0.99.31 Logo and Gif
 

 Merge pull request #81 from gdrplatform/GDR-3464

[GDR-3464] Update doc for PRISM dataset 

 docs: update doc for PRISM dataset
 

 Fix loadGDS() and reopenGDS() for R 4.6.1 vignette build (v2.7.1).

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

 fix another bug in AHub
 

 Merge branch 'main' into devel
 

 Merge pull request #87 from PNNL-CompBio/doc-updates

Improved documentation. Added updated Rd files and bumped version 

 Improved documentation.

Added additional information and algorithmic details to the documentation of:
- calc_spatial_diff_ex.R
- distance_based_analysis.R
- enrich_ORA.R
- impute_spe.R
 

 more package dependencies
 

 fixed potential build issue
 

 added software dependency
 

 version bump again
 

 tests: add new tests to check NSE with upstream S4Vectors changes
 

 updating the new tile functionality
 

 Merge pull request #126 from smped/devel

Respect column names in mutate 

 Respect column names in mutate
 

 dont run some examples
 

 defunct and cleanup
 

 Devel version 1.3.1; minor citation and contact changes.
 

 update citation and contact e-mail
 

 Merge pull request #82 from DiseaseTranscriptomicsLab/default

v1.2 

 release bioc 3.23
 

 Merge pull request #79 from DiseaseTranscriptomicsLab/main

v1.1.1 

 clarify vignettes
 

 Reapply "Merge pull request #75 from DiseaseTranscriptomicsLab/main"

This reverts commit 2447feb4c3bc67ced6a5e0d4d3656d0c604c3446.
 

 Merge pull request #75 from DiseaseTranscriptomicsLab/main

bioconductor changes in main to default 

 small rewrites
 

 Merge pull request #1 from plger/knn

merge knn-variant and variability estimates into devel 

 version bump
 

 added brief section on kNN approach
 

 version bump
 

 fixed error with dgeMatrix
 

 changed default weighing to linear
 

 added kNN-based background
 

 Matrix::rowMeans...
 

 fixed doc, fixed right rowMeans import
 

 added missing files...
 

 version bump
 

 more informative error message on empty peaks
 

 Fix installed check metadata tests
 

 Merge pull request #3 from MingLi-929/devel

fix: modernize upsetplot and tidyselect usage 

 bump version
 

 Merge pull request #1 from Treywea/devel

fix typo and test dependency 

 fix typo and test dependency
 

 version bump 1.81.1
 

 update R version to 4.6.0
 

 bump version to 1.7.2 and add ragg to Suggests
 

 Merge pull request #95 from AnthonyChristidis/main

Merge latest changes for scDiagnostics 

 fix: add "Query_" prefix to top 6 anomaly names to match distance_data matrix
 

 fix: update pc_subset default in examples and move title to ggpairs with updated styling
 

 feat: add v1.8.0 changes to NEWS.md
 

 Change default `n_hvgs` from 1000 to 100 in `detectAnomaly`.
 

 `docs: add pkgdown website URL to DESCRIPTION`
 

 refactor(calculateGeneShifts): add MAD-based anomaly thresholding and cleanup

- Replace single `anomaly_threshold` with `threshold_method` ("MAD"/"absolute"), `mad_multiplier`, and updated `anomaly_threshold` (default 0.5)
- Add `median`/`mad` to `@importFrom stats`
- Enforce `pc_subset` cannot be NULL
- Pass new threshold parameters to `detectAnomaly`
- Fix `@param` cross-references to use `\link[SingleCellExperiment:...]` syntax
- Remove internal `processGenesSimple` roxygen docs and minor comment cleanup
- Update Rd man page accordingly
 

 feat(detectAnomaly): add HVG support, MAD thresholding, and heatmap visualization

- Add `n_hvgs` parameter for HVG selection when `pc_subset = NULL` (uses `scran`)
- Replace fixed `anomaly_threshold` with `threshold_method` ("MAD" or "absolute") and `mad_multiplier`
- Store `applied_threshold` in output list for traceability
- Add ComplexHeatmap visualization path in `plot.detectAnomalyObject` for HVG-based results
- Add `data_type = "both"` option (HVG heatmaps only) to show reference and query together
- Add `draw_plot` parameter to control whether plot is rendered immediately
- Fix ellipse angle calculation bug (use `vectors` instead of `values`)
- Update docs, examples, and tests accordingly
 

 Add circlize to Suggests and update RoxygenNote to 7.3.3
 

 Merge pull request #23 from ccb-hms/main

Merge changes from ccb-hms. 

 Merge pull request #21 from ccb-hms/main

Update color for non-anomalous cells in barplot and heatmap for gene … 

 Merge branch 'ccb-hms:main' into main
 

 Merge branch 'ccb-hms:main' into main
 

 Merge branch 'ccb-hms:main' into main
 

 Merge pull request #19 from ccb-hms/main

Fix anomaly detection plot and add assay selection option for gene im… 

 GenomicAlignments 1.49.1: Defunct CIGAR utilities and sequenceLayer()

These were deprecated in GenomicAlignments 1.45.5 (BioC 3.22).
 

 Release 0.99.21: Bioconductor second review response
 

 bump version and update NEWS
 

 Update citation
 

 update package description text
 

 Release 0.99.20: fix BiocCheck load-error signal NOTE

Use warning() instead of message(sprintf()) for attach load errors.
 

 version bump, 1.21.1
 

 rerendered manpages
 

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

 Release 0.99.19: BiocCheck fixes for SPB rebuild

- Add Normalization and NetworkEnrichment biocViews
- Fix coding-practice notes in utils_shiny_app.R (seq_len, sprintf, no <<-)
- R CMD check and BiocCheck: 0 ERRORs, 0 WARNINGs locally
 

 MultipleAlignment 0.99.5: Use new detail() S4 generic from BiocGenerics
 

 Release 0.99.18: ML Venn improvements, plot downloads, check clean

- Show all selected ML methods in Venn/UpSet with explicit zero overlap
- JPG/PDF plot export across Shiny tabs; fix local library path clash
- R CMD check: 0 ERRORs, 0 WARNINGs (drop rmda from Suggests)
 

 chore: version bump; fix pkgdown
 

 fix: bambu errors when .fai not present
 

 fix: pass genome as FaFile to bambu for offline use

bambu's checkInputSequence call BSgenome::available.genomes() which
errors out when no internet avaliable
 

 fixed missing BNPARAM doc
 

 Merge pull request #24 from zeehio/claude/update-news

Update NEWS.md with tuneInPeakInfo fixes and deprecations 

 Clarify deprecated functions are internal/unexported
 

 Merge pull request #23 from zeehio/claude/cleanup-redundant-triple-colon

Drop redundant ::: qualifiers in test files 

 Drop over-explanatory comments about testthat and unexported functions

Anyone writing testthat tests already knows unexported functions
resolve fine in test files; no need to spell out why.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01QSVH82XMPFq38YQWaTAaaN
 

 Drop redundant ::: qualifiers in test files

Unexported functions (extendLength, extendNBase, findLocalMaxWinSize,
cwt_classic) don't need MassSpecWavelet::: in test files: testthat's
test environment is a clone of the package namespace
(testthat:::test_env() -> env_clone(asNamespace(package))), so they
resolve by their bare name, same as exported functions -- confirmed by
running the suite with the qualifiers removed. The comment in
test-findLocalMaxWinSize.R claiming ::: was "how it is actually
reachable today" was wrong.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01QSVH82XMPFq38YQWaTAaaN
 

 Deprecate getRidgeValue(), i2u(), u2i(), mzInd2vRange(), mzV2indRange(), smoothDWT()

Verified none of these six functions are called anywhere internally in
MassSpecWavelet, nor by xcms (the one known downstream package
depending on this package's peak-detection internals; checked its
full source directly). None are exported, so this only affects code
reaching them via `:::`.

Each now calls .Deprecated() with a message explaining the situation
and inviting anyone relying on it to open an issue within the next
year before removal. Roxygen docs for the four functions that already
had a man page (getRidgeValue, mzInd2vRange, mzV2indRange, smoothDWT)
gained a matching deprecation note; NAMESPACE is unaffected since none
of these were ever exported.

mzInd2vRange()/mzV2indRange() call i2u()/u2i() internally in a loop
(once per input element), so their internal calls are wrapped in
suppressWarnings() to avoid emitting one deprecation warning per
element in addition to their own -- manually confirmed this matters by
sabotaging the suppression, which turned 1 warning into 21 for a
10-element input.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01QSVH82XMPFq38YQWaTAaaN
 

 Fix findLocalMaxWinSize()'s roxygen block and mark it internal

The @return tag's continuation lines used two-space indentation
(#'  ...) instead of one, which made roxygen2 treat the following
@export and @examples lines as more @return prose instead of parsing
them as tags -- they were literally dumped as text at the end of the
generated \value{} section, and the function was never actually
exported despite the source claiming @export (confirmed with
roxygen2::parse_file(): only a "return" tag existed, no "export" or
"examples" tag was ever produced).

Now that @keywords/@examples parse correctly, mark this function
@keywords internal instead of (recognized-for-the-first-time) @export:
it's explicitly documented as experimental and untested until the
previous commit, so it shouldn't become part of the public API by
accident. This matches the existing convention for the package's other
internal-but-documented helpers (extendLength(), extendNBase()).
NAMESPACE is unaffected (the function was never in it to begin with).

Also wrapped the example in \donttest{}, matching extendLength()'s
precedent: now that @examples is a real tag, its bare (non-exported)
function call needs to be donttest-skipped or R CMD check's example
step would try to run it under a plain library(MassSpecWavelet) and
fail with "could not find function". Verified this is skipped
correctly (and that the pre-existing tag-swallowing bug is fixed) via
roxygen2::parse_file() and a real R CMD check example run.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01QSVH82XMPFq38YQWaTAaaN
 

 Merge pull request #20 from zeehio/claude/test-mexh-getRidgeLength

Add unit tests for getRidgeLength() and mexh() 

 Merge pull request #18 from zeehio/claude/test-tuneInPeakInfo

Fix three tuneInPeakInfo() crashes and add direct unit tests 

 Fix three crashes in tuneInPeakInfo()

Found while adding direct unit tests for this function:

1. If a peak's local refinement window (re-cwt()/getRidge() segment
   around the peak) happens to contain no ridges (e.g. a quiet/flat
   neighborhood), getRidge() returns an empty list, names() is NULL,
   and strsplit(NULL, "_") crashes with "non-character argument" --
   the same class of bug fixed earlier in identifyMajorPeaks(). Now
   that peak is left unprocessed (original values kept, reported in
   unProcessedPeak) instead of crashing.

2. When called via the direct peakIndex/peakScale arguments (instead
   of majorPeakInfo), peakValue/peakSNR are NULL. If any peak ends up
   unprocessed (the case above, or the pre-existing
   length(scales.i) <= 1 case), appending peakValue[i] (NULL[i] is
   NULL) silently dropped an element instead of keeping the output
   vectors aligned by position, and crashed later with "attempt to
   set an attribute on NULL" once names<- ran on the (possibly still
   NULL) result. Now NA is used as the placeholder when there is no
   original value to fall back on.

3. `for (i in 1:length(peakIndex))` iterates i = 1, 0 when peakIndex
   has length 0 (e.g. peakDetectionCWT(tuneIn = TRUE) on a
   flat/constant signal, whose majorPeakInfo$peakIndex is empty per
   the earlier flat-signal fix), crashing with "missing value where
   TRUE/FALSE needed". Switched to seq_along(), and the accumulator
   vectors now start as numeric(0)/integer(0) instead of NULL so a
   zero-peak call returns a well-formed empty result.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01QSVH82XMPFq38YQWaTAaaN
 

 Add unit tests for getLocalMaximumCWT()

This function's relative amp.Th / exclude0scaleAmpThresh thresholding
has been the source of several past bugfixes (see NEWS.md), but was
only ever exercised indirectly through getRidge()/peakDetectionCWT()
tests using their own defaults. These tests build a small wCoefs
matrix with a scale-0 (raw signal) column whose baseline dwarfs the
wavelet-scale columns -- exactly the scenario exclude0scaleAmpThresh
is meant to fix -- and cover:

- The default (no threshold) local maximum detection.
- An absolute amp.Th filtering out low-amplitude peaks.
- A relative amp.Th being dominated by the scale-0 baseline when
  exclude0scaleAmpThresh = FALSE.
- exclude0scaleAmpThresh = TRUE correctly excluding the scale-0
  column from the relative threshold calculation.
- exclude0scaleAmpThresh having no effect when there is no scale-0
  column.
- minWinSize overriding the scale-derived window size.
- Row/column names being preserved.

Every expectation was derived from the fixture's actual, empirically
verified output, and manually confirmed to fail when the
exclude0scaleAmpThresh logic is broken (exactly the 2 assertions
tied to that rule fail, nothing else).

No version bump: more test-coverage work is planned before the next
Bioconductor push.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01QSVH82XMPFq38YQWaTAaaN
 

 Add unit tests for extendLength() and extendNBase()

These internal helpers pad a signal/matrix before cwt() runs the
wavelet transform, and are correctness-critical: an off-by-one here
silently corrupts every CWT coefficient near the signal edges. Only
the default combination (method = "reflection", direction = "right")
was ever exercised indirectly through cwt(); the other 8
method/direction combinations, matrix input, addLength = 0, and the
argument-validation paths had no coverage at all.

Every expectation was derived from the functions' actual, empirically
verified output, and manually confirmed to fail when the underlying
method dispatch is broken (forcing "circular" regardless of the
requested method breaks exactly the reflection/open assertions).

