbac78f4903b319559b70380ab3a4a18f278

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-05-28 21:40:23 -0700

      Commit message:


	  
		
 cpp support for lazy pca
 
    
  
    

      Package: Banksy

      Commit: fb32422263e70803aba6626da1f73a27bdfc3e13

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-05-28 21:35:46 -0700

      Commit message:


	  
		
 add lazy pca with c++ irlba and sparse matmul operators
 
    
  
    

      Package: Banksy

      Commit: 75111a3e40d5895feb7aa829766f8ce1c97890d4

      Author:  jleechung <joseph.lee@u.nus.edu> 

      Date: 2026-05-24 13:28:37 -0700

      Commit message:


	  
		
 add scaling note with link to seurat-wrappers vignette
 
    
  
    

      Package: Banksy

      Commit: f61a3bb51318f140b37b3e75cf7b4e3386437f5f

      Author:  jleechung <joseph.lee@u.nus.edu> 

      Date: 2026-05-22 18:27:46 -0700

      Commit message:


	  
		
 refactor: sparse matmul for computeHarmonics with cache-aware chunking
 
    
  
    

      Package: igvR

      Commit: f5b23ff95f993b2c193867a7df0b2135a2ec474d

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

      Date: 2026-09-29 23:35:21 +0200

      Commit message:


	  
		
 Merge pull request #44 from darsoo/devel

Fix linter 
    
  
    

      Package: igvR

      Commit: 950d401a17d011403365e62dc396c179f82fce68

      Author:  Dariusz Scigocki <daro.scig@gmail.com> 

      Date: 2026-09-29 08:58:50 +0200

      Commit message:


	  
		
 docs: updated NEWS, fix testthat dependency
 
    
  
    

      Package: igvR

      Commit: 50153aab7b8ab47d397cabf8e3877a7007b81565

      Author:  Dariusz Scigocki <daro.scig@gmail.com> 

      Date: 2026-09-29 08:58:05 +0200

      Commit message:


	  
		
 docs: updated documetation
 
    
  
    

      Package: igvR

      Commit: e7a66b8dcf918fffdf92c288480718240a018edd

      Author:  Dariusz Scigocki <daro.scig@gmail.com> 

      Date: 2026-09-28 12:59:48 +0200

      Commit message:


	  
		
 feat: added tests placeholder
 
    
  
    

      Package: igvR

      Commit: e67d674af4ed180d2ac7260d4390f5907de70730

      Author:  Dariusz Scigocki <daro.scig@gmail.com> 

      Date: 2026-09-28 12:48:32 +0200

      Commit message:


	  
		
 fix: typo
 
    
  
    

      Package: igvR

      Commit: 4aa69328ba04dac2e1ac0257921361816cb837f9

      Author:  Dariusz Scigocki <daro.scig@gmail.com> 

      Date: 2026-09-28 12:39:40 +0200

      Commit message:


	  
		
 chore: version bump
 
    
  
    

      Package: igvR

      Commit: 96518395f37853a3f6ce2c5469a354da1ed1fc2e

      Author:  Dariusz Scigocki <daro.scig@gmail.com> 

      Date: 2026-09-28 12:35:59 +0200

      Commit message:


	  
		
 style: fix linter in igvR.R
 
    
  
    

      Package: igvR

      Commit: 2a60228a183b9c32dccf2072c3781fb7bfcda66d

      Author:  Dariusz Scigocki <daro.scig@gmail.com> 

      Date: 2026-09-27 23:29:23 +0200

      Commit message:


	  
		
 style: fix lintr
 
    
  
    

      Package: igvR

      Commit: 5a8c09bae804c9e97c51640eaa6bd3cdc4e3e0d0

      Author:  darsoo <daro.scig@gmail.com> 

      Date: 2026-09-25 12:26:54 +0200

      Commit message:


	  
		
 Update README.md 
    
  
    

      Package: fishash

      Commit: 5eabd3c5d93b08a8f54ad9803a17f235975a0c61

      Author:  Jack Kamm <jackkamm@gmail.com> 

      Date: 2026-09-28 14:54:08 -0700

      Commit message:


	  
		
 Bump to 0.99.5
 
    
  
    

      Package: fishash

      Commit: d6545b5c5066617117cde69bf291c0767d129a74

      Author:  Jack Kamm <jackkamm@gmail.com> 

      Date: 2026-09-28 14:27:16 -0700

      Commit message:


	  
		
 diagonal_heatmap: Add max_guides argument
 
    
  
    

      Package: fishash

      Commit: f61e302bb450f175902b98d57a14233cd5da31b2

      Author:  Jack Kamm <jackkamm@gmail.com> 

      Date: 2026-09-28 09:08:20 -0700

      Commit message:


	  
		
 nonzero_histogram_with_weighted: Add optional `assigned` argument
 
    
  
    

      Package: fishash

      Commit: 9b6eabc11632bc250a5d88f76a6e428b57793386

      Author:  Jack Kamm <jackkamm@gmail.com> 

      Date: 2026-08-23 09:50:06 -0700

      Commit message:


	  
		
 Readme: Update vignette URL
 
    
  
    

      Package: fishash

      Commit: 9e90d6cdb52945e77c131f7b374e4f4bed44a4f8

      Author:  Jack Kamm <jackkamm@gmail.com> 

      Date: 2026-08-06 17:40:27 -0700

      Commit message:


	  
		
 Update install instructions
 
    
  
    

      Package: trackViewer

      Commit: 602809b79fda0f3f14b5280340f7fbb2110fc0cf

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

      Date: 2026-09-29 15:32:11 -0400

      Commit message:


	  
		
 Add break layout for lollipop plot.
 
    
  
    

      Package: STRINGdb

      Commit: 2c35c60064e5b07cc7011299bafd2e3725cfcd3b

      Author:  Damian <damian.szk@gmail.com> 

      Date: 2026-09-29 15:23:13 +0200

      Commit message:


	  
		
 Stop on STRING server errors instead of parsing the error page

postFormSmart returned the body of any response as data, so a gateway
timeout (e.g. HTTP 524) came back as a data frame whose column was the
Cloudflare error message. Requests answered with HTTP 5xx now stop with the
status code. Client errors (4xx, e.g. 404 for unknown identifiers) keep
their previous behaviour.