No version bump: more test-coverage work is planned before the next
Bioconductor push.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01QSVH82XMPFq38YQWaTAaaN
 

 Add direct unit tests for identifyMajorPeaks()

Previously identifyMajorPeaks() was only exercised indirectly through
peakDetectionCWT() integration tests, using peakDetectionCWT()'s own
default parameters. These tests call identifyMajorPeaks() directly
against a synthetic ridgeList/wCoefs fixture with three peaks tuned to
exercise each filtering rule in isolation:

- ridgeLength: filters short ridges from peakIndex while keeping them
  in allPeakIndex.
- nearbyPeak: rescues a short ridge located near a qualifying long
  ridge.
- SNR.Th: filters low-SNR peaks; SNR.Th=0 disables the rule.
- excludeBoundariesSize: filters peaks near the signal edges;
  excludeBoundariesSize=0 disables the rule.
- SNR.method: invalid values raise the documented error.
- minNoiseLevel: a named "fixed" value is used as-is instead of being
  scaled by max(wCoefs).
- An empty ridgeList returns the well-formed empty result.

Every expectation was derived from the fixture's actual, verified
behavior, and manually confirmed to fail when the corresponding rule
is broken.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01QSVH82XMPFq38YQWaTAaaN
 

 Migrate unit test suite from RUnit to testthat

Moves tests from inst/tests/runit.*.R + tests/runit.R to the standard
testthat layout (tests/testthat/test-*.R + tests/testthat.R),
switching Suggests from RUnit to testthat (>= 3.0.0) with the 3rd
edition. Test logic and coverage are unchanged, only the assertion
API (checkEquals/checkTrue -> expect_equal/expect_true/...) and file
layout.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01QSVH82XMPFq38YQWaTAaaN
 

 fixes #140 by treating the S4 prototype as an instance, thus supporting both S4 objects and S3 objects with an old class
 

 version bump 1.31.12
 

 allow recursive input to be character as in tools::package_dependencies
 

 scrapper (#155)

* omit logNormCounts & computeLibraryFactors in mmDS
* clear scrapper-and UpSetR-related warnings in vignettes
* address R CMD check NOTE re: no visible binding
* v1.27.4 

 version bump 1.31.11
 

 use size check as additional criteria for needsUpdate

assisted-by: gemini 3.5 flash and claude sonnet 5
 

 chore: remove unused shinytest2 from Suggests

shinytest2 was declared in Suggests but had zero references in the entire
codebase (no AppDriver, no record_test, no tests/testthat references). On
environments without shinytest2 installed, R CMD check would ERROR at the
dependency-check stage. Removed to eliminate the dead dependency declaration.
 

 fix(joint-canvas): repair copy-code observer ID + sync docs via roxygenise

Bug found by R CMD check (M3 subagent): the joint canvas copy-code
observer was still bound to the removed 'export_code_btn' input ID
instead of the new 'jc_copy_code' ID, making the 'Copy R Code' button
dead in module 14. The earlier insert_edit_into_file replacement had
only partially applied.

Fix:
- R/14_shiny_mod_joint_canvas.R: replace the dangling
  observeEvent(input, ...) with the correct
  observeEvent(input, ...) + .jc_export_code() reactive,
  matching module 12/13 pattern (clipr + manual-copy fallback).
- Remove the stale 'Generated R Code' modalDialog scaffold that was
  left behind by the incomplete replacement.

Doc sync (addresses R CMD check WARNINGs 1 & 2):
- Run roxygen2::roxygenise() to regenerate all man/*.Rd files.
- This adds generate_combined_plot_code.Rd (was missing after the
  function was added to R/15_code_generator.R) and adds it to NAMESPACE.
- This also synchronizes the margin_top/margin_bottom/margin_left/
  margin_right \item entries for generate_volcano_code,
  generate_de_volcano_code, generate_network_code, generate_hubgene_code,
  and generate_boxplot_image_code (codoc mismatch warnings).
 

 fix(dotplot): use data-driven scale domain (drop fixed limits), align with enrichplot

Remove the fixed 'limits = c(0,50)' / 'c(0,500)' from scale_size_continuous.
The fixed domain was compressing actual data range (e.g. CoreCount 10-30)
into a small fraction of the scale, making bubbles appear nearly identical.

Now ggplot2 auto-derives the scale domain from current data min/max, so the
full point_range (default c(3,8) mm) is always utilized. CoreCount 10->30
now maps across the entire 3-8mm diameter range (2.25:1 area ratio, the
theoretical max for this range), vs ~1.7:1 before.

This mirrors enrichplot::.dotplot_internal which uses scale_size(range=c(3,8))
without explicit limits. Data clamp (pmin/pmax) is retained to guard against
extreme outliers; the clamp threshold stays as the soft cap (50/500) but no
longer gates the visual scale.

Also update subtitle: 'sqrt scale' -> 'linear, data-driven scale'.
 

 feat(export): add Combined Pathway Plotting export, fix dotplot bubble size, refine Pathway Volcano labels

- R/12_shiny_mod_multi_plot.R: Add full image export modal (PDF/PNG/SVG/TIFF)
  mirroring Joint Canvas. Extract plot computation to .combined_plot reactive
  so both main renderPlot and export modal share the same patchwork object.
  Includes Dimensions (W/H inch + DPI) and Live Preview (res=72, v3 dims).

- R/15_code_generator.R: Widen dotplot default point_range from c(3,8) to
  c(2,12). Old range compressed CoreCount 10->30 to 1.72:1 area ratio (below
  2.25:1 perception threshold); new range yields 2.27:1. Keeping limits fixed
  preserves cross-contrast visual comparability (vs dynamic limits which would
  make same pathway appear different sizes across datasets).

- R/15_code_generator.R: Pathway Volcano direction labels 'Up in' -> 'Enriched in'
  in generate_volcano_code. GSEA NES direction is enrichment direction, not
  gene-level expression up/down; 'Enriched in LeftGroup/RightGroup' is accurate.

- R/13_shiny_mod_pathway_relation.R: Sync dotplot slider default and fallback
  point_range to c(2,12) to match new generator default.
 

 ui: allow scrollbars in Live Preview pane for large figures

With res fixed at 72 and pixel dims computed as inch*72, large figures
(e.g. 16x12 inch -> 1152x864 px) can exceed the 520px-tall preview pane
and get clipped by overflow:hidden. Switch to overflow:auto so users
can scroll to inspect the full figure when width/height exceed the pane.

Applied to all 5 preview containers (box/vol/de in R/10, network in
R/13, hubgene in R/16).
 

 fix: real cause of 'non-numeric argument' — margin NA passed to sprintf

Previous fix only patched the dims helpers, but the actual error was
in the 5 generator CALL SITES. The margin guard was 'if (is.null(...))'
which does NOT catch NA. When a user clears the margin numericInput,
Shiny returns NA, the guard passes, NA reaches generate_*_code, and
sprintf('%d', NA) embeds 'NA' into the code string as
'margin(NA, NA, NA, NA)'. ggplot's margin() rejects NA and throws
'non-numeric argument to binary operator' — only in Live Preview
because that's the only path that eval()s the generated code.

Fix: add '|| is.na()' to all 20 margin guards (4 margins x 5 call sites
across R/10 box/vol/de, R/13 network, R/16 hubgene) so NA falls back
to the default just like NULL.
 

 renderPlot preview: match export PHYSICAL size for accurate layout

Rewrite the 3 preview-dims helpers (.vol_preview_dims in R/10 shared by
box/vol/de, .preview_dims in R/13, .hub_preview_dims in R/16) so the
preview device's physical size (inches) always equals the user's
width x height inputs. margin() and base_size are in POINTS (1/72 inch),
so they only occupy the same proportion of the figure when the device
inches match the export inches — this is what makes the preview match
the exported layout.

Implementation: res = dpi * scale where scale = min(1, 1600 / (max(w,h)
* dpi)), so the longer pixel side is capped at 1600 (memory protection
for large figures like 24x24@600dpi) while physical inches are always
preserved. renderPlot's res/width/height now all read dpi from the
corresponding numericInput.

Verified: 5x5@300->1500x1500@300dpi=5x5in; 8x6@300->1600x1200@200dpi=8x6in;
24x24@600->1600x1600@67dpi=24x24in. Physical inches exact in all cases.
 

 Live Preview: clean up previous temp PNG before writing new one

Each of the 5 preview reactives (box/vol/de in R/10, network in R/13,
hubgene in R/16) now keeps a plain env (NOT reactiveValues, to avoid
re-triggering reactive dependencies) holding the path to the previous
temp PNG. Before ggsave-ing a new one, unlink the old file so only one
temp PNG per preview stays on disk at any time.
 

 revert plotly labels to v0.99.14; parameterize canvas margins with UI controls

- Revert Pathway Volcano plotly annotation layout from radial-distribute
  back to the v0.99.14 simple scheme (ay=-30, ax alternating 0/50).
  Live Preview display logic is left untouched.
- Add margin_top/bottom/left/right parameters to 5 code generators in
  15_code_generator.R (volcano, de_volcano, network, hubgene, boxplot_image).
  Margins are injected into the generated code string via sprintf/paste0.
- Add Canvas Margin (pt) UI block (4 numericInputs: T/B/L/R) to all 5
  export modals across 10/13/16 modules, so users can adjust per-figure
  breathing room instead of being stuck with hardcoded values.
 

 feat: add boxplot publication export, fix pathway volcano labels, dual-mode preview

- Add Boxplot Image Export Center (panel 4) with auto-extract data,
  live preview, and reproducible R code generator
- Remove obsolete 'Export Code' block from Holographic module bottom
  (was using deprecated generate_pathway_plot_code)
- Fix Pathway Volcano label occlusion in plotly: 8-direction radial
  distribution replaces stacked ay=-30 layout
- Fix ggrepel label occlusion in exported volcano: nudge_y + force +
  finite max.overlaps (was Inf, forcing all labels to render)
- Add Internal/External dual-mode preview to all export modals
  (Pathway/DE Volcano, Boxplot, Joint Canvas, DotPlot/Network, HubGene)
- External Canvas renders full-size PNG and opens in new browser tab
  (bypasses the 720px internal preview cap for detail inspection)
- Register shinyjs::useShinyjs() and addResourcePath for canvas dir
 

 chore: tidy for R CMD check (DESCRIPTION Authors@R, rd examples) and repair UTF-8 comments in R/ (no version bump)
 

 v0.99.13: add .gitignore for tools/ and IDEA.md (local dev only)
 

 v0.99.12: keep all user/pathway genes in DE Volcano export trim so non-significant markers still get labelled
 

 v0.99.12: fix DotPlot export missing bubbles + DE Volcano export code generator

- R/15_code_generator.R (DotPlot missing bubbles): generate_dotplot_code()
  emitted scale_size_continuous(limits=c(0,50/500), trans='sqrt'), but
  ggplot2 4.x removed the oob argument, so pathways with CoreCount>50 or
  setSize>500 were silently censored at render time -- bubbles vanished
  from Live Preview/PDF/PNG with only a stderr warning the modal does not
  show. Misperceived as 'long names drop bubbles' because large gene sets
  tend to have long names. Fix: clamp the active size column to the scale
  limits in data preprocessing (mirroring the plotly pmin/pmax path) so
  'limits' becomes a pure visual anchor, not a censoring gate. Also
  migrate deprecated trans='sqrt' to transform='sqrt'. Verified e2e with
  9 MSigDB pathways (setSize 80-1800, CoreCount 8-95, names up to 60
  chars): 9/9 bubbles render in all 4 size/color combos, zero warnings.

- R/10_shiny_mod_quadrant.R (DE Volcano export generator): the reactive
  behind the Quadrant DE Volcano 'Export Publication Plot' button was
  calling generate_boxplot_image_code() (boxplot generator) with boxplot
  arguments, so the clipboard-copied R code did not reproduce the
  interactive DE Volcano. Switched to generate_de_volcano_code() with
  the correct arguments (user_genes, pathway_genes, logfc_thresh,
  pval_thresh, show_annotations) sourced from the matching reactives.
 

 v0.99.11: make export annotations checkbox-controlled

Per user request: "加这些标签可以是一个对钩选项，选上了就加入，
没有就跟之前一样".

Both volcano export modals now have a checkbox (default unchecked):
- Pathway Volcano: "Show stats subtitle (pathways / selected / significant)"
- DE Volcano: "Show stats + direction banners (Up/Down | High-in)"

When unchecked, the generated ggplot2 code produces a clean figure with
title + axes only (identical to pre-annotation behavior). When checked:
- Pathway Volcano adds subtitle "X pathways | Y selected | Z significant"
- DE Volcano adds subtitle "Up X | Down Y | NS Z | ..." plus two corner
  annotations mirroring the interactive plotly: right-top red
  "High in ", left-top blue "High in ",
  using actual group names (e.g. "High in WT").

Implementation: labs/annotate blocks built via paste0 (embedding group
names as string literals) and injected into the sprintf template via %s,
avoiding nested-sprintf %% escaping. Both generators gain a
show_annotations=FALSE argument; R/10 reads the checkbox via isTRUE(input$...).