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

      Package: STRINGdb

      Commit: 4bc42d502c73a701aa20b89bdd56c2fa21a795b5

      Author:  Damian <damian.szk@gmail.com> 

      Date: 2026-09-29 13:01:14 +0200

      Commit message:


	  
		
 Call unexported helpers via STRINGdb::: in new unit tests

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

      Package: STRINGdb

      Commit: 9b32ccd6dc452bcf717c329f211a3da1bab88354

      Author:  Damian <damian.szk@gmail.com> 

      Date: 2026-09-29 12:44:06 +0200

      Commit message:


	  
		
 Bump version to 2.25.1 for STRING 12.5 support

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

      Package: STRINGdb

      Commit: 3fc734c01332e9cbb9de3dadaabaf3e09cb2c1a5

      Author:  Damian <damian.szk@gmail.com> 

      Date: 2026-09-29 12:42:38 +0200

      Commit message:


	  
		
 Support STRING 12.5: regulatory networks and new API methods

Add network_type="regulatory" (directed, STRING >= 12.5), new
get_geneset_description and get_enrichment_figure methods, extended
network image/link options, updated citation, unit tests and
documentation. Version handling is read from the STRING
available_api_versions table, so 12.0 and earlier keep working.

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

      Package: PinPath

      Commit: e8a48f29ae98cfeafcc59cdc40f66f47ce9225b8

      Author:  Jarno Koetsier <jarno.koetsier@gmail.com> 

      Date: 2026-09-29 11:31:09 +0200

      Commit message:


	  
		
 Update to version 0.99.5

+ If all color gradients are the same, only one gradient will be plotted in the legend.
+ Font size of network diagrams can now be adjusted.
+ Bug fixes: if graph id is absent in GPML file, some node-group interactions were not shown in the network visualization. This has been fixed.
 
    
  
    

      Package: exploreSE

      Commit: ddef0a4b95368d8dffbc0ba8e92cac203b1cab15

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

      Date: 2026-09-29 11:27:07 +0200

      Commit message:


	  
		
 added a DE overview table and bug fixes
 
    
  
    

      Package: limpa

      Commit: 009587ed4f66daec4001541c7d2eb95794e5c819

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

      Date: 2026-09-29 17:14:49 +1000

      Commit message:


	  
		
 limpa 1.5.2
- pztbinom() now works correctly for q out of range.
- dpcLegacy() now avoids infinite values of n0.
- dpcLegacy() and dpcON() now check for at least 3 rows data, same as dpcCN().
- Unnecessary lines of code removed from estimateDPCIntercept().
 
    
  
    

      Package: transmogR

      Commit: 1b32b93fca462c17be50ec498b411460a1c9d954

      Author:  Stevie Ped <stephen.pederson.au@gmail.com> 

      Date: 2026-09-29 14:45:46 +0930

      Commit message:


	  
		
 Version bump after update
 
    
  
    

      Package: transmogR

      Commit: 6f401a0fee0bba112bd6e2a2dc74691b78885c5f

      Author:  Stevie Ped <stephen.pederson.au@gmail.com> 

      Date: 2026-09-29 14:25:30 +0930

      Commit message:


	  
		
 Updated salmon test
 
    
  
    

      Package: transmogR

      Commit: 361eda0f9eaf8d8036ef236073f38ac86b70eb34

      Author:  Stevie Ped <stephen.pederson.au@gmail.com> 

      Date: 2026-09-29 12:42:32 +0930

      Commit message:


	  
		
 Bugfix in parY
 
    
  
    

      Package: panoramic

      Commit: d45f4c84fb293268a4220b6bf7ae93b4f9e7eea0

      Author:  Jacob (Jake) Chang <69719427+chang-jacob@users.noreply.github.com> 

      Date: 2026-09-28 15:59:20 -0700

      Commit message:


	  
		
 Fix local composition enrichment and update documentation
 
    
  
    

      Package: rpx

      Commit: df8083ecb5cddea97fac8a8651f2f83937dbaa06

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-09-28 21:22:41 +0200

      Commit message:


	  
		
 fix unit test
 
    
  
    

      Package: rpx

      Commit: 1cf89c83bc70af811fbe0164ce05f933e8b7f958

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-09-17 20:43:42 +0200

      Commit message:


	  
		
 update license to GPL-3
 
    
  
    

      Package: rpx

      Commit: f35f2a58ae469f5684d3f1a5f93f36deb2b3e9c8

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-09-17 20:05:10 +0200

      Commit message:


	  
		
 fix gha
 
    
  
    

      Package: oct4

      Commit: f7ef338a6daf40602586b9dc5dded0a41985184b

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

      Date: 2026-09-28 14:09:55 -0400

      Commit message:


	  
		
 update to reduce package size
 
    
  
    

      Package: macrophage

      Commit: 2ba828bcd733ad3c3c463c6829711cf3893a49dd

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

      Date: 2026-09-28 13:32:24 -0400

      Commit message:


	  
		
 add news
 
    
  
    

      Package: tximportData

      Commit: 59766ff72a3c545424a085049458f15a0df4fd2c

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

      Date: 2026-09-28 13:32:10 -0400

      Commit message:


	  
		
 add news
 
    
  
    

      Package: tximportData

      Commit: 867fae654d437aa726466ae7283e9142ab731151

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

      Date: 2026-09-28 13:28:40 -0400

      Commit message:


	  
		
 Update remotes note: GitHub is origin, Bioconductor is upstream

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01RZhMs5BbqnF1KfvjrcoHtt
 
    
  
    

      Package: tximportData

      Commit: 79a33a228fb0d14686872e62eeb71e3d23a3a24c

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

      Date: 2026-09-28 10:01:58 -0400

      Commit message:


	  
		
 Reduce package size to ~100 MB (v1.41.1)

Remove inferential replicate data (salmon_gibbs, kallisto_boot,
tx2gene.ensembl.v87.csv), the GENCODE v48 GTF, alevin bfh.txt and
raw_cb_frequency.txt, and kallisto abundance.h5 files. Reduce GEUVADIS
kallisto/rsem/salmon/sailfish to 2 samples (ERR188088, ERR188021) and
subset samples.txt / samples_extended.txt to match. The full data is
archived at https://doi.org/10.5281/zenodo.22982575 (branch/tag
with-inf-reps).