Files changed:
- R/10_shiny_mod_quadrant.R: add checkboxes to both export modals,
  pass show_annotations through .volcano_export_code / .de_volcano_export_code.
- R/15_code_generator.R: generate_volcano_code / generate_de_volcano_code
  gain show_annotations param + conditional labs_annot_block.
 </pre>
    </div>
  
    

      Package: GSEAlens

      Commit: 8208e2cd25f38d0b77d695441f7649a769d9ae76

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-06-30 13:03:11 +0800

      Commit message:


	  
		
 v0.99.11: sync export code labels with interactive plotly

Three user-reported issues addressed:

1. DotPlot export subtitle now reflects Color by / Size by selection.
   Previously the subtitle was hardcoded "Color = significance |
   Size = gene-set magnitude" regardless of the user's choices; now
   it dynamically references color_title / size_title so the saved
   figure documents the active aesthetic (e.g. "Color: |NES|
   (viridis, reversed) | Size: Set Size (sqrt scale)").

2. Pathway Volcano export now carries the same statistics banner as
   the interactive plotly title. generate_volcano_code() gains an
   n_selected argument; the generated labs(subtitle=...) renders
   "X pathways | Y selected | Z significant (P<0.25)" computed from
   the live data. R/10 passes length(selected_pathway_ids()) through.

3. DE Volcano export now reproduces both the plotly stats banner and
   the "High in " corner labels. labs(subtitle=...) renders
   "Up X | Down Y | NS Z | Selected U | Pway V | Both W" computed
   from the de_df category column, and two annotate("text", ...) calls
   place red/blue "High in " / "High in " banners in the
   top corners (mirroring the interactive plotly annotations), with
   coord_cartesian(clip="off") + plot.margin so the labels stay visible.

4. Modal CSS (R/07): fix scroll-to-top bug. Previously only .modal-body
   had max-height: 85vh, while .modal-dialog was unconstrained and
   Bootstrap centered it vertically, so once the Live Preview image
   pushed the modal taller than the viewport the browser clipped the
   header above the fold and the body scrollbar could not reach it.
   Switch to a flex layout: .modal becomes a scrolling viewport,
   .modal-content is a flex column bounded to 92vh, header and footer
   are pinned (flex: 0 0 auto), only .modal-body scrolls. Now any
   tall Live Preview can be scrolled all the way back to the title bar.

Files changed:
- R/07_shiny_app.R: modal CSS overhaul (flex layout, pinned header/footer).
- R/10_shiny_mod_quadrant.R: pass n_selected to generate_volcano_code.
- R/15_code_generator.R: dynamic subtitle in generate_dotplot_code,
  stats subtitle + n_selected arg in generate_volcano_code, stats
  subtitle + High-in annotations in generate_de_volcano_code.
 </pre>
    </div>
  
    

      Package: GSEAlens

      Commit: 3d83efcdc6d9c4e2e5d57fd59c49b2bb2a6f89d3

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-06-30 12:15:40 +0800

      Commit message:


	  
		
 v0.99.11: aspect-ratio preview + ggrepel labels for Network/HubGene

USER REPORT
-----------
"Image overflows the preview pane; when width exceeds 8 inch (or 9 for
Joint Canvas), the preview stops refreshing horizontally. Should render
the actual aspect ratio, scaled to fit in the Live Preview pane. If too
long, the long side is bounded by the renderable area. Also: pathway
relationship network labels are dark-on-dark and completely cover the
underlying nodes — should learn from clusterProfiler's plotting, place
labels above the annotated node, and stagger labels that would overlap."

FIX 1: Aspect-ratio-correct preview (all 5 export modals)
---------------------------------------------------------
Previous: width/height were capped INDEPENDENTLY at 720/540 px, which
distorted aspect ratio and stopped growing horizontally beyond ~7.2
inch of width (because min(w*100, 720) saturated).

New algorithm (.xxx_preview_dims helper per module):
  * Take the user's width_in / height_in (inches)
  * Find which is the longer side, pin it to max_dim (720 px)
  * Scale the shorter side by the SAME ratio
  * Result: on-screen proportions always match the saved figure
    - 16x4 banner  -> 720x180 (wide-and-short)
    - 9x7 default  -> 720x560 (matches saved file)
    - 4x16 column  -> 180x720 (tall-and-narrow, container scrolls)

Modal containers also got max-height:560px + overflow:auto + flexbox
centering so tall banners become browseable (scroll) instead of
overflowing the modal.

FIX 2: ggrepel labels for Network & HubGene static exports
----------------------------------------------------------
Previous: geom_label was drawn at the node's (x, y) center, so the
label box completely covered the node circle/diamond underneath.

New: ggrepel::geom_label_repel with:
  * nudge_y = 0.18  -> label starts ABOVE the node (not on top)
  * min.segment.length = 0 -> always draw connector segment
  * segment.color = "grey55" -> visible but unobtrusive
  * direction = "both" + max.overlaps = Inf -> auto-stagger
    overlapping labels in BOTH axes (clusterProfiler / enrichplot
    convention)
  * fill = "white", color = "#222" -> readable on any node color
  * box.padding = 0.45 -> breathing room between label and node

No new dependency added: enrichplot (already in Imports) brings
ggrepel transitively, and `library(ggrepel)` is now emitted at the
top of generate_network_code / generate_hubgene_code so the
clipboard-copy path also works standalone.

Verified in a real Shiny test app:
  * Network renders with labels above nodes, no node occlusion
  * Width/height changes (16x4, 9x7, 4x16) all produce correctly
    proportioned previews, zero errors in the R console.
 
    
  
    

      Package: GSEAlens

      Commit: 1b1b81c3f8aad9280173db04c59fb60555e35932

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-06-30 11:37:23 +0800

      Commit message:


	  
		
 v0.99.11: fix live-preview crash — renderPlot res must be scalar, not function

ROOT CAUSE (confirmed via real Shiny app reproduction on port 4567):
  Warning: Error in *: non-numeric argument to binary operator
    152: list2
    151: startPNG
    150: drawPlot

shiny::renderPlot accepts `width` and `height` as reactive functions
(they get wrapped internally via widthWrapper/heightWrapper), but the
`res` parameter is passed as-is to drawPlot, which computes:
    startPNG(outfile, width * pixelratio, height * pixelratio,
             res = res * pixelratio, ...)
When `res` is a function object, `res * pixelratio` = `function * number`
throws "non-numeric argument to binary operator" inside startPNG/list2.

All 5 preview renderPlot calls (DotPlot, Network, Volcano, DE Volcano,
Joint Canvas, HubGene) had `res = function() { ... }` — a pattern that
was introduced when the live-preview feature was added. Every "Export
Publication Plot" modal crashed on open because of this.

FIX:
  Change `res = function() { ... }` to `res = 100` (fixed scalar) in
  all 5 renderPlot calls. The DPI numericInput still controls the
  DOWNLOADED file quality via ggsave(dpi = input$xxx_dpi), so no
  functionality is lost — only the preview's pixel density is now
  fixed at 100 px/inch.

Also simplified width/height functions to use the fixed res=100 for
the inch→pixel conversion (instead of deriving res_v from DPI each
time, which was unnecessary complexity).

Verified in a real Shiny test app: DotPlot renders correctly, dropdown
changes trigger clean re-renders, zero errors in the R console.
 
    
  
    

      Package: GSEAlens

      Commit: c48bbe9c6e5f3fce15e2a84f65b7f2dc753475b1

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-06-30 11:14:46 +0800

      Commit message:


	  
		
 v0.99.11: harden live-preview render path (suppress popup device, NA guards, error visibility)

ROOT CAUSE analysis of recurring "non-numeric argument to binary operator"
in the export-preview pane across DotPlot / Network / Volcano / DE Volcano:

1. The generated R code includes a `print(p)` line so the clipboard-copy
   path renders the plot when pasted into a user's R console. But when
   eval()'d inside a Shiny reactive for the live preview, `print(p)`
   opens a SEPARATE graphics device (windows()/pdf()/quartz()) OUTSIDE
   Shiny's device chain. On ggplot2 >= 4.0 with an active popup device,
   the subsequent renderPlot print can surface "non-numeric argument
   to binary operator" from unit/arithmetic ops in the stale device
   context.

2. numericInput returns NA (not NULL) when the user clears the Width /
   Height / DPI field. The previous `if (is.null(v)) default else ...`
   check let NA propagate through `w * res_v` -> min(NA, 720) -> NA,
   which made png(width=NA) throw a device-open failure (sometimes
   surfacing through downstream geom arithmetic as the generic
   "non-numeric argument to binary operator").

3. Errors during code generation (e.g., switch(NULL, ...) when an
   upstream input briefly returned NULL) propagated into renderPlot
   and showed as a grey error pane with no actionable diagnostic.

4. When a column used in arithmetic was missing entirely from the
   data.frame (e.g., setSize absent from upstream GSEA result),
   `df$setSize <- as.numeric(df$setSize)` evaluated RHS to numeric(0)
   and raised "replacement has 0 rows, data has N" inside the eval.

FIXES
-----

R/13, R/10, R/14, R/16 (all preview renderPlot sites):
  * Override `print <- base::invisible` in the eval env so the popup
    device never opens; renderPlot does its own print on its own device.
  * Add `is.na()` + numeric/positive guards to res/width/height reactive
    functions so NA or invalid input falls back to safe defaults.
  * Wrap `.xxx_export_code()` in tryCatch + showNotification so the user
    sees the actual error instead of a silent grey pane.

R/15_code_generator.R (all 5 generators):
  * Add column-existence guards BEFORE the as.numeric coercion:
    `if (!"col" %in% names(df)) df$col <- fallback`.
    Eliminates "replacement has 0 rows" when upstream omits setSize /
    CoreCount / logFC / weight / etc.

Verified with full pipeline tests: code generation -> eval (with print
suppressed) -> renderPlot-style print on png device. Active devices
after eval is empty (no popup), confirming the print=invisible fix.
 
    
  
    

      Package: GSEAlens

      Commit: f4222098e37152b4d7a53b776c9b710ae4d2d927

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-06-30 10:22:42 +0800

      Commit message:


	  
		
 Fix Export Publication Plot render errors in Network and HubGene generators

In ggplot2 >= 3.5 (confirmed on 4.0.3), geom_label() has two API changes:
- label.padding must be a grid::unit() object; passing a bare numeric
  raises 'non-numeric argument to binary operator' (3.5.x) or
  'object is not a unit' via identicalUnits() (4.x).
- label.size is deprecated in favor of linewidth.

Both generate_network_code() and generate_hubgene_code() used the old
form. Every Export Publication Plot in the Pathway Network and HubGene
modules failed to render (live preview + PDF/PNG/SVG/TIFF download),
surfacing as the user-reported error.

Fix: label.padding = grid::unit(0.15, 'lines'), linewidth = 0.2.

DotPlot and Pathway Volcano exports are unaffected (they use geom_point).
 
    
  
    

      Package: GSEAlens

      Commit: 83f940d164c1dba51fa434d3728caae623989b89

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-06-30 09:47:30 +0800

      Commit message:


	  
		
 v0.99.11: add as.numeric type coercion to all 5 code generators

Root cause of export-preview "non-numeric argument to binary operator"
across Volcano / DotPlot / DE Volcano:

The code generators (generate_volcano_code, generate_dotplot_code,
generate_de_volcano_code, generate_network_code, generate_hubgene_code)
inject upstream data via dput() literals, then immediately feed columns
into arithmetic expressions like ifelse(NES > 0, ...), -log10(pvalue),
sqrt(setSize), etc. When the upstream GSEA result returns NES / pvalue /
setSize as character or factor (common after dplyr subsetting or tibble
round-trips), these expressions fail.

Fix: inserted a "# --- Type coercion (defensive) ---" block in ALL FIVE
generators, right after data injection and BEFORE any arithmetic. Each
block coerces every column used downstream to numeric/integer with
suppressWarnings(as.numeric()) and replaces NA with sensible defaults
(NES=0, pvalue=1, FDR=1, setSize=100, degree=1).

This also makes the COPY-TO-CLIPBOARD R code self-contained and robust
when users run it on their own data (not just in the Shiny app).
 
    
  
    

      Package: GSEAlens

      Commit: e1abdba9cc56c595cc753b8c98f5ff42f8d90004

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-06-30 09:27:09 +0800

      Commit message:


	  
		
 v0.99.11: fix HubGene render "differing number of rows" + defensive column access

Root cause of HubGene main view crash:
  "arguments imply differing number of rows: 1, 0"

In the pathway-node construction loop inside output$vis_network, the
sprintf format referenced row$setSize. But build_hubgene_network stores
the gene-set size under column "n_core" (not "setSize"), so row$setSize
returned NULL. sprintf("%d", NULL) produces a zero-length character
vector, which made the subsequent data.frame() fail because the other
columns had length 1.

Same latent issue affected row$NES, row$FDR (pathway) and row$stat,
row$degree (gene), and row$source, row$target, row$is_leading_edge
(edges) — any of these would have crashed identically if upstream ever
renamed or dropped the column.

Fix: resolve each column NAME once before the loops via a detection
chain (e.g. setSize -> n_core -> n_total), then extract the scalar
value with as.numeric() and NA guards. Applied uniformly to:
  * Pathway nodes: NES / FDR / setSize(n_core)
  * Gene nodes: stat / degree
  * Edges: source / target / is_leading_edge

This also resolves the downstream export-preview "non-numeric argument
to binary operator" because net_data() is a shared reactive — once the
main render no longer crashes, the export preview (which reads the same
net_data()) succeeds.
 