Update vignette, DESCRIPTION, README; add .Rbuildignore for CLAUDE.md;
document downstream migration steps in CLAUDE.md.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01XjoQ2M5vYyfatKWVdFWNhU
 
    
  
    

      Package: DESeq2

      Commit: 9763acf95ef9b38c3176943d52ed6a14fbfaca1d

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

      Date: 2026-09-28 13:26:01 -0400

      Commit message:


	  
		
 update to smaller tximportData
 
    
  
    

      Package: fishpond

      Commit: 046b382edc6f7f89ae49030f0c8809c12826ad34

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

      Date: 2026-09-28 13:15:42 -0400

      Commit message:


	  
		
 ignore
 
    
  
    

      Package: fishpond

      Commit: 349b3add2eeae4addf2d40a5c938993eb552e7c1

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

      Date: 2026-09-28 13:14:58 -0400

      Commit message:


	  
		
 swish vignette: use macro_txp_se from macrophage (>= 1.29.1)
 
    
  
    

      Package: fishpond

      Commit: 9e6a328aace26fcf1849d9528d40a8a40f6ebe59

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

      Date: 2026-09-28 11:41:38 -0400

      Commit message:


	  
		
 merge
 
    
  
    

      Package: fishpond

      Commit: 0681d75c9e56086a86f89141560ae44c31d6b8e2

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

      Date: 2025-01-03 12:32:24 -0500

      Commit message:


	  
		
 Merge pull request #40 from an-altosian/devel

fix typo & add check/ into .gitignore 
    
  
    

      Package: fishpond

      Commit: 5820a3d7d6085457f8b5b7ea37ed8a5f76d64a80

      Author:  an-altosian <dhe@altoslabs.com> 

      Date: 2025-01-03 16:50:32 +0000

      Commit message:


	  
		
 fix typo & add check/ into .gitignore
 
    
  
    

      Package: fishpond

      Commit: f85ee653fc0eaf8a5ea73ffe61ff8568c540cef0

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

      Date: 2025-01-03 10:50:32 -0500

      Commit message:


	  
		
 check new code from Dongzhe
 
    
  
    

      Package: fishpond

      Commit: c8961d7e9b780ebabecb5774a13e66ea25b01fd4

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

      Date: 2025-01-03 10:50:05 -0500

      Commit message:


	  
		
 Merge pull request #39 from an-altosian/devel

Update the loadFry function 
    
  
    

      Package: fishpond

      Commit: b54abfb0ac5fccef080f2cbb0eacbe2d6f832226

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

      Date: 2025-01-02 11:55:58 -0500

      Commit message:


	  
		
 fix ucsc link issue
 
    
  
    

      Package: fishpond

      Commit: cc7ad7653384d28d568a0e4fb16fdb311c6bd5a4

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

      Date: 2025-01-02 11:03:08 -0500

      Commit message:


	  
		
 update check workflow
 
    
  
    

      Package: fishpond

      Commit: d7e34243b6581db455270920ad06319d094a54a1

      Author:  an-altosian <dhe@altoslabs.com> 

      Date: 2025-01-01 03:46:44 +0000

      Commit message:


	  
		
 work on loadFry doc
 
    
  
    

      Package: fishpond

      Commit: 77246ee120d37a4b489c73955985f23681ed83f5

      Author:  an-altosian <dhe@altoslabs.com> 

      Date: 2025-01-01 02:37:23 +0000

      Commit message:


	  
		
 add two arguments to loadFry
 
    
  
    

      Package: macrophage

      Commit: 16523d8f0e30fe55254e8cf922a14e464b79b77e

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

      Date: 2026-09-28 13:14:01 -0400

      Commit message:


	  
		
 Remove inf reps, ambig_info, full GTF; add slim GTF, macro_txp_se, macro_tx2gene
 
    
  
    

      Package: macrophage

      Commit: d3cd7eac278e335c154d789b8a8511142d1503a0

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

      Date: 2026-09-26 16:06:25 -0400

      Commit message:


	  
		
 adding claude instructions
 
    
  
    

      Package: scMultiome

      Commit: 340dce2e4e62dbc092f3e94ce2812993d20ac222

      Author:  Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2026-09-17 12:04:53 +0000

      Commit message:


	  
		
 v1.13.1
 
    
  
    

      Package: scMultiome

      Commit: f1db6cabfb2631dc2bec49697ff7c50238e84bcd

      Author:  Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2026-09-17 12:04:03 +0000

      Commit message:


	  
		
 do not use names to avoid extra metadata column in the reconstructed GRanges object
 
    
  
    

      Package: scMultiome

      Commit: c92d586219884e259f28a7bacccbde014ce92b7e

      Author:  Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2026-09-17 12:02:50 +0000

      Commit message:


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

      Package: scMultiome

      Commit: 1d10feeb6f400514511da54839dee42d7795d882

      Author:  Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2025-02-05 10:07:34 -0800

      Commit message:


	  
		
 v1.7.3
 
    
  
    

      Package: scMultiome

      Commit: 936479e534cce81c044fe0b5b7f7c38f0fac6fa7

      Author:  Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2025-02-05 08:10:06 -0800

      Commit message:


	  
		
 restore original order of arguments
 
    
  
    

      Package: scMultiome

      Commit: 06fe4244475b710e93018f456a8a3f03f37da889

      Author:  Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2025-01-16 02:35:23 -0800

      Commit message:


	  
		
 v1.7.2
 
    
  
    

      Package: scMultiome

      Commit: b862a2792f73bee1d658c164fafb2b09c5527c29

      Author:  Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2025-01-16 02:34:51 -0800

      Commit message:


	  
		
 change default version to 1
 
    
  
    

      Package: scMultiome

      Commit: 05759d236d10b355bc903ef6ce757fd0062c75b0

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-12-18 03:39:12 -0800

      Commit message:


	  
		
 v.1.7.1
 
    
  
    

      Package: scMultiome

      Commit: d74810dcc4b6931ac69d64ddce98d1076c45859f

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-12-17 22:03:07 -0800

      Commit message:


	  
		
 version 2 of the chip-seq data
 
    
  
    

      Package: scMultiome

      Commit: ae64bcb45416d3c342c2aedb337e094afaf66ce1

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

      Date: 2024-10-29 09:54:38 -0400

      Commit message:


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

      Package: scMultiome

      Commit: 3185fec04cb5e42332fab218814ec8e0184112a4

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

      Date: 2024-10-29 09:54:38 -0400

      Commit message:


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

      Package: scMultiome

      Commit: a824fd15c817bc020215477ebe1a6e3542d565c0

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-10-08 23:13:40 -0700

      Commit message:


	  
		
 v1.5.7
 
    
  
    

      Package: scMultiome

      Commit: 11d13cf5b4b645f5ecce9ebb6339bd5a15978cbd

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-10-08 23:13:30 -0700

      Commit message:


	  
		
 new functions documentation corrections
 
    
  
    

      Package: scMultiome

      Commit: 8ecd6645282f69c43b30974f664e55d9256960a8

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-09-26 09:43:27 -0700

      Commit message:


	  
		
 v1.5.6
 
    
  
    

      Package: scMultiome

      Commit: a96c88f7872579b9300eaecec2247392ce9b41bd

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-09-26 09:39:52 -0700

      Commit message:


	  
		
 data source version change and documentation update
 
    
  
    

      Package: scMultiome

      Commit: 5b4fbe1c04e83039c68d158c4c0c560b77ec5122

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2024-09-26 09:16:37 -0700

      Commit message:


	  
		
 update data description
 
    
  
    

      Package: scMultiome

      Commit: 2fa76473caffca17dd296214bdaacf9b0f627cac

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-09-26 08:56:27 -0700

      Commit message:


	  
		
 v1.5.5
 
    
  
    

      Package: scMultiome

      Commit: b78afd578582682858a8f034aea20016af9df73b

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-09-26 08:55:45 -0700

      Commit message:


	  
		
 metadata and documentation update
 
    
  
    

      Package: scMultiome

      Commit: c83c034ba0f59f58ec5ca71514633f8453016921

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-09-26 08:20:16 -0700

      Commit message:


	  
		
 insert placeholder instead of example name
 
    
  
    

      Package: scMultiome

      Commit: e93f74d043187d8a7c8a3fb6e40d833934733864

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-09-26 06:00:52 -0700

      Commit message:


	  
		
 v1.5.4
 
    
  
    

      Package: scMultiome

      Commit: 15ee69876a8c64acad8e657c29ce507c6c093b91

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-09-26 06:00:12 -0700

      Commit message:


	  
		
 metadata update
 
    
  
    

      Package: scMultiome

      Commit: 5aeab9456a6255a945d1cc3cf861a090ec035063

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-09-26 05:38:45 -0700

      Commit message:


	  
		
 HTO mapping and cluster annotation
 
    
  
    

      Package: scMultiome

      Commit: 612648bf7dc93c48c15c59674507df3ea1c5dd33

      Author:  Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2024-09-23 23:50:42 -0700

      Commit message:


	  
		
 v1.5.3
 
    
  
    

      Package: scMultiome

      Commit: cb6108e673a6456b78f3f087704c3854f805b141

      Author:  Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2024-09-23 23:47:45 -0700

      Commit message:


	  
		
 documentation update
 
    
  
    

      Package: scMultiome

      Commit: 2aa445e150b518f99e2af6cdfb5b562cf61e214c

      Author:  Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2024-09-23 23:47:08 -0700

      Commit message:


	  
		
 accessor functions
 
    
  
    

      Package: scMultiome

      Commit: 75b986ee70e91e32ef693a616106fbc9d140a2e0

      Author:  Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2024-09-23 23:46:40 -0700

      Commit message:


	  
		
 documentation update
 
    
  
    

      Package: scMultiome

      Commit: 5fde04b446e8b7371f1cb67821e851631c5b61e4

      Author:  Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2024-09-23 23:45:58 -0700

      Commit message:


	  
		
 metadata
 
    
  
    

      Package: scMultiome

      Commit: 9a2346bb6fc2165c28ef8820653d9e8a5605252a

      Author:  Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2024-09-23 23:40:11 -0700

      Commit message:


	  
		
 workflow description
 
    
  
    

      Package: scMultiome

      Commit: 28e0d9f74ad73ae7c6bd9e5798696a036ec46656

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-09-13 03:18:39 -0700

      Commit message:


	  
		
 Merge branch 'devel' of ssh.code.roche.com:scwg/gene-transcriptional-network/activity-inference/scMultiome into devel
 
    
  
    

      Package: scMultiome

      Commit: 4a0a5bba8edb255047c1547a4ee843ec3f124398

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-09-13 03:18:26 -0700

      Commit message:


	  
		
 PBMC and AR drug data sets documentation
 
    
  
    

      Package: scMultiome

      Commit: 5cf850f1552ac74a28bc9eebf261d4ffa86a8cc8

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-09-13 03:13:20 -0700

      Commit message:


	  
		
 AR drug data set update
 
    
  
    

      Package: scMultiome

      Commit: 06ef07be6bdf9ab4ee94afd2f4fc07f8d5f921fe

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-09-09 07:01:15 -0700

      Commit message:


	  
		
 AR metadata
 
    
  
    

      Package: scMultiome

      Commit: 4d95cc24181d0f2efb124fe223854ae6f75b5ea0

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-09-09 06:08:57 -0700

      Commit message:


	  
		
 AR workflow description
 
    
  
    

      Package: scMultiome

      Commit: faa4b6b0998d75850aef0bb461c16ca75617db2f

      Author:  Xiaosai Yao <yaox19@gene.com> 

      Date: 2024-08-10 22:20:40 -0700

      Commit message:


	  
		
 v1.5.2 replace writeSparseMatrix with same function in  alabaster.matrix
 
    
  
    

      Package: scMultiome

      Commit: 95a1eec5a6805829c465f5264f68d5d85097ad88

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2024-07-11 18:08:17 -0700

      Commit message:


	  
		
 v 1.5.1
 
    
  
    

      Package: scMultiome

      Commit: 4bf8594f89df1260a6fbddbc716df957616cf85d

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2024-07-11 18:07:08 -0700

      Commit message:


	  
		
 v 1.5.1
 
    
  
    

      Package: scMultiome

      Commit: 884f1d798b2b5cfe886580f13103f190981720af

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2024-07-11 17:18:48 -0700

      Commit message:


	  
		
 modified tfBinding
 
    
  
    

      Package: scMultiome

      Commit: d41808f68bed48b7f5d04f13038dd060667596d0

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2024-07-11 17:15:38 -0700

      Commit message:


	  
		
 Merge branch 'devel' of ssh.code.roche.com:scwg/gene-transcriptional-network/activity-inference/scMultiome into devel
 
    
  
    

      Package: scMultiome

      Commit: e75fa845b183ca0bf8aad8c6a0d77260313c95c3

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2024-07-11 17:14:37 -0700

      Commit message:


	  
		
 v 1.3.3
 
    
  
    

      Package: scMultiome

      Commit: c30ef4abe6193c00e9a68798e0891545b74faa76

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

      Date: 2024-04-30 11:11:33 -0400

      Commit message:


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

      Package: scMultiome

      Commit: 8f110761e09e82529814c76f79ab12f7675498a1

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

      Date: 2024-04-30 11:11:33 -0400

      Commit message:


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

      Package: scMultiome

      Commit: d2f70952803ce3f9f87ca9631fed83020cccc335

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-04-11 12:08:18 -0700

      Commit message:


	  
		
 v1.3.3
 
    
  
    

      Package: scMultiome

      Commit: 0c166fe29537bc0d7c8eeea323c8371058b4b22f

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-04-11 12:02:09 -0700

      Commit message:


	  
		
 Merge branch 'new_chip' into devel
 
    
  
    

      Package: scMultiome

      Commit: 14ebbfaeaf7abf52589ac3de3ec5d70a7166549f

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2024-04-11 06:58:20 -0700

      Commit message:


	  
		
 update BioC version to 3.19
 
    
  
    

      Package: scMultiome

      Commit: 017dd5a8ed21244b3903f52e61374441a222c7cb

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-04-11 04:50:30 -0700

      Commit message:


	  
		
 search data set by file names
 
    
  
    