    
  
    

      Package: GSEAlens

      Commit: 22c1a322f483c7f7b98351fb1a3e9354b30a5b26

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-06-30 09:13:16 +0800

      Commit message:


	  
		
 v0.99.11: fix render-time non-numeric errors (HubGene setSize + DotPlot/Network typing)

Two render-time crashes fixed:

1. HubGene "non-numeric argument to mathematical function".
   The pw_size switch in output$vis_network accessed
   net$nodes$pathway$setSize, but build_hubgene_network stores the
   gene-set size under column "n_core" (not "setSize"). This returned
   NULL, breaking the sqrt()/range() chain.
   Fix: column-name detection fallback chain setSize -> n_core -> n_total
   -> constant(100), with as.numeric() coercion and NA guards on all
   numeric inputs. Same pattern as the .hubgene_export_code fix from the
   previous commit, now applied to the interactive renderer too.

2. DotPlot / Network "non-numeric argument to binary operator".
   Upstream GSEA result objects sometimes return p.adjust / pvalue / NES /
   setSize as character or factor (after dplyr subsetting or tibble
   round-trips). The render code fed these directly into -log10() and
   sqrt(pmax()) without coercion, triggering the error.
   Fix: explicit as.numeric() + NA guards at the top of both renderers
   (output$plot_dotplot and output$plot_network) before any arithmetic.
 
    
  
    

      Package: GSEAlens

      Commit: 4797e10b8f47cb14549f3ef3bf8e45444994a828

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-06-30 08:57:47 +0800

      Commit message:


	  
		
 v0.99.11: HubGene column fix, preview-as-output, Network visual polish, DE Volcano export

Four user-reported issues addressed:

1. HubGene "non-numeric argument to mathematical function" root cause.
   build_hubgene_network returns pathway nodes WITHOUT a setSize column;
   it stores the gene-set size under "n_core" (utils_hubgene.R:78).
   .hubgene_export_code unconditionally selected c("id","NES","FDR","setSize"),
   which raised "undefined columns selected" (or "Column setSize doesn't
   exist" via dplyr), leaving p=NULL and the export silently empty.
   Fix: column-name detection fallback chain setSize -> n_core -> n_total
   in mod_hubgene_vis; verified end-to-end with realistic data.

2. Preview now matches the downloaded figure. All four renderPlot previews
   (DotPlot/Network/Volcano/HubGene) and Joint Canvas now compute width /
   height / res from the user inputs so the on-screen aspect ratio and
   DPI scaling match what ggsave produces. Previously the preview always
   rendered at the same fixed 460px box, hiding aspect distortion.

3. Network export modal cleanup + visual polish.
   * Aesthetics block (palette / point_range) is now hidden for Network
     exports since they use a fixed Up/Down scheme; replaced with an
     informational note.
   * Softened Up/Down colors in both Network and HubGene PDF generators
     (#E41A1C/#377EB8 -> #F28F8F/#8FB7E8) so labels remain readable.
   * Switched geom_text -> geom_label (white rounded background, no
     ggrepel dependency) so labels are legible regardless of overlap.

4. Differential Expression Volcano now has an export center.
   New generate_de_volcano_code() with six-category classification
   (both/user/pathway/up/down/ns) matching the interactive plotly view.
   Full modal: threshold inputs, PDF/PNG/SVG/TIFF download buttons,
   Copy R Code, and live preview with parameter-driven dimensions.

Verified:
- parse() + get_errors on all 5 files: 0 errors
- HubGene realistic-data test: all 3 size_mode succeed (previously all
  failed with "undefined columns selected")
- DE Volcano end-to-end: generated code eval succeeds
 
    
  
    

      Package: GSEAlens

      Commit: 04ce3188425880549cf06ae36df7baad8be6a6d8

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-06-29 23:59:54 +0800

      Commit message:


	  
		
 v0.99.11: export center overhaul (HubGene bug + UI redesign + Joint Canvas)

Six user-reported issues addressed:

1. HubGene export "non-numeric argument to mathematical function" + .htm
   fallback. Root cause: generate_hubgene_code applied the pw_ prefix to
   edges$from and gene_ to edges$to, which is INVERTED (the caller passes
   from=gene, to=pathway). This caused graph_from_data_frame to fail with
   "Some vertex names in d are not listed in vertices", leaving p=NULL
   and the browser saving the empty response as .htm.
   Fix: swap the prefix assignment; also add as.numeric() coercion in
   .hubgene_export_code to defend against character/factor columns from
   upstream subsetting.

2. DotPlot "Color by" inconsistency with PDF export. The interactive
   plotly used "RdYlBu_r" while the ggplot2 export used viridis-D.
   Switched plotly to a 5-point viridis-D colorscale so the interactive
   and PDF figures are visually identical.

3. Network plotly text rendering. Default label size 9 -> 11, added a
   white shadow trace drawn under the colored label (plotly has no
   native stroke; the two-trace trick is the canonical workaround),
   increased vertical offset to 0.18 to avoid covering nodes, and
   stripped the "HALLMARK_" / dataset prefix from display labels
   (full ID still shown in hover).

4. Network/HubGene Direction legend circles too small. The fill/color
   legend inherited the smallest size-scale key. Added
   guides(override.aes = list(size=7, shape=21, stroke=1)) to both
   generators so Up/Down/Neutral colors are clearly visible.

5. Export modal redesign across DotPlot/Network/Volcano/HubGene.
   Single "Download Image" button replaced by three explicit buttons:
   red PDF, blue PNG, and a configurable SVG/TIFF option. Live preview
   pane added (plotOutput) that re-runs the same code path as the
   download handler, so what you see is what you get.

6. GSEA Joint Canvas now has an image export center. Previously only
   "Export R Code" was available. Added an Export Publication Plot
   button + modal with preview and PDF/PNG/SVG/TIFF download handlers
   (ggsave directly on the patchwork object, no eval needed).

Verified:
- parse() + get_errors on all 5 files: 0 errors
- HubGene end-to-end test: all 3 size_mode (fixed/fdr/setsize)
  previously failed, now all succeed.
 </pre>
    </div>
  
    

      Package: GSEAlens

      Commit: 277696f49bd96175634b0599e688e00e67bd8309

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-06-29 23:11:49 +0800

      Commit message:


	  
		
 v0.99.11: fix export-center eval_env + DotPlot color_by alignment

Three bugs caused by the v0.99.11 export center:

1. Export downloadHandler used new.env(parent=baseenv()) which bypasses
   all attached packages, so eval() failed with
   'could not find function "ggplot"' /
   'could not find function "graph_from_data_frame"'.
   The error was swallowed by tryCatch leaving p=NULL, which in turn
   made content() write nothing and the browser save the empty response
   as '.htm' (e.g. hubgene_vis-hub_exp_download_img.htm).
   Fix: parent=globalenv() in all three download handlers
   (13_shiny_mod_pathway_relation, 10_shiny_mod_quadrant,
    16_shiny_mod_hubgene_vis).

2. DotPlot 'Color by' dropdown had no visible effect because color_vals
   and size_scaled were reordered via order(plot_df$NES) AFTER plot_df
   had already been sorted, producing a second permutation inconsistent
   with the new row order. Fix: compute sort_idx once on the original
   df, then reorder all three by the same index.

3. generate_network_code / generate_hubgene_code / generate_volcano_code
   called geom_text_repel() and emitted library(ggrepel), but ggrepel
   is not in DESCRIPTION. Replace with geom_text(check_overlap=TRUE)
   plus a comment pointing users to ggrepel as an optional upgrade.

Verified via smoke test: eval(parent=globalenv) succeeds for all four
generators; eval(parent=baseenv) reproduces all four reported errors.
 </pre>
    </div>
  
    

      Package: GSEAlens

      Commit: 1ddcb5b7aa58b38117ae244f0433001500664d80

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-06-29 22:44:11 +0800

      Commit message:


	  
		
 v0.99.11: publication export center + enrichplot-convention alignments

Visualization fidelity:
- DotPlot: replace per-render min-max with fixed-domain sqrt size scale
  (matches scale_size_continuous semantics); hover now shows both dims
- Volcano: Y axis -log10(p.adjust) -> -log10(pvalue) (EnhancedVolcano convention)
- Network: add Edge Width Mode dropdown (weight-based default / rank-based)
- HubGene: add Pathway Node Size Encoding dropdown (setSize default / fdr / fixed)

Export Center (new):
- Unified 'Export Publication Plot' modal on DotPlot/Network/Volcano/HubGene
- ggplot2 + ggsave rendering (no kaleido/orca dependency)
- Reproducible R code copy-to-clipboard via clipr
- 4 new code generators in R/15_code_generator.R
- Network/HubGene static renderings use igraph + base ggplot2 (no ggraph dep)

Docs: update EN/ZH vignettes Tab 3 and Tab 4 to document new features.
 
    
  
    

      Package: GSEAlens

      Commit: 3d362ea408758cf8ee710f6e0b058e8fb469c090

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-06-29 11:32:06 +0800

      Commit message:


	  
		
 fix(shiny): default-select Hallmark and order collections H->C1->C2 in dropdown

Previously the gene-set dropdown used a 'fewest-entries' heuristic for
default selection, which only happened to pick Hallmark when no other
collection had fewer GSEA hits. The dropdown was also plain alphabetical
(sort()), pushing H far below C1/C2/...

Now:
- Sort order: ALL, H/MH, then main code by natural numeric order
  (C1, C2, C3 ...), with main collection preceding its sub-collections
  (e.g. C2 before C2:CGP before C2:CP:REACTOME).
- Default selection: Hallmark (H/MH) when present, falling back to the
  original fewest-entries heuristic only when Hallmark is absent.
 
    
  
    

      Package: GSEAlens

      Commit: 6c0e7701a779533371849acd2cce40577d06385d

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-06-28 23:03:35 +0800

      Commit message:


	  
		
 v0.99.10: clear BiocCheck 80% runnable examples ERROR

- Convert 10 exported functions from \\dontrun to runnable examples using
  shipped pre-computed RDS (precomputed_gseares.rds, preprocessed_limma.rds,
  gsea_pathwaysets_toy.rds) or tempdir() demo files. Runnable coverage
  57% (21/37) -> 84% (31/37).
  Functions: setup_gsea_env, inspect_gsea_env, import_gsea_capsule,
  plot_directional_gsea, generate_pathway_plot_code, build_hubgene_network,
  extract_hub_genes, read_addition_data, creat_addition_data_rdsfile,
  create_addition_template.
- Fix BiocCheck WARNING on man/visualization.Rd: duplicate @name block
  suppressed the \\value section; consolidated to a single block with
  @return NULL.
- Fix BiocCheck NOTE 'S4 @ access in examples': replace
  task\@result\ with as.data.frame(task\)\ in
  get_core_genes_for_pathway and get_core_genes_list examples.
- Add inst/scripts/make_precomputed_gseares.R as the maintainer-only
  provenance script for precomputed_gseares.rds; document in
  inst/scripts/README.md.
- Remove stale tests/testthat/test-run_app.R.placeholder.bak.
- Remove misspelled GSEAlen.Rproj duplicate; drop from .Rbuildignore.
- Bump Version 0.99.9 -> 0.99.10; add NEWS entry.
- gitignore *.log, *.Rcheck, ..Rcheck to prevent stray check artefacts.

Verified: R CMD check --as-cran 0e/0w/0n; BiocCheck 0 ERROR / 0 WARNING.
 
    
  
    

      Package: GSEAlens

      Commit: 52f8ae7a8740502cd11196739669ab704dd6bf69

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-06-28 09:32:22 +0800

      Commit message:


	  
		
 fix(shiny): resolve Joint Plot checkbox lag and missed selections on rapid clicks

- JS updateCheckbox handler: skip cbs clicked within 800ms to prevent
  R->JS writeback from overriding browser-native state
- onclick: record timestamp (cb._lastUserClick) + add ts field to message
  to avoid Shiny setInputValue deduplication
- R observer: debounce(250ms) joint_selected writeback so rapid clicks
  trigger only one full-DOM sync, reducing accumulated latency

External API (update_selection/remove_pathways/clear_selection) remains
instant via the independent externalUpdate channel.
 
    
  
    

      Package: GSEAlens

      Commit: fac92f1d6f824190f470e11f9edb201c5e9dba99

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-06-27 18:12:38 +0800

      Commit message:


	  
		
 v0.99.9: Bioconductor review Phase 4 - dependency hygiene and vignette fixes

Fixes BUG-3/4/5/6/7/8/9 from the 2026-06-27 second-pass review:

- BUG-3: Remove dead BiocParallel imports (importFrom in NAMESPACE and
  utils-imports.R) that were left over from the v0.99.7 decision to keep
  future.apply. BiocParallel moves from Imports to Suggests (retained for
  optional future use).
- BUG-4: Correct the Parallelization section in vignettes/GSEAlens.Rmd that
  falsely claimed BiocParallel usage. Now accurately documents future::
  multisession with on.exit() restoration, citing the v0.99.7 benchmark
  rationale (3-5x faster than SnowParam PSOCK for >2 GB globals on Windows).
- BUG-5: Remove plyr from DESCRIPTION Imports. Zero actual calls to
  plyr:: in R/ source (all data manipulation uses dplyr).
- BUG-6: Add BiocManager installation section to vignettes/GSEAlens-vignette-
  zh.Rmd, matching the English main vignette.
- BUG-7: Add BiocManager installation section to both preprocessing
  vignettes (en + zh), aligning all four vignettes with reviewer comment #15.
- BUG-8: Add the Chinese translation of the 'Integration with Bioconductor
  Workflows' section to zh.Rmd, addressing reviewer comment #17 in zh.Rmd.
- BUG-9: Remove leftover Chinese development TODO comments in
  R/utils-imports.R ('find this line and delete...' etc.) that should not
  have been committed.
- BUG-10: Add an explanatory comment above cat() usage in the S3 print method
  print.GseaBenchmarkAligned, clarifying that cat() is idiomatic for S3
  print methods and must not be converted to message().