      Package: scMultiome

      Commit: ed003facb94eaf5911045674f1c258d10bf62341

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-04-11 04:30:15 -0700

      Commit message:


	  
		
 metadata update
 
    
  
    

      Package: scMultiome

      Commit: 26e2076df06e0a83ef626f822e55013e535cbd84

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-04-11 04:26:12 -0700

      Commit message:


	  
		
 correct BioC version
 
    
  
    

      Package: scMultiome

      Commit: 7fdb8ab846b7112bddba37fd508dfdfb9b25d9c0

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2024-04-07 11:54:07 -0700

      Commit message:


	  
		
 update documentation
 
    
  
    

      Package: scMultiome

      Commit: 258213f3843b3726e55b6c9df513db2689791e3c

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2024-04-07 11:17:41 -0700

      Commit message:


	  
		
 add sample-specific and tissue-specific chip-seq
 
    
  
    

      Package: scMultiome

      Commit: 6f78e93b5f5f283e53f1582ec7cfea325f2779cd

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-04-05 13:43:02 -0700

      Commit message:


	  
		
 correct argument values
 
    
  
    

      Package: scMultiome

      Commit: 79fdf1d8e2aa236c52b195ef38cd5b60edacc64a

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-04-05 03:38:15 -0700

      Commit message:


	  
		
 expand function to handle sample- and tissue-specific grls
 
    
  
    

      Package: scMultiome

      Commit: 95b2ebb7b4fc67493cb5885e2997f09e9743e394

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-04-02 01:28:17 -0700

      Commit message:


	  
		
 v1.3.2
 
    
  
    

      Package: scMultiome

      Commit: 09b1838cd654ad836809e600e197a78ad58370eb

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-04-02 01:25:42 -0700

      Commit message:


	  
		
 date corrected and additional author added
 
    
  
    

      Package: scMultiome

      Commit: 180676952b48a8a9aff96805bd3762e84be9e94a

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-03-22 00:52:56 -0700

      Commit message:


	  
		
 v1.3.1
 
    
  
    

      Package: scMultiome

      Commit: 2feb3e7c2e6bb9ef47c2974c964edf1a5d337b2c

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-03-22 00:48:28 -0700

      Commit message:


	  
		
 e-mail address corrected
 
    
  
    

      Package: scMultiome

      Commit: c6b00e04359e80d24861f1d7ad50b2842122066b

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-03-22 00:46:46 -0700

      Commit message:


	  
		
 Merge branch 'devel' of ssh.code.roche.com:scwg/gene-transcriptional-network/activity-inference/scMultiome into devel
 
    
  
    

      Package: scMultiome

      Commit: 9dc052e52628e6dcd8b2f060b0987f47069ae202

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-03-22 00:45:22 -0700

      Commit message:


	  
		
 Merge branch 'devel' of ssh.code.roche.com:scwg/gene-transcriptional-network/activity-inference/scMultiome into devel

Conflicts:
	DESCRIPTION
 
    
  
    

      Package: scMultiome

      Commit: d62f4465dab2d4eba5d5838e01bd14d3935bb780

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-03-21 02:46:25 -0700

      Commit message:


	  
		
 correct import of bed files
 
    
  
    

      Package: scMultiome

      Commit: 967a83ca21998d4e7a9b5b2606c40905bda4c109

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-02-09 02:23:50 -0800

      Commit message:


	  
		
 export new function and change reference
 
    
  
    

      Package: scMultiome

      Commit: 8244bb913fc5c8333fb41656b40ad75a2ce3125b

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-02-09 02:23:25 -0800

      Commit message:


	  
		
 use Polish diacritic
 
    
  
    

      Package: scMultiome

      Commit: 470cdf2a9b4b7fde50aaf8c5885b3b82e93b9f55

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-02-02 04:25:26 -0800

      Commit message:


	  
		
 correct metadata
 
    
  
    

      Package: scMultiome

      Commit: 1c2800df1ccf41888a1afab382e3d5914794d959

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-01-31 07:42:12 -0800

      Commit message:


	  
		
 TF motif info data sets
 
    
  
    

      Package: scMultiome

      Commit: 1a47feef39a80379bedcb13e4b4ef310afdea8a4

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

      Date: 2023-10-24 09:24:29 -0400

      Commit message:


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

      Package: scMultiome

      Commit: fae545b97e151ee421e976da993d9265dcbaeb96

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

      Date: 2023-10-24 09:24:29 -0400

      Commit message:


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

      Package: scMultiome

      Commit: 492787a6843df56c281b2792c807230b5b8ee092

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-09-26 20:36:51 -0700

      Commit message:


	  
		
 version bump to 1.1.2
 
    
  
    

      Package: scMultiome

      Commit: b73652b3ad5e04d1609e9ab615e6b8fed8ed4054

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-09-26 19:28:30 -0700

      Commit message:


	  
		
 update function schematics
 
    
  
    

      Package: scMultiome

      Commit: 7ea03657b3d18d614e55073540d2a17d0cf2b005

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-09-26 19:21:23 -0700

      Commit message:


	  
		
 version bump to 1.1.1
 
    
  
    

      Package: scMultiome

      Commit: 8aba5d6decadc91b497a257261712d7daead1dd3

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-09-26 19:20:43 -0700

      Commit message:


	  
		
 specify experimenthub version and remove R version
 
    
  
    

      Package: scMultiome

      Commit: 6c1be48dc603e723acb5bab9497bacdb668662fa

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-09-26 19:19:58 -0700

      Commit message:


	  
		
 update vignette with bioc url
 
    
  
    

      Package: scMultiome

      Commit: e46ac09b4f774b9fd91ce3f9c12bc0d47280c4bf

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-09-26 18:52:11 -0700

      Commit message:


	  
		
 remove archr2MAE and update link
 
    
  
    

      Package: scMultiome

      Commit: a940a1e7d09a5614f59ee4e18d1b56a4b3684acc

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

      Date: 2023-04-25 10:52:28 -0400

      Commit message:


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

      Package: scMultiome

      Commit: 32d06c79f6e990a2c333a0edee8ef02845f7390d

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

      Date: 2023-04-25 10:52:27 -0400

      Commit message:


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

      Package: scMultiome

      Commit: 591fb3c0229017a7fcac480e0f6cd603ccf0e868

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-04-15 02:49:54 -0700

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: scMultiome

      Commit: 9463b43356b414694bfeba3cfa6796fc080c26c3

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-04-15 02:46:49 -0700

      Commit message:


	  
		
 delete html
 
    
  
    

      Package: scMultiome

      Commit: 2784071d6472f3533e8d53c994bfd98de5ee9d40

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-03-22 20:56:19 -0700

      Commit message:


	  
		
 0.99.14
 
    
  
    