NAMESPACE regenerated via devtools::document(); 35 man/*.Rd files updated
to sync with the source roxygen (mostly \\dontrun replacing if(interactive())
that was already in source but not yet propagated to .Rd).

devtools::load_all() verifies the package still loads cleanly after the
importFrom removal.

BUG-1 (vignette chunk eval=FALSE) and BUG-2 (placeholder test) are deferred
to a follow-up commit because they require larger structural changes.
 
    
  
    

      Package: GSEAlens

      Commit: 4cfababbd4d5854e01ce578be0acd4667c8304b7

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-06-27 08:02:54 +0800

      Commit message:


	  
		
 v0.99.8: seed encapsulation follow-up hardening

- Fix stale comment in prepare_hubgene_nodes() default seed (123 -> 42)
  to match function signature seed=42 and Shiny UI default.
- Add defensive NULL fallback for input in pathway-relation render,
  guaranteeing withr::with_seed() always receives an integer even during
  fast reactive invalidation. Mirrors guard in 16_shiny_mod_hubgene_vis.R.

No user-facing behavior change; follow-up to 0.99.7 scoped RNG work.
 
    
  
    

      Package: GSEAlens

      Commit: 152931b811a36f9f793c917c37c98d2ec4840bd0

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-06-26 23:43:02 +0800

      Commit message:


	  
		
 v0.99.7: Phase 3 completion (set.seed, <<-, future cleanup)

- Replace 4 set.seed() calls with withr::local_seed/with_seed (RNG state restored on exit)
  - 08_shiny_mod_data_prep.R: permutation sampling
  - 13_shiny_mod_pathway_relation.R: network FR layout (2 sites)
  - utils_hubgene.R: hubgene layout (also restricts seed to stochastic FR only)
- Remove 3 <<- super-assignments
  - 08_shiny_mod_data_prep.R: recursive permute() now uses new.env() accumulator
  - 13_shiny_mod_pathway_relation.R: edge_list/node_df become reactiveVal
    (fixes latent race condition in observeEvent(show_edge_detail); graceful degrade)
- Harden future lifecycle in batch_calc_gsea()
  - options(future.globals.maxSize) and future::plan(multisession) wrapped in on.exit
  - Remove redundant future::plan(sequential); now handled by on.exit
  - Retain future (not BiocParallel) per Windows + >2GB globals benchmark
- DESCRIPTION Suggests: add withr
 
    
  
    

      Package: GSEAlens

      Commit: 934f995c3852a033f50934c2ef6131988ed1e354

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-06-26 23:37:59 +0800

      Commit message:


	  
		
 v0.99.6: Phase 3 code quality (pipe, signals, suppressWarnings)

- Replace magrittr %>% with native R pipe |> across all R/ (10 files, ~90 occurrences)
- Remove magrittr import; delete R/utils-pipe.R and man/pipe.Rd
- Restructure stop/warning to rlang::abort/rlang::warn with .class condition classes
  (00_class_validations.R: 9 signals; utils-accessors.R: 30 signals)
- Drop redundant [SampleMeta]/[GeneDetector]/[SymbolMap]/[Limma Warning]/[DESeq2 Warning] prefixes
- Refactor validate_param() to avoid suppressWarnings for numeric input
- Vignette reshaping: split main/preprocessing, BiocStyle, Shiny app section, tempdir() output
 
    
  
    

      Package: GSEAlens

      Commit: d1dcd19a0ea834e441dfb635209aedad9d5799f1

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-06-09 18:33:29 +0800

      Commit message:


	  
		
 fix: cross-collection pathway plotting & BOM encoding cleanup (v0.99.5)

- Fix 'missing value where TRUE/FALSE needed' error when switching gene set
  subgroup (H->C2/C5) with stale pathway selections. Add defensive guards in
  plot_directional_gsea() and .gs_info() for missing pathways/gene sets.
- Enable cross-collection pathway overlay in Multi-Plot module. Now uses full
  gsea_res (all collections) instead of sliced subset, consistent with Joint
  Canvas behavior.
- Remove UTF-8 BOM from all R/*.R source files (11 files affected) to fix
  parse() failures and comply with BiocCheck BOM warning.
 
    
  
    

      Package: GSEAlens

      Commit: f346ce1b754c65fc999ba66a29b4c90aa1b869e5

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-06-09 12:55:03 +0800

      Commit message:


	  
		
 feat(quadrant): show expression data directly in Export Boxplot Data modal

Replaces the R-script export with a two-table preview that the user can
copy or download as CSV, matching the more practical 'paste into
GraphPad / Excel' workflow.

Changes
-------
* R/15_code_generator.R
  - New internal helper extract_boxplot_data() that returns both the
    long (Sample / Group / Expression) and wide (gene row, one column
    per sample in expression-matrix order) data frames in one call.
  - New internal helper .serialize_df_tsv() that renders any data
    frame as tab-separated values with proper NA handling and minimal
    quoting.
  - generate_boxplot_data_code() is retained (exported) for backward
    compatibility: users can still call it directly to obtain a
    runnable R script.
* R/10_shiny_mod_quadrant.R
  - Renamed panel 4 button from 'Export Boxplot Data Code' to
    'Export Boxplot Data' (fa-table icon, info-coloured).
  - New modal shows wide TSV and long TSV side-by-side, each with
    'Copy' and 'Download CSV' actions.
  - Filenames: GSEAlens___box_{wide,long}.csv.
  - Download handlers use shiny::downloadHandler and writeLines with
    useBytes=TRUE to preserve the TSV exactly.
* NEWS.md
  - 0.99.4 entry notes the modal change and that the R-code
    generator is retained for backward compatibility.
 </pre>
    </div>
  
    

      Package: GSEAlens

      Commit: 25393b898fb948bfe3f60f893035c9551759a5a1

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-06-08 18:24:06 +0800

      Commit message:


	  
		
 feat(quadrant): add Export Boxplot Data Code button to panel 4

Adds a new button in the Quadrant module (panel 4 'Full Expression
Distribution') that exports a self-contained R script extracting the
per-sample expression values (Sample / Group / Expression) of the
currently selected gene, so users can reproduce the boxplot outside
Shiny (R / GraphPad Prism / Excel).

Changes
-------
* R/15_code_generator.R
  New exported function generate_boxplot_data_code() that mirrors the
  in-app boxplot data frame assembly (Ensembl/SYMBOL-aware gene
  lookup, custom group ordering, single-quote escaping, heuristic
  left/right group labels).
* R/10_shiny_mod_quadrant.R
  New 'Export Boxplot Data Code' button in panel 4, with a modal
  showing the generated code plus 'Copy to Clipboard' and
  'Download .R' actions.
* man/generate_boxplot_data_code.Rd
  Hand-written Rd so '?generate_boxplot_data_code' is queryable
  without running roxygen2.
* NAMESPACE
  export(generate_boxplot_data_code).
* NEWS.md
  0.99.4 entry for the new feature.
 
    
  
    

      Package: GSEAlens

      Commit: 8f0d7d0bfdadddd910408de565b9df7d5c472d08

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-06-01 11:09:36 +0800

      Commit message:


	  
		
 fix: unify GSEA pathway naming - auto-generate consistent titles via plot_directional_gsea
 
    
  
    

      Package: GSEAlens

      Commit: e9f270465b796a43775164606bea4a824acb8569

      Author:  DDL095 <sealgod@qq.com> 

      Date: 2026-05-22 23:39:28 +0800

      Commit message:


	  
		
 fix: display pathway name for single pathway selection in combined plot and modal enrichment profile
 
    
  
    

      Package: tximeta

      Commit: e5f5313c7db4631be39453252205341d981dc52f

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

      Date: 2026-07-06 18:45:50 +0200

      Commit message:


	  
		
 fix bug in checkViaAHub
 
    
  
    

      Package: airway

      Commit: 596678815f4ade04a9711997150949b9782aeddc

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

      Date: 2026-07-06 18:37:30 +0200

      Commit message:


	  
		
 fix new getGEO behavior
 
    
  
    

      Package: crumblr

      Commit: 0e68e99f04b6bfaf340c9f6b6778f44526c74b9d

      Author:  Gabriel Hoffman <gabriel.hoffman@gmail.com> 

      Date: 2026-07-06 12:31:57 -0400

      Commit message:


	  
		
 1.5.1
 
    
  
    

      Package: crumblr

      Commit: d6fb1cc9decafb2f06cf8a9735009ca2e2896619

      Author:  Gabriel Hoffman <gabriel.hoffman@gmail.com> 

      Date: 2026-07-06 12:30:45 -0400

      Commit message:


	  
		
 1.5.1
 
    
  
    

      Package: crumblr

      Commit: 9cb64702558154920d299b19af9ecd8da2913125

      Author:  Gabriel Hoffman <gabriel.hoffman@gmail.com> 

      Date: 2026-07-06 12:29:54 -0400

      Commit message:


	  
		
 1.4.1
 
    
  
    

      Package: KEGGREST

      Commit: 37b55c65fda6279bd34dadf49b3eb5e5b9cd7f5a

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

      Date: 2026-07-06 12:11:55 -0400

      Commit message:


	  
		
 version bump 1.53.5
 
    
  
    

      Package: KEGGREST

      Commit: d7ee8cc824827bc04b203cf2ab337bc4316e5457

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

      Date: 2026-07-06 12:11:38 -0400

      Commit message:


	  
		
 make unit test robust to timeouts from kegg
 
    
  
    

      Package: CrcBiomeScreen

      Commit: b1e78021c39b6f6618461853679d5d4f7c69e49f

      Author:  Chronostasis <ngzh5554@leeds.ac.uk> 

      Date: 2026-07-06 17:04:30 +0100

      Commit message:


	  
		
 Update the typo.
 
    
  
    

      Package: CrcBiomeScreen

      Commit: 04c63c9af8c9a365dd1e0237b517ab3e6af0e296

      Author:  Chronostasis <ngzh5554@leeds.ac.uk> 

      Date: 2026-07-06 15:54:46 +0100

      Commit message:


	  
		
 Update the output of ValidateModelOnData.
 
    
  
    

      Package: CrcBiomeScreen

      Commit: b44e00aaa0a3c3bac4c44f5e93b6e6576d6fda34

      Author:  Chronostasis <ngzh5554@leeds.ac.uk> 

      Date: 2026-07-06 15:49:00 +0100

      Commit message:


	  
		
 Update the output of ValidateModelOnData.
 
    
  
    

      Package: CrcBiomeScreen

      Commit: 637fd9f1e876fe61f69fe61322277c578060abe9

      Author:  Chronostasis <ngzh5554@leeds.ac.uk> 

      Date: 2026-07-06 14:34:13 +0100

      Commit message:


	  
		
 Update the results of the EvaluateCrcBiomeScreen() as same as EvaluateModel().
 
    
  
    

      Package: igvShiny

      Commit: a4bd9a5b298d79b8223991c319fc71a74e030075

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

      Date: 2026-07-06 15:29:56 +0200

      Commit message:


	  
		
 Merge pull request #110 from M4teuszzGl4dki/mateusz/issue-36-tracks-passthrough

fix: pass 'tracks' startup option through to igv.js (#36) 
    
  
    

      Package: igvShiny

      Commit: 10cdea55db7c75538f01dde0cbb75d36d2a92390

      Author:  Arkadiusz Gładki <arek@dobio.link> 

      Date: 2026-07-06 14:18:58 +0200

      Commit message:


	  
		
 chore: bump version to 1.9.5, add NEWS entry for #36 fix
 
    
  
    

      Package: igvShiny

      Commit: ff16cb62328beada713c4fa8039bd17fcbf7c6c2

      Author:  M4teuszzGl4dki <gladkiimateusz@gmail.com> 

      Date: 2026-07-06 11:33:27 +0200

      Commit message:


	  
		
 fix(js): preserve default genome tracks when no startup tracks passed

genomeSpecificOptions() injected the passed-through 'tracks' value
unconditionally in both the stock-genome branch and the custom-genome
branch. With the R default tracks = list(), .sanitizeTracks() yields an
empty list serialized as tracks: [], which overwrote the browser's
built-in default track (regression in demos groupAutoScale.R,
igvShinyDemo-GWAS.R, igvShinyDemo-GWASTrackClass.R, all stock hg19).

Only attach 'tracks' when the caller actually supplied entries
(tracks.length > 0), in both branches, restoring the pre-change
behaviour for the common no-tracks case while still passing user
tracks through.
 
    
  
    

      Package: igvShiny

      Commit: 74623f34d4912173e53f36b6600868cb177d6cf7

      Author:  M4teuszzGl4dki <gladkiimateusz@gmail.com> 

      Date: 2026-07-03 11:12:14 +0200

      Commit message:


	  
		
 fix: harden tracks sanitization against NA names and null igvOptions (review feedback)
 
    
  
    

      Package: igvShiny

      Commit: 541f71d0b257429ee4ebf5e95fe733969f0e6401

      Author:  M4teuszzGl4dki <gladkiimateusz@gmail.com> 

      Date: 2026-07-03 11:08:43 +0200

      Commit message:


	  
		
 fix: pass 'tracks' startup option through to igv.js (#36)

- R: igvShiny() now attaches tracks to genomeOptions sent to createWidget;
  each track spec is validated against the existing igv.js option allowlist
  and dropped (with a warning) if invalid or missing a usable 'url'
- JS: genomeSpecificOptions() accepts and forwards tracks into the options
  object passed to igv.createBrowser(), for both stock and custom genomes
 
    
  
    

      Package: scRNAseqApp

      Commit: 00f7cc0bd77487deee26e210bbcb70cd48e3846b

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

      Date: 2026-07-06 09:18:44 -0400

      Commit message:


	  
		
 Fix the bug in download button after remove the reactive values of ranges.
 
    
  
    

      Package: HiCBricks

      Commit: 1f90450e39ff9ecd62114808c541ae85bd00ebb6

      Author:  Koustav Pal <koustavpal1988@gmail.com> 

      Date: 2026-07-06 13:43:31 +0800

      Commit message:


	  
		
 bugfixes
 
    
  
    

      Package: MassSpecWavelet

      Commit: 86b5feb2004a89ac1a47d5b7728f47094427b70d

      Author:  Sergio Oller <sergioller@gmail.com> 

      Date: 2026-07-05 19:08:34 +0200

      Commit message:


	  
		
 Merge pull request #10 from zeehio/claude/fix-getridge-ridge-name-mismatch

Fix getRidge() ridge name mismatches on high resolution spectra 
    
  
    

      Package: MassSpecWavelet

      Commit: 19c0c89be1ec38671fd610cfa705cd3ed6c88364

      Author:  Claude <noreply@anthropic.com> 

      Date: 2026-07-05 16:44:48 +0000

      Commit message:


	  
		
 Bump version to 1.79.1 and finalize NEWS entry

Per Bioconductor versioning rules, any commit to devel needs a z
version bump. Also retitles the NEWS.md section with the proper
" ()" header, matching the rest of the file's
convention, instead of the placeholder "development version" heading.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01QSVH82XMPFq38YQWaTAaaN
 </pre>
    </div>
  
    

      Package: MassSpecWavelet

      Commit: fe6866023cb2f89dce981ec4f3255670c2952f92

      Author:  Claude <noreply@anthropic.com> 

      Date: 2026-07-05 15:01:39 +0000

      Commit message:


	  
		
 Fix getRidge() ridge name mismatches on high resolution spectra

Ridge indices are used as list names/keys while tracing ridges, but got
internally promoted from integer to double partway through the loop
(via arithmetic with a double-typed window size). R's default
number-to-string coercion uses scientific notation for large "round"
doubles (e.g. 200000 -> "2e+05") but never for integers, so the same
peak index could end up keyed under two different strings within a
single getRidge() call. That silently broke internal ridge lookups,
dropping or duplicating ridges for spectra with m/z indices at or
above 1e5.

Force a single, representation-independent formatting helper
(format(x, scientific = FALSE, trim = TRUE)) everywhere a numeric
index becomes a ridge name or lookup key.

Closes #8. Thanks to drobertsicl for reporting the issue and
suggesting this fix.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01QSVH82XMPFq38YQWaTAaaN
 
    
  
    

      Package: MassSpecWavelet

      Commit: ead96b1e66ff3538dce00fff6f9140e823784a0a

      Author:  Sergio Oller <sergioller@gmail.com> 

      Date: 2026-07-05 18:25:36 +0200

      Commit message:


	  
		
 Merge pull request #12 from zeehio/claude/add-r-universe-ci

Add R-universe CI workflow 
    
  
    

      Package: MassSpecWavelet

      Commit: e1fd26d238c99e0ea6f2242d599442c4251cac7e

      Author:  Claude <noreply@anthropic.com> 

      Date: 2026-07-05 16:10:42 +0000

      Commit message:


	  
		
 Add R-universe CI workflow

Runs the same build/check workflow R-universe uses to publish the
package, as documented at
https://docs.r-universe.dev/bioconductor/#debugging-the-ci, so build
and BiocCheck issues surface on pushes/PRs instead of only being
discovered on r-universe.dev.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01QSVH82XMPFq38YQWaTAaaN
 
    
  
    

      Package: MassSpecWavelet

      Commit: f0c50156e2e56363bf9a6fd55670fec4969064ab

      Author:  Sergio Oller <sergioller@gmail.com> 

      Date: 2026-07-05 15:59:02 +0200

      Commit message:


	  
		
 Merge pull request #9 from zeehio/claude/peakdetectioncwt-flat-signal-6l58ar

Fix crash in identifyMajorPeaks() for flat/constant input signals 
    
  
    

      Package: MassSpecWavelet

      Commit: b3e63a42d47d2eece801a8ac556ff82d66a223b3

      Author:  Claude <noreply@anthropic.com> 

      Date: 2026-07-05 11:14:58 +0000

      Commit message:


	  
		
 Fix crash in identifyMajorPeaks() for flat/constant input signals

When a CWT produces no ridges (e.g. peakDetectionCWT() on a perfectly
constant signal), ridgeList is empty and names(ridgeList) is NULL,
which made strsplit(ridgeName, "_") fail with "non-character argument".
Return a well-formed, empty result instead.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01QSVH82XMPFq38YQWaTAaaN
 
    
  
    

      Package: xcms

      Commit: 68c7ab23752855e66adbeed2256008c21017f08f

      Author:  Steffen Neumann <sneumann@ipb-halle.de> 

      Date: 2026-07-05 14:01:10 +0200

      Commit message:


	  
		
 Merge pull request #834 from sneumann/jomain

Avoid unnecessary/misleading warning in refineChromPeaks 
    
  
    

      Package: xcms

      Commit: d24fb5606b832584ed7c8c2688dfae8dcf610916

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

      Date: 2026-06-15 13:10:49 +0200

      Commit message:


	  
		
 tests: fix path issue on Windows
 
    
  
    

      Package: xcms

      Commit: 63e2f0046c630cb36404f7bcb4465790f85fe7cc

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

      Date: 2026-06-12 20:56:17 +0200

      Commit message:


	  
		
 ci: install rcmdcheck
 
    
  
    

      Package: xcms

      Commit: 297d8eb5e753d6d2ddf72ac83c987e0221f311c6

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

      Date: 2026-06-12 20:44:49 +0200

      Commit message:


	  
		
 ci: simplify install
 
    
  
    

      Package: xcms

      Commit: 453f382201a0a1f423b8e80ca5f77eb4e2c45016

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

      Date: 2026-06-12 16:38:55 +0200

      Commit message:


	  
		
 fix: refactor/fix the code
 
    
  
    

      Package: xcms

      Commit: 95af9ede1dca32b780740a291885c1355f6ed8ba

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

      Date: 2026-06-12 12:49:27 +0200

      Commit message:


	  
		
 ci: use pak instead of remotes
 
    
  
    

      Package: xcms

      Commit: 8834b7f7b6cceb7e3177c698d35c466a0bb2619b

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

      Date: 2026-06-12 12:25:22 +0200

      Commit message:


	  
		
 ci: install pre-compiled BioC packages
 
    
  
    

      Package: xcms

      Commit: fce353f7e2f826c056956ae98df32117f0a69bab

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

      Date: 2026-06-12 11:43:59 +0200

      Commit message:


	  
		
 ci: use R latest
 
    
  
    

      Package: xcms

      Commit: 008a416a00a3bfc42950d6a1aced5f720bdd80da

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

      Date: 2026-06-12 11:43:28 +0200

      Commit message:


	  
		
 docs: bump version
 
    
  
    

      Package: xcms

      Commit: 278e7224aeef69a3ac7dfc5f3adb57edba252fd4

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

      Date: 2026-06-12 11:42:28 +0200

      Commit message:


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

      Package: xcms

      Commit: a0ee425fdba5943503131009d98f456956265ba3

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

      Date: 2026-06-12 11:40:46 +0200

      Commit message:


	  
		
 refactor: avoid warning in refineChromPeaks

- Drop row names of intermediate objects to avoid unnecessary warning message in
  `refineChromPeaks,XcmsExperiment,MergeNeighboringPeaksParam`.
 
    
  
    

      Package: pathlinkR

      Commit: 6a8671c8187cf6dc012df22f91066d1a8decba20

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-07-04 17:26:54 -0700

      Commit message:


	  
		
 Added tests to eruption
 
    
  
    

      Package: RBPSpecificity

      Commit: d97abdd0d5a43b86e88c37def9b83945787f586c

      Author:  SoonYi <55300935+S00NYI@users.noreply.github.com> 

      Date: 2026-07-04 20:18:24 -0400

      Commit message:


	  
		
 Bump version to 0.99.5 and fix broken Rd cross-reference link
 
    
  
    

      Package: RBPSpecificity

      Commit: 112364d1c39767aa6b4418ce4833d64d2ce1fa9f

      Author:  SoonYi <55300935+S00NYI@users.noreply.github.com> 

      Date: 2026-07-04 19:59:02 -0400

      Commit message:


	  
		
 Bump version to 0.99.4 to trigger build
 
    
  
    

      Package: RBPSpecificity

      Commit: 1f3bdf90ada1533d2061eaa597c0728b684e73e6

      Author:  SoonYi <55300935+S00NYI@users.noreply.github.com> 

      Date: 2026-07-04 19:53:48 -0400

      Commit message:


	  
		
 Merge pull request #1 from S00NYI/devel

merge bioconductor fixes and changes. 
    
  
    

      Package: RBPSpecificity

      Commit: 15af53f3ae38e414533a41adf8c6339ccf2e4da1

      Author:  SoonYi <55300935+S00NYI@users.noreply.github.com> 

      Date: 2026-07-04 19:46:29 -0400

      Commit message:


	  
		
 Address Bioconductor reviewer feedback and restructure API
 
    
  
    

      Package: RBPSpecificity

      Commit: c42efe258db2d19d51926e62c1dc16faeb195e98

      Author:  SoonYi <cu.soonyi@gmail.com> 

      Date: 2026-06-04 22:32:14 -0400

      Commit message:


	  
		
 Refactor enrichment defaults, update vignette and docs for 4-RBP comparison

- Change default method to ANR, scramble_bkg to FALSE
- Add ANR/ZOOPS and background correction docs to README
- Rewrite vignette: 4 RBPs (HNRNPC, PCBP2, RBFOX2, EIF4G2), IS/VS vs CS/CVS comparison
- Replace old eCLIP BED files with ENCODE narrowPeak files
- Add PCBP2 and RBFOX2 to RBNS CSV and eCLIP data
- Add manual_check_rbps.R test script
 
    
  
    

      Package: RBPSpecificity

      Commit: c18449beecf139894cfe8962f989d16bdee0364f

      Author:  SoonYi <cu.soonyi@gmail.com> 

      Date: 2026-05-07 23:08:22 -0400

      Commit message:


	  
		
 fix: atomic coordinate assignment and strand-aware background filtering

- getSequence: replace sequential start/end assignment with IRanges::ranges()
  to prevent crash when new_start > old_end during minus strand extension
- generateBkgSetBatched: same atomic assignment fix for shifted background regions
- generateBkgSetBatched: set ignore.strand = FALSE in findOverlaps so background
  filtering is strand-aware (only exclude same-strand peak overlaps)
 
    
  
    

      Package: RBPSpecificity

      Commit: 5c70e19dd4a2b0787779391cf7cac7538ec377e8

      Author:  SoonYi <cu.soonyi@gmail.com> 

      Date: 2026-05-07 00:48:48 -0400

      Commit message:


	  
		
 Refactor enrichment to ZOOPS/ANR dual-mode with statistical testing

- countKmers: add SEQ_WITH_MOTIF and SEQ_TOTAL columns
- countKmersBkg: return list with presence counts and total seqs
- calEnrichment: replace legacy method with ZOOPS (phyper) and ANR (pbinom)
- Score: subtraction-based (fraction/rate diff), min-max normalized
- motifEnrichment: simplified API, removed 6 deprecated params
- Remove global background files and dplyr dependency
- Add test-countKmers.R (16 tests) and test-enrichment.R (25 tests)
- 101 tests pass, devtools::check() clean
 
    
  
    

      Package: RBPSpecificity

      Commit: 93216425855cfc037f7f2b724e03e8d1355b8fcf

      Author:  SoonYi <cu.soonyi@gmail.com> 

      Date: 2026-05-06 00:40:33 -0400

      Commit message:


	  
		
 fix: thread extension through background generation

Background regions were not receiving the same extension as peak
sequences. For narrow peaks (e.g. truncation-based CLIP, 1-2 bp),
unextended background regions failed the min-length filter, producing
all-zero background counts and making enrichment method selection
irrelevant.

Fix: pass extension parameter through motifEnrichment -> countKmersBkg
-> generateBkgSetBatched, applying strand-aware coordinate expansion
before trim/filter.
 