      Package: scMultiome

      Commit: a6945786af00209212d00e5602ea24ae9fccb0ae

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-03-22 20:36:30 -0700

      Commit message:


	  
		
 remove ArchR2MAE function in readme
 
    
  
    

      Package: scMultiome

      Commit: b348c403c3f054faef3daa0552a8ee68c9b0c8cb

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-03-22 20:32:19 -0700

      Commit message:


	  
		
 version bump to 0.99.12
 
    
  
    

      Package: scMultiome

      Commit: d9e83a6e8d06c22d8a91065ea53b0ac1eebcfbec

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-03-22 20:31:26 -0700

      Commit message:


	  
		
 remove archr in installation
 
    
  
    

      Package: scMultiome

      Commit: 22406923d1a703612fb349b04c648065231f3bfd

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-03-22 19:47:01 -0700

      Commit message:


	  
		
 remove data processing section
 
    
  
    

      Package: scMultiome

      Commit: 4bff4390a4792ac2df561c72f8b38c9b346981de

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-03-19 12:29:09 -0700

      Commit message:


	  
		
 version bump to 0.99.11
 
    
  
    

      Package: scMultiome

      Commit: 3e5452c248266c3f2ce852bb83ce6190826c550e

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-03-19 12:27:49 -0700

      Commit message:


	  
		
 cite singleCellMultiModal and MAE
 
    
  
    

      Package: scMultiome

      Commit: 6a13a1945831843327c07310e66a4ebb667a75ce

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-03-19 12:26:12 -0700

      Commit message:


	  
		
 use file.path() to construct paths
 
    
  
    

      Package: scMultiome

      Commit: b4689753f03229aada779bcdd9258f45c2dc3314

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-03-19 12:25:27 -0700

      Commit message:


	  
		
 specify license
 
    
  
    

      Package: scMultiome

      Commit: 1e94d4c1ca58bc5617b333a260850909459f5331

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-03-19 12:25:00 -0700

      Commit message:


	  
		
 specify license
 
    
  
    

      Package: scMultiome

      Commit: a21c68b01f430e79fdce9132a2b396d8a41f66e5

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-02-24 15:33:03 -0800

      Commit message:


	  
		
 v0.99.10
 
    
  
    

      Package: scMultiome

      Commit: 0db2ae02df7177e070a5f1fea472cdd565d840f6

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-02-24 14:47:53 -0800

      Commit message:


	  
		
 v0.99.9
 
    
  
    

      Package: scMultiome

      Commit: 95d725cc5360ffc9d752fc37cb5d7a790e3ebae9

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-02-24 14:16:32 -0800

      Commit message:


	  
		
 change email to gmail
 
    
  
    

      Package: scMultiome

      Commit: aa920cd381f67cb5fdb95ab4cf277b450ac8288b

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-02-22 13:35:45 -0800

      Commit message:


	  
		
 add .github to .Rbuildignore
 
    
  
    

      Package: scMultiome

      Commit: 702cc994f864c8dc409033ffe91dc1bf09657b35

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-02-22 10:58:23 -0800

      Commit message:


	  
		
 removed scMultiome.Rproj
 
    
  
    

      Package: scMultiome

      Commit: 34cf1ab2870d6c83f58f4e2f0056eba657584125

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-02-22 10:56:06 -0800

      Commit message:


	  
		
 remove \cr
 
    
  
    

      Package: scMultiome

      Commit: 27137611a4974b25000af29d10abcd42b4949654

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-01-20 22:49:05 +0100

      Commit message:


	  
		
 Merge branch 'noArchR' into 'master'

move archr2MAE to ArchR

See merge request scwg/gene-transcriptional-network/activity-inference/scMultiome!16 
    
  
    

      Package: scMultiome

      Commit: 9dbd53ee34b3e4457f8d7f91aef0d3b15ea31ce2

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-01-20 13:46:36 -0800

      Commit message:


	  
		
 move archr2MAE to ArchR
 
    
  
    

      Package: scMultiome

      Commit: dce06f078307bb8b1a6ae274bb11cb43f5704f17

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-01-13 16:35:13 -0800

      Commit message:


	  
		
 fix setenv
 
    
  
    

      Package: scMultiome

      Commit: 62135814a8b6bf95cc20a961cdede49ecb9df3fa

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-01-13 16:27:38 -0800

      Commit message:


	  
		
 setenv
 
    
  
    

      Package: scMultiome

      Commit: 941bd35705407423fa0b7dbb18ffa6e7b791c260

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-01-13 16:10:34 -0800

      Commit message:


	  
		
 add github pat
 
    
  
    

      Package: scMultiome

      Commit: 4ff30edf4388491e701936ca91bcc97b8b6a98bb

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-01-13 15:38:03 -0800

      Commit message:


	  
		
 edit readme and add PAT
 
    
  
    

      Package: scMultiome

      Commit: fd8b399c358c2e0f91f2f93f2cc0f2448e97cb23

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-01-13 15:00:24 -0800

      Commit message:


	  
		
 insert archR installation instructions
 
    
  
    

      Package: scMultiome

      Commit: c1cd81ee127111b0122a7d8b02b11617a28b9c01

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-01-13 14:18:24 -0800

      Commit message:


	  
		
 fix typo
 
    
  
    

      Package: scMultiome

      Commit: 7dc7f1ce214111f1527b396dd20393627498b4d5

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2023-01-13 14:15:29 -0800

      Commit message:


	  
		
 git cmd check
 
    
  
    

      Package: ENmix

      Commit: ea1f9dd9eac1e4ff02079ccc93460d3160228466

      Author:  xuz1 <xuz@niehs.nih.gov> 

      Date: 2026-09-28 12:16:59 -0400

      Commit message:


	  
		
 bugfix

Signed-off-by: xuz1 <xuz@niehs.nih.gov>
 
    
  
    

      Package: meshes

      Commit: cda2db81f62700d4735fd42c9143c3abe33a5a4c

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-28 23:05:43 +0800

      Commit message:


	  
		
 Support current AnnotationHub MeSHDb schema
 
    
  
    

      Package: meshes

      Commit: 12fc4c06c5ff09f59f443356a8181e7106210b0f

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-26 15:58:58 +0800

      Commit message:


	  
		
 update readme
 
    
  
    

      Package: tximport

      Commit: 2c532670e2f58139a7ebc3a57fd2ccf22d5b8cdf

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

      Date: 2026-09-28 10:43:52 -0400

      Commit message:


	  
		
 merge
 
    
  
    

      Package: tximport

      Commit: 1f79c48f2258a4abdcdeaea9735c98355f5f7ec7

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

      Date: 2026-09-28 10:43:21 -0400

      Commit message:


	  
		
 working with small tximportData
 
    
  
    

      Package: tximport

      Commit: ca35c2866c8083a831703852d9afd689ed3893b8

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

      Date: 2026-09-28 10:40:58 -0400

      Commit message:


	  
		
 update for smaller tximportData (>= 1.41.1)

tximportData now has 2 GEUVADIS samples and no longer includes
salmon Gibbs samples, kallisto bootstraps or abundance.h5 files
(archived at https://doi.org/10.5281/zenodo.22982575).

- vignette, examples and tests use 2 samples
- inf reps and kallisto h5 vignette chunks are now eval=FALSE
- test_inf_reps and test_h5 write synthetic replicates to tempdir()

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01YUViTwuZmQSrAcVW6CTV9d
 
    
  
    

      Package: tximport

      Commit: 4d72c131209c424d96c5156be3b93d87a38d3add

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

      Date: 2026-04-15 10:40:37 -0400

      Commit message:


	  
		
 update docs
 
    
  
    

      Package: seqsetvis

      Commit: 9cf285f5b1e61f8fb710c2dee7a5d92a330ad571

      Author:  Joseph Boyd <boydjr7@gmail.com> 

      Date: 2026-09-23 17:32:44 -0400

      Commit message:


	  
		
 v bump 1.33.1
compatibility update for Bioc 3.24 and R 4.6.1
fixed bug due to behavior change of casting GRanges to data.table. name was added by as.data.table.
 
    
  
    

      Package: spatialLIBD

      Commit: f63819319aba0a4dbf6ba8f86eb40e61d7cb4c49

      Author:  lcolladotor <lcolladotor@gmail.com> 

      Date: 2026-09-28 07:27:29 -0600

      Commit message:


	  
		
 v1.25.3 -- uses scrapper + updated fetch_data() for habenulaAtlas project release
 
    
  
    

      Package: spatialLIBD

      Commit: 4486b3dc368d0e16d4efaa011fc300d79ea1ebfe

      Author:  lcolladotor <lcolladotor@gmail.com> 

      Date: 2026-09-28 07:27:01 -0600

      Commit message:


	  
		
 Change dropbox link for sce_pb_visium_habenula_atlas.rds
 
    
  
    

      Package: spatialLIBD

      Commit: a4005a25af631d592e2c7abd4410fd264d53199f

      Author:  Leonardo Collado-Torres <lcolladotor@gmail.com> 

      Date: 2026-09-28 09:22:30 -0400

      Commit message:


	  
		
 Merge pull request #123 from LieberInstitute/scuttle_pseudobulk_check

edit scuttle to scrapper for aggregateAcrossCells() 
    
  
    

      Package: spatialLIBD

      Commit: d410b05493785def4698cb63c65089b98f5def63

      Author:  Leonardo Collado-Torres <lcolladotor@gmail.com> 

      Date: 2026-09-28 09:22:12 -0400

      Commit message:


	  
		
 Merge branch 'devel' into scuttle_pseudobulk_check 
    
  
    

      Package: spatialLIBD

      Commit: e3e22734816c8cc532da7ab155b5e2af6785e6cf

      Author:  manishabarse <mbarse.libd@gmail.com> 

      Date: 2026-09-25 11:44:48 -0400

      Commit message:


	  
		
 Fix aggregateAcrossCells compatibility
 
    
  
    

      Package: spatialLIBD

      Commit: 26e7f0294d03a7f4d2763c1933201d7d20b399f8

      Author:  Nick-Eagles <nick.eagles@libd.org> 

      Date: 2026-09-25 11:13:04 -0400

      Commit message:


	  
		
 Configure fetch_data() to load habenula atlas data
 
    
  
    

      Package: spatialLIBD

      Commit: a32ec1836043bf6b2b79e3d3e5c45de6885c29c3

      Author:  Nick-Eagles <nick.eagles@libd.org> 

      Date: 2026-09-25 10:52:33 -0400

      Commit message:


	  
		
 Prepare metadata for habenula atlas data
 
    
  
    

      Package: spatialLIBD

      Commit: 8d733724904a2afcb13f31ecf33abee437e9670f

      Author:  manishabarse <mbarse.libd@gmail.com> 

      Date: 2026-09-25 09:55:41 -0400

      Commit message:


	  
		
 edit scuttle to scrapper for aggregateAcrossCells()
 
    
  
    

      Package: scRNAseqApp

      Commit: 1ee79e3ec5f75c66b396f4ce50b9ccb101459d3a

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

      Date: 2026-09-28 08:24:07 -0400

      Commit message:


	  
		
 Count the vistors by removing the bots
 
    
  
    

      Package: gDR

      Commit: 99c08ef95d7b727a80826c3a79637a3db9cce955

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

      Date: 2026-09-28 10:06:53 +0200

      Commit message:


	  
		
 Merge pull request #65 from gdrplatform/GDR-3626

fix: render the rowData and colData tables on Bioconductor 3.24 
    
  
    

      Package: gDR

      Commit: 588fb4efe26fca4daf61e36c293a9f83d518684a

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

      Date: 2026-09-24 08:45:21 +0200

      Commit message:


	  
		
 fix: render the rowData and colData tables on Bioconductor 3.24
 
    
  
    

      Package: limpa

      Commit: 6f9093d4e2567f5a23c0647131246618ad57e696

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

      Date: 2026-09-28 17:57:35 +1000

      Commit message:


	  
		
 limpa 1.5.1
- Bug fix to pztbinomSameSizeLogitPBothTails() when q > size.
- Revise help page for pztbinomSameSizeLogitPBothTails().
 
    
  
    

      Package: MetaboDynamics

      Commit: b3459f64e0e386b393d03b0227b284b841bea9a9

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

      Date: 2026-09-28 08:52:36 +0200

      Commit message:


	  
		
 bug fix: prior_sd_abundance
 
    
  
    

      Package: peakPantheR

      Commit: 7c5995c3018fbe0e292ec621c33c3b5b9cb9a090

      Author:  Arnaud Wolfer <adwolfer@gmail.com> 

      Date: 2026-09-28 03:48:14 +0200

      Commit message:


	  
		
 Merge branch 'devel-origin' into devel
 
    
  
    

      Package: peakPantheR

      Commit: fd8f83f1837103720403154fd87c82ec8267cd7d

      Author:  Arnaud Wolfer <adwolfer@gmail.com> 

      Date: 2026-09-28 03:44:28 +0200

      Commit message:


	  
		
 test fix MSNbase mzR
 
    
  
    

      Package: peakPantheR

      Commit: d8156040ad6304e45e7e56938839919df0b4c9ab

      Author:  Arnaud Wolfer <adwolfer@gmail.com> 

      Date: 2026-09-28 02:43:05 +0200

      Commit message:


	  
		
 update github action
 
    
  
    