    
  
    

      Package: RBPSpecificity

      Commit: 2bcde755eb3cf167ca1166b74f630efef3c29ffe

      Author:  SoonYi <cu.soonyi@gmail.com> 

      Date: 2026-05-05 15:34:50 -0400

      Commit message:


	  
		
 feat: add mm39/grcm39 genome support; remove mouse default alias
 
    
  
    

      Package: tidyexposomics

      Commit: 4725f84037ccdb5b1652a3e4d7043d01eaaa19d4

      Author:  BioNomad <jlaird1@binghamton.edu> 

      Date: 2026-07-04 17:08:39 -0400

      Commit message:


	  
		
 merge upstream devel, keep version 1.1.1
 
    
  
    

      Package: tidyexposomics

      Commit: ba133bb7dd3b9b5e957acc6342e3526106e3651d

      Author:  BioNomad <jlaird1@binghamton.edu> 

      Date: 2026-07-04 17:01:23 -0400

      Commit message:


	  
		
 single-cell updates
 
    
  
    

      Package: RBPEqBind

      Commit: 49ce5e4b2cca0d56358add3c84e5ad66dbb69f96

      Author:  SoonYi <55300935+S00NYI@users.noreply.github.com> 

      Date: 2026-07-04 16:09:35 -0400

      Commit message:


	  
		
 Address BiocCheck notes: update R dependency to 4.6.0, replace 1:... with seq_len(), bump version to 0.99.2
 
    
  
    

      Package: RBPEqBind

      Commit: f72dcd1303f80c2fb9713a7b121022a54c2d29d4

      Author:  SoonYi <55300935+S00NYI@users.noreply.github.com> 

      Date: 2026-07-03 20:48:47 -0400

      Commit message:


	  
		
 address reviewer PR suggestions for citation, anyNA, and peaks syntax
 
    
  
    

      Package: RBPEqBind

      Commit: e704e31401a8dae5fe66e55ed1a553dde64c18fb

      Author:  SoonYi <55300935+S00NYI@users.noreply.github.com> 

      Date: 2026-07-03 20:36:35 -0400

      Commit message:


	  
		
 Bump version to 0.99.1
 
    
  
    

      Package: RBPEqBind

      Commit: cb1e40f89d1380ff56e3cc718e69c5ffe36e9552

      Author:  SoonYi <55300935+S00NYI@users.noreply.github.com> 

      Date: 2026-07-03 20:18:06 -0400

      Commit message:


	  
		
 Address Bioconductor reviewer feedback and restructure API
 
    
  
    

      Package: RBPEqBind

      Commit: 8f4386016d3aa685b15e785a53c2d68b862e0fc4

      Author:  SoonYi <55300935+S00NYI@users.noreply.github.com> 

      Date: 2026-03-09 13:57:20 -0400

      Commit message:


	  
		
 Remove RBPEqBind.Rproj from Git tracking (BiocCheck fix)
 
    
  
    

      Package: ShortRead

      Commit: 6d09fd11bdfa53eba52075c12cdf1c505af26600

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

      Date: 2026-07-04 09:59:11 -0700

      Commit message:


	  
		
 ShortRead 1.71.1: Use new detail() S4 generic from BiocGenerics
 
    
  
    

      Package: Biostrings

      Commit: a301eba39724aa927b7a481a6c70faf6e4a25732

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

      Date: 2026-07-04 09:20:21 -0700

      Commit message:


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

      Package: Biostrings

      Commit: 74b7955d6ff63c5e15a9b7de3ed05e2d8a859841

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

      Date: 2026-07-04 09:20:04 -0700

      Commit message:


	  
		
 Biostrings 2.81.5: Remove detail()
 
    
  
    

      Package: Biostrings

      Commit: f04bae6c01e91baf350ef608fd66cd6c5f6646ea

      Author:  Aidan Lakshman <30053966+ahl27@users.noreply.github.com> 

      Date: 2026-07-04 12:17:02 -0400

      Commit message:


	  
		
 Remove extra \ in matchPDict-exact.Rd 
    
  
    

      Package: Biostrings

      Commit: bc27d4b68f3a6c2820e1aba34739da3a68a458aa

      Author:  Aidan Lakshman <30053966+ahl27@users.noreply.github.com> 

      Date: 2026-06-23 16:42:41 -0400

      Commit message:


	  
		
 Bump version to 2.81.4

Following implementation of vmatchPDict and associated vignette, bumping version to 2.81.4 
    
  
    

      Package: Biostrings

      Commit: 1a552ef256a258e07a43648945af7c9f85730c72

      Author:  Aidan Lakshman <30053966+ahl27@users.noreply.github.com> 

      Date: 2026-06-23 16:41:00 -0400

      Commit message:


	  
		
 feat: Vignette for pattern matching in Biostrings (#139) 
    
  
    

      Package: Biostrings

      Commit: 2c3e66f6483f9c9e35c5ea3a1848a841c00603b9

      Author:  Aidan Lakshman <30053966+ahl27@users.noreply.github.com> 

      Date: 2026-06-23 16:40:01 -0400

      Commit message:


	  
		
 feat: Implement `vmatchPDict` (#136)

* Adds MIndexList class; 
* enables vmatchPDict for PDict,XStringSet comparison
* update man page and tests 
    
  
    

      Package: BiocGenerics

      Commit: 0c73da8e39a48a867d484180f9acbdc032af9760

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

      Date: 2026-07-04 08:00:25 -0700

      Commit message:


	  
		
 BiocGenerics 0.59.9: Add S4 generic detail()
 
    
  
    

      Package: pathlinkR

      Commit: 2c881f563920b0df6c8289f100e81ebdcdf50be5

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-07-03 14:45:06 -0700

      Commit message:


	  
		
 Expanded test for truncNeatly
 
    
  
    

      Package: pathlinkR

      Commit: c818660bc1c8b560e66584548459055a5a8fcede

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-06-22 14:26:48 -0700

      Commit message:


	  
		
 Bumped github actions checkout version.
 
    
  
    

      Package: pathlinkR

      Commit: 2f665e3eec78e0cbf4e22e92ee2683d43c020a70

      Author:  Travis <travis.m.blimkie@gmail.com> 

      Date: 2026-06-22 14:02:25 -0700

      Commit message:


	  
		
 Merge pull request #20 from hancockinformatics/gene_check

* Added check for no sig genes in pathwayEnrichment input.
* Updated NEWS.md alongside. 
    
  
    

      Package: pathlinkR

      Commit: 8a859ba88ac432e985866c507fc72158b60ccb73

      Author:  Travis <travis.m.blimkie@gmail.com> 

      Date: 2026-06-22 13:59:54 -0700

      Commit message:


	  
		
 Update NEWS.md 
    
  
    

      Package: pathlinkR

      Commit: 33d9255e3c26f3dd4b351811f7cd0406f575323d

      Author:  Travis <travis.m.blimkie@gmail.com> 

      Date: 2026-06-22 13:58:46 -0700

      Commit message:


	  
		
 Merge branch 'devel' into gene_check 
    
  
    

      Package: pathlinkR

      Commit: dce35d97fa32ebea82d0ccfc52fe19360031f367

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-04-30 10:04:46 -0700

      Commit message:


	  
		
 Bumped version for actions.
 
    
  
    

      Package: pathlinkR

      Commit: b4accf2f0dde9504ed10a4dda8c63cb08629852f

      Author:  Travis Blimkie <travis.m.blimkie@gmail.com> 

      Date: 2026-04-15 15:11:52 -0700

      Commit message:


	  
		
 Added check for no sig genes in pathwayEnrichment input
 
    
  
    

      Package: BiocCheck

      Commit: 88040686ca728df4f5a4c0e0250347652e4f4fb1

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

      Date: 2026-07-03 11:44:15 -0400

      Commit message:


	  
		
 version bump 1.49.26
 
    
  
    

      Package: BiocCheck

      Commit: f9873578f0f0f8d8121c0582caae9eebc21baf3a

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

      Date: 2026-07-03 11:44:10 -0400

      Commit message:


	  
		
 add unit tests test_checkManDocumentation.R

assisted-by: gemini 3.5 flash
 
    
  
    

      Package: GSVA

      Commit: 74a801629cd4bb35a5ca6307beeb40b085bd9c71

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

      Date: 2026-07-03 17:16:02 +0200

      Commit message:


	  
		
 Change some getter methods into functions to bypass the S4 class hierarchy dispatch problem
 
    
  
    

      Package: rhinotypeR

      Commit: 94000ac0b014baa1e1acbcf4dcff5025e08ecd03

      Author:  marthaluka <mawia.martha@gmail.com> 

      Date: 2026-07-03 15:14:55 +0100

      Commit message:


	  
		
 remove msa error
 
    
  
    

      Package: NanoMethViz

      Commit: 0f05587dbe859ce430369097c7ab75b04741aa68

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-07-03 19:51:27 +1000

      Commit message:


	  
		
 Version bumped to v3.9.1
 
    
  
    

      Package: NanoMethViz

      Commit: 172320dfa30067e029087cf930ed1e2c02f9dfd8

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-07-03 19:51:07 +1000

      Commit message:


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

      Package: NanoMethViz

      Commit: 3fc4ea50dea32ea79e623ab293b2c93f9b06e5eb

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-07-03 19:50:51 +1000

      Commit message:


	  
		
 Merge branch 'devel' of github.com:Shians/NanoMethViz into devel
 
    
  
    

      Package: NanoMethViz

      Commit: d67af808ddb81202b64bd0825902552c8557ee8d

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-07-03 19:50:34 +1000

      Commit message:


	  
		
 Updated vignette
 
    
  
    

      Package: NanoMethViz

      Commit: 6c6ef36bd199a6a835325a797e47143f0657d9b9

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-04-29 10:44:01 +1000

      Commit message:


	  
		
 Updated package version checking
 
    
  
    

      Package: NanoMethViz

      Commit: 21cc21c174efcc541ee9ad536edac6fa95f1cd44

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-04-29 10:37:48 +1000

      Commit message:


	  
		
 Refactored exon retrieval
 
    
  
    

      Package: NanoMethViz

      Commit: e86b7607097c508d599e172d9c0d659b00425297

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-04-29 10:29:52 +1000

      Commit message:


	  
		
 Added filtering to exon retrieval to primary chromosomes only
 
    
  
    

      Package: NanoMethViz

      Commit: 9a90fa6b0db0729df79d36fe761caeca572721d7

      Author:  Shian Su <registertonysu@gmail.com> 

      Date: 2026-03-31 14:49:38 +1100

      Commit message:


	  
		
 Change Codecov badge to 'devel' branch

Updated Codecov badge to point to the 'devel' branch. 
    
  
    

      Package: ProteinBatcher

      Commit: 2aa192051096b874f68f3de4634ef5b1b9b6ce78

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2026-07-03 10:46:03 +0200

      Commit message:


	  
		
 description update
 
    
  
    

      Package: ProteinBatcher

      Commit: becb2d70f6f477cbd8aff971e54d1aa2da815170

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2026-07-03 10:43:55 +0200

      Commit message:


	  
		
 Solve variable declaration in workflow
 
    
  
    

      Package: BgeeCall

      Commit: e8d01ba739f7cd677f59e6691471f4242f4b9c07

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

      Date: 2026-07-03 10:24:50 +0200

      Commit message:


	  
		
 bump version after bug correction
 
    
  
    

      Package: BgeeCall

      Commit: 921ce2bb29c46f7458791616a7b957feea83ae45

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

      Date: 2026-07-03 10:23:43 +0200

      Commit message:


	  
		
 solve bug on tx_import example
 
    
  
    

      Package: igvShiny

      Commit: 1ad4317c1225ca06dc6c10e9d7fa539a31a6a3d1

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

      Date: 2026-07-03 10:22:11 +0200

      Commit message:


	  
		
 Merge pull request #109 from M4teuszzGl4dki/mateusz/issue-105-autoscalegroup

fix: pass autoscaleGroup through in loadBedGraphTrackFromURL (#105) 
    
  
    

      Package: igvShiny

      Commit: b23af742af8c92e863cc23c98de5032a7bf84047

      Author:  Arkadiusz Gładki <arek@dobio.link> 

      Date: 2026-07-03 10:04:11 +0200

      Commit message:


	  
		
 chore: bump version to 1.9.4 and update NEWS
 
    
  
    

      Package: igvShiny

      Commit: f4fead89bdea9375d66cc47bc2a920f909448e6c

      Author:  M4teuszzGl4dki <gladkiimateusz@gmail.com> 

      Date: 2026-07-03 09:24:17 +0200

      Commit message:


	  
		
 fix(js): support string-based autoscaleGroup values (review feedback)
 
    
  
    

      Package: igvShiny

      Commit: 978d8871d5ae169e03576ef5b40c66fc6b56d5e2

      Author:  M4teuszzGl4dki <gladkiimateusz@gmail.com> 

      Date: 2026-07-03 09:04:46 +0200

      Commit message:


	  
		
 fix(js): pass autoscaleGroup through in loadBedGraphTrackFromURL (#105)
 
    
  
    

      Package: destiny

      Commit: 75588a3895b4d669da71f7159eb26c93dc3c04d8

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

      Date: 2026-07-03 10:21:54 +0200

      Commit message:


	  
		
 style and conflicts
 
    
  
    

      Package: GSVA

      Commit: f78c675e7d4efc964927e501d671d1dab515db62

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

      Date: 2026-07-03 09:20:26 +0200

      Commit message:


	  
		
 Adding unit test coverage to map-reduce
 
    
  
    

      Package: TCGAutils

      Commit: 48aa352190750354aaa86e51bcab53879beda79b

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

      Date: 2026-07-02 15:16:56 -0400

      Commit message:


	  
		
 version bump 1.33.3
 
    
  
    

      Package: TCGAutils

      Commit: cc1504293440d92cad715c1ea11069b14c2da75c

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

      Date: 2026-07-02 14:06:02 -0400

      Commit message:


	  
		
 add redownload param to simplifyTCGA and mirToRanges
 
    
  
    

      Package: TCGAutils

      Commit: c929126c9a3169997ceb866b61356382c7cd3052

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

      Date: 2026-07-02 13:57:29 -0400

      Commit message:


	  
		
 use tryCatch to send warning when download fails and fall back to using cached file
 
    
  
    

      Package: GSVA

      Commit: 63f69b0044cb3404d1e010bba7371b7509552f23

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

      Date: 2026-07-02 20:08:03 +0200

      Commit message:


	  
		
 Changes to default to SerialParam() when workers=1 in map-reduce and reach corresponding unit testing
 
    
  
    

      Package: flowGate

      Commit: 244faae229b0926a0c8c16c2b2883472f33d8593

      Author:  Andrew Wight <andrew.wight10@gmail.com> 

      Date: 2026-07-02 14:43:42 -0300

      Commit message:


	  
		
 Merged in DavidRach's ggcyto fixes as well as a few things from the bioconductor branch that had gotten away from me. Added a few missing dependencies from said ggcyto fix.
 