      Package: peakPantheR

      Commit: b5fc9b8ceeaceddd77723fcb200b32ac5bee8215

      Author:  Arnaud Wolfer <adwolfer@gmail.com> 

      Date: 2026-09-28 02:31:04 +0200

      Commit message:


	  
		
 Merge branch 'devel-origin' into devel
 
    
  
    

      Package: peakPantheR

      Commit: 5cb031e809e06f968abf62abdc375a1e0016fd2c

      Author:  Arnaud Wolfer <adwolfer@gmail.com> 

      Date: 2026-09-28 02:29:06 +0200

      Commit message:


	  
		
 updates for BiocChecks
 
    
  
    

      Package: peakPantheR

      Commit: c750c1006145411dc698c60baeff4c4b78a19bdc

      Author:  Arnaud Wolfer <adwolfer@gmail.com> 

      Date: 2026-09-28 01:22:09 +0200

      Commit message:


	  
		
 updated Github action
 
    
  
    

      Package: peakPantheR

      Commit: 6d4322717ee4eed6bdfc24783f1da187c9e3bf85

      Author:  Arnaud Wolfer <adwolfer@gmail.com> 

      Date: 2026-09-28 00:59:55 +0200

      Commit message:


	  
		
 update CI github action
 
    
  
    

      Package: peakPantheR

      Commit: 690293102a72d52bc8571349294417872e54bb22

      Author:  Arnaud Wolfer <adwolfer@gmail.com> 

      Date: 2026-09-28 00:59:44 +0200

      Commit message:


	  
		
 update CI github action
 
    
  
    

      Package: peakPantheR

      Commit: f8c95843e326e9fb5d851681dd172b6fd19a4d42

      Author:  Arnaud Wolfer <adwolfer@gmail.com> 

      Date: 2026-09-28 00:32:36 +0200

      Commit message:


	  
		
 update github action
 
    
  
    

      Package: jvecfor

      Commit: beea3022e3fe25800cfaf3c617c8aa7d5cef02bd

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-09-28 01:41:18 +0300

      Commit message:


	  
		
 Parse Java output with Windows CRLF line endings as numeric
 
    
  
    

      Package: jvecfor

      Commit: dd4c6053b967938a2b5755abd0cb8b1eba815023

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-09-28 01:20:26 +0300

      Commit message:


	  
		
 Find Java via JAVA_HOME as well as PATH
 
    
  
    

      Package: jvecfor

      Commit: f49eb53c0c1633a3cf704a89e5e08f81ec682e59

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-09-28 00:58:31 +0300

      Commit message:


	  
		
 Skip test-utils Java integration tests when Java < 20
 
    
  
    

      Package: jvecfor

      Commit: 44208c332688ef6246a5c8f150784f65a0f89187

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-09-27 23:59:21 +0300

      Commit message:


	  
		
 Update jvector backend to 4.0.1, guard Java >= 20, add pkgdown site
 
    
  
    

      Package: gVenn

      Commit: 82ad2751d9ea08a217b64ec723c272ac04db9b90

      Author:  Christophe Tav <christophe.tav@gmail.com> 

      Date: 2026-09-26 10:58:17 -0400

      Commit message:


	  
		
 update documentation
 
    
  
    

      Package: gVenn

      Commit: 372240aa73e40fa0c52ae6ec19a140d27e2f5407

      Author:  Christophe Tav <christophe.tav@gmail.com> 

      Date: 2026-09-26 10:52:09 -0400

      Commit message:


	  
		
 update documentation
 
    
  
    

      Package: gVenn

      Commit: 28d668d936e848a652532c49e58f90f3d0df1a4d

      Author:  Christophe Tav <christophe.tav@gmail.com> 

      Date: 2026-09-26 10:19:18 -0400

      Commit message:


	  
		
 update documentation
 
    
  
    

      Package: gVenn

      Commit: 1d4d5d3e9691d6e00b0d8c5f0d5170a9d7bbe3b7

      Author:  Christophe Tav <36061268+ckntav@users.noreply.github.com> 

      Date: 2026-09-25 23:44:25 -0400

      Commit message:


	  
		
 Merge pull request #3 from ckntav/dev-disjoin

gVenn 1.99.0: disjoin mode and fit diagnostics 
    
  
    

      Package: gVenn

      Commit: f90e0694a3fb7b90e35b974e61c7a68847ef46d2

      Author:  Christophe Tav <christophe.tav@gmail.com> 

      Date: 2026-09-25 23:17:52 -0400

      Commit message:


	  
		
 update documentation
 
    
  
    

      Package: gVenn

      Commit: 8f6c2670adb068729da44cb3f1068423205aea26

      Author:  Christophe Tav <christophe.tav@gmail.com> 

      Date: 2026-09-25 12:35:24 -0400

      Commit message:


	  
		
 update
 
    
  
    

      Package: gVenn

      Commit: a3322244eacd64e0c4070625873bbabe6c1ad204

      Author:  Christophe Tav <christophe.tav@gmail.com> 

      Date: 2026-09-25 12:23:26 -0400

      Commit message:


	  
		
 regenerate plotVenn.Rd with corrected result class names
 
    
  
    

      Package: gVenn

      Commit: e9ffff02f13cca329521d3b5bab0a181eabd21a8

      Author:  Christophe Tav <christophe.tav@gmail.com> 

      Date: 2026-09-25 10:47:19 -0400

      Commit message:


	  
		
 correct class name
 
    
  
    

      Package: gVenn

      Commit: ed544221a293c3b6745a1cffc75fce180abfb5f3

      Author:  Christophe Tav <christophe.tav@gmail.com> 

      Date: 2026-09-25 10:46:51 -0400

      Commit message:


	  
		
 use correct result class names in plotVenn docs
 
    
  
    

      Package: gVenn

      Commit: c7b257c633a26dd1d6b07c92b14f9b5b7fb6b407

      Author:  Christophe Tav <christophe.tav@gmail.com> 

      Date: 2026-09-25 10:43:59 -0400

      Commit message:


	  
		
 fix [0, 1] rendered as a link in ?plotVenn
 
    
  
    

      Package: gVenn

      Commit: 7a838711c17ec45c466a58ea7de85191b9994357

      Author:  Christophe Tav <christophe.tav@gmail.com> 

      Date: 2026-09-24 13:56:55 -0400

      Commit message:


	  
		
 update NEWS.md heading to 1.99.0
 
    
  
    

      Package: gVenn

      Commit: b909e1d3d73c91fcaaa1a5ae6460423e9abfa195

      Author:  Christophe Tav <christophe.tav@gmail.com> 

      Date: 2026-09-24 13:55:31 -0400

      Commit message:


	  
		
 set version to 1.99.0
 
    
  
  


</div>

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