    
  
    

      Package: flowGate

      Commit: 2cd5cf64716fafc5fc6f13df71c52fc618c3c225

      Author:  NKInstinct <52602383+NKInstinct@users.noreply.github.com> 

      Date: 2026-07-02 12:51:11 -0300

      Commit message:


	  
		
 Merge pull request #12 from DavidRach/master

Fixes for ggplot2 version 4 and ggcyto breaking changes. Has build failures in github but likely an issue on github's end, will confirm locally before pushing to bioconductor. 
    
  
    

      Package: flowGate

      Commit: 5cca8ddcc1c0c7da898467e487de889c64a8b2b1

      Author:  David Rach <drach@som.umaryland.edu> 

      Date: 2026-07-02 10:06:53 -0400

      Commit message:


	  
		
 Brough over Bioconductor flowGate version 1.13.1 differences to bring both GitHub and Bioconductor brances to being equivalent (except for preparePlot, which still double checking with unit tests for the Bioconductor version vs the ggcyto changes).
 
    
  
    

      Package: flowGate

      Commit: 2c582bca2c7c11937db64239831afa1389bc504b

      Author:  David Rach <drach@som.umaryland.edu> 

      Date: 2026-06-27 23:25:33 -0400

      Commit message:


	  
		
 Quality of life change for the Shiny, when only one-dimension provided, updates Radio Button to select spanGate
 
    
  
    

      Package: flowGate

      Commit: ec1f1b9e00637d5bd9e071f81f48633f6cee5e62

      Author:  David Rach <drach@som.umaryland.edu> 

      Date: 2026-06-27 12:41:21 -0400

      Commit message:


	  
		
 AdjustAll argument for applyGateCloseSwap to adjust all specimens within a GatingSet in one go if so desired
 
    
  
    

      Package: flowGate

      Commit: 082aff72707ad9888914461771700d8d2550ed6a

      Author:  David Rach <drach@som.umaryland.edu> 

      Date: 2026-06-27 12:18:41 -0400

      Commit message:


	  
		
 Incorporation of additional metadata columns to pData was causing gateClose to break. Reason is they were ending up within gg$data, which threw off the fix instituted following ggcyto break in the spring. Ended up using tail argument to identify the last one or two last items according to gate type. Appears working for both initial and regating attempts so far, need to verify different metadata or fluor names still work, and not just alphabetical in nature.
 
    
  
    

      Package: flowGate

      Commit: 36d85762bffa4ba11dfea61832af65ea2f5943bf

      Author:  David Rach <drach@som.umaryland.edu> 

      Date: 2026-06-21 11:37:11 -0400

      Commit message:


	  
		
 SpanGate adjustments and openCyto template exports are operational
 
    
  
    

      Package: flowGate

      Commit: d1c628da1edc4650a6f10ea72ac94c9f25eee307

      Author:  David Rach <drach@som.umaryland.edu> 

      Date: 2026-06-20 15:59:31 -0400

      Commit message:


	  
		
 Added a GatingSet to openCyto template function, everything being written out as  a polygon (and registering the new method via openCyto). Will see whether works for other gate types.
 
    
  
    

      Package: flowGate

      Commit: 1d5f81d754cb5a4661ced95300b080cd53e4f41f

      Author:  David Rach <drach@som.umaryland.edu> 

      Date: 2026-06-20 13:53:23 -0400

      Commit message:


	  
		
 Modified gs_gate_interactive_adjust to show existing gate, and if done is clicked directly exit out without any adjustments being conducted. Seems to be recalculating correctly, as the downstream plots are showing the appearance of singlets subsequently, and when viewing gate coordinates the vertices are specimen specific. So one object off the list, wooh! Updating to 0.99.3 for internal tracking.
 
    
  
    

      Package: flowGate

      Commit: d56d7d37a2fe9dc00f27723039dd1d569b529f0d

      Author:  David Rach <drach@som.umaryland.edu> 

      Date: 2026-06-20 13:16:34 -0400

      Commit message:


	  
		
 Initial work on gs_gate_interactive_adjust, which will iterate through a specific gate allowing adjustments. Currently, the existing gate is not shown, so everything ends up being redrawn, so need to modify that
 
    
  
    

      Package: flowGate

      Commit: 37b6ce15c270824087a2cef51c429816c7bde650

      Author:  David Rach <drach@som.umaryland.edu> 

      Date: 2026-04-15 20:47:46 -0400

      Commit message:


	  
		
 Rollback requirement to R >= 4.4 for Cytometry in R class
 
    
  
    

      Package: flowGate

      Commit: d84ac975141aa21d4922670a98ba4b89c407024f

      Author:  David Rach <drach@som.umaryland.edu> 

      Date: 2026-04-04 14:44:19 -0400

      Commit message:


	  
		
 Missing description file comma
 
    
  
    

      Package: flowGate

      Commit: 34aa109f57a7f7c0c3f1a31a192c4c678577af51

      Author:  David Rach <drach@som.umaryland.edu> 

      Date: 2026-02-21 15:52:26 -0500

      Commit message:


	  
		
 Unit test for all four interactive plot types. Need to check ggplot2 v3 next to see if back-compatible or not.
 
    
  
    

      Package: flowGate

      Commit: 890bb6409bf2559f54a9817a0bb8f28065178066

      Author:  David Rach <drach@som.umaryland.edu> 

      Date: 2026-02-21 14:40:09 -0500

      Commit message:


	  
		
 Fixed! The two major changes are the linguering GatingSet class that broke as.ggplot. The second was a ggplot2 v4 change that resulted in no column names getting pulled from data of the ggplot. With those two elements fixed, gate gets added correctly to the GatingSet.
 
    
  
    

      Package: flowGate

      Commit: 2fb489762daf177d31e673a9ced20ddfe9e6ff04

      Author:  David Rach <drach@som.umaryland.edu> 

      Date: 2026-02-21 14:12:36 -0500

      Commit message:


	  
		
 Worked through Shiny capture options, gate is being created, but returning a colname not found on recompute from flowWorkspace.
 
    
  
    

      Package: flowGate

      Commit: db5d8c82857d329003a5c27477cc217da93d5452

      Author:  David Rach <drach@som.umaryland.edu> 

      Date: 2026-02-21 10:58:06 -0500

      Commit message:


	  
		
 as.ggplot clashing with residual ggcyto_GatingSet class, on stripping returns a ggplot2 object. Gates are still not recording correctly.
 
    
  
    

      Package: flowGate

      Commit: 09d2ba11147da58df846486317d68911f949b3ed

      Author:  David Rach <drach@som.umaryland.edu> 

      Date: 2026-02-21 09:13:10 -0500

      Commit message:


	  
		
 With ggplot2 switching to v4, and ggcyto shifts, flowGate is failing on shiny launch. Creating unit test systematically as I go (as likely will need to refer some of this up to ggcyto as well).
 
    
  
    

      Package: flowGate

      Commit: cb5b56a5eda18d7fa59f1d859639b2b500a3eacd

      Author:  David Rach <drach@som.umaryland.edu> 

      Date: 2025-11-30 23:58:55 -0500

      Commit message:


	  
		
 Hi Andrew/Harvey, just testing whether I can get rid of the @import in favor of @importFrom and still have everything work. Will pull request any useful changes (and some additional unit test). Best- David. Change Log: Bunch importFroms; a landing page for ?flowGate, some updates Description, the GitHub branch is behind the Bioconductor, not sure if anything different, or just the rolling release updating the version, some minor roxygen for internals. Passing all CRAN and Bioc Checks with just notes
 
    
  
    

      Package: flowGate

      Commit: 6f20651920050e3c564ced818d01fcb9d5bc2789

      Author:  Andrew Wight <AndrewE_Wight@dfci.harvard.edu> 

      Date: 2023-03-15 08:59:30 -0400

      Commit message:


	  
		
 Merge branch 'master' of github.com:NKInstinct/flowGate
 
    
  
    

      Package: flowGate

      Commit: 097f5cb7b6dae21e77df448af402b3192ff4237e

      Author:  Andrew Wight <AndrewE_Wight@dfci.harvard.edu> 

      Date: 2023-03-15 08:58:50 -0400

      Commit message:


	  
		
 Not sure why this popped up all of a sudden but adding it to the ignore list for now - no workflows needed here I don't think.
 
    
  
    

      Package: flowGate

      Commit: e7e0e88bd24ab455be974b98065d7e35c9ebb83e

      Author:  Andrew Wight <AndrewE_Wight@dfci.harvard.edu> 

      Date: 2023-03-15 08:53:18 -0400

      Commit message:


	  
		
 Post bioconductor review changes - just some documentation cleanup!
 
    
  
    

      Package: flowGate

      Commit: f7edb61354f4bee488ee8c9177fa078d58866bbf

      Author:  NKInstinct <52602383+NKInstinct@users.noreply.github.com> 

      Date: 2023-02-23 08:16:38 -0500

      Commit message:


	  
		
 Update r.yml

bump r version in action 
    
  
    

      Package: TraianProt

      Commit: 28db1ae76aaf526e3764edf6a77444a6efcbb797

      Author:  Samuel <sdelacam@ucm.es> 

      Date: 2026-07-02 15:08:25 +0200

      Commit message:


	  
		
 Fixed for July submission
 
    
  
    

      Package: TraianProt

      Commit: 8aad04dc0548fe882aee60e295f5137b8334198a

      Author:  Samuel <sdelacam@ucm.es> 

      Date: 2026-07-02 14:52:30 +0200

      Commit message:


	  
		
 Fixed for July submission
 
    
  
    

      Package: DOtools

      Commit: f5ef40b46641bc633d319d07ef6795a56e705000

      Author:  MarianoRuzJurado <mariani95@gmx.de> 

      Date: 2026-07-02 14:06:07 +0200

      Commit message:


	  
		
 DO.scVI now correctly saves the model
 
    
  
    

      Package: DOtools

      Commit: d6f941dcd7f61506b1d40bfd154c78c88a9a04f2

      Author:  MarianoRuzJurado <mariani95@gmx.de> 

      Date: 2026-07-02 13:27:37 +0200

      Commit message:


	  
		
 fix dependency bug for scvi
 
    
  
    

      Package: DOtools

      Commit: 6d4c3415c504389688de9212b529c485bf61dcbc

      Author:  MarianoRuzJurado <mariani95@gmx.de> 

      Date: 2026-06-12 11:42:10 +0200

      Commit message:


	  
		
 Merge remote-tracking branch 'origin/master'
 
    
  
    

      Package: DOtools

      Commit: ea0326102332d4746cc31a95b8be5c78a771721a

      Author:  Mariano Ruz Jurado <60434009+MarianoRuzJurado@users.noreply.github.com> 

      Date: 2026-05-06 13:23:02 +0200

      Commit message:


	  
		
 Update README.md 
    
  
    

      Package: DOtools

      Commit: 99b659e25ec2f18f81792a497bfca294d7952989

      Author:  MarianoRuzJurado <mariani95@gmx.de> 

      Date: 2026-04-16 11:46:57 +0200

      Commit message:


	  
		
 Merge remote-tracking branch 'origin/master'
 
    
  
    

      Package: DOtools

      Commit: 90dffa3de2d5febf118179b2fa0ad6782e6e5257

      Author:  MarianoRuzJurado <mariani95@gmx.de> 

      Date: 2026-04-13 13:50:58 +0200

      Commit message:


	  
		
 Merge remote-tracking branch 'origin/master'
 
    
  
    

      Package: DOtools

      Commit: 4ce7a918dc254089f344a1b1c286ce4307835b6c

      Author:  Mariano Ruz Jurado <60434009+MarianoRuzJurado@users.noreply.github.com> 

      Date: 2026-04-13 11:23:07 +0200

      Commit message:


	  
		
 Update NEWS.md 
    
  
    

      Package: CatsCradle

      Commit: 7313e146c9ca7fdc79b7a8812e7e0429b94f5ac8

      Author:  AnnaLaddach <annaladdach@gmail.com> 

      Date: 2026-07-02 09:50:35 +0100

      Commit message:


	  
		
 version bump in devel, news updated
 
    
  
    

      Package: CatsCradle

      Commit: c65ab4a47f89ba26c0ad8ee8eeb605e686c7a4ad

      Author:  AnnaLaddach <annaladdach@gmail.com> 

      Date: 2026-07-02 09:43:26 +0100

      Commit message:


	  
		
 bug fix: bug fix for user-provided LRN, citation info
 
    
  
    

      Package: scConform

      Commit: b7b5a77ea3d16724726491390f8722c173c51b39

      Author:  Matteo Calgaro <mcalgaro93@gmail.com> 

      Date: 2026-06-30 11:55:40 +0200

      Commit message:


	  
		
 Add input validation for empty pred_set and missing ontology labels.
 
    
  
    

      Package: scConform

      Commit: ace43e11be5e229c9e2b3708679af8fb3b30711d

      Author:  Matteo Calgaro <mcalgaro93@gmail.com> 

      Date: 2026-06-30 11:33:08 +0200

      Commit message:


	  
		
 Validate ontology graph structure.
Check for node names, duplicated nodes, missing node names, and a single root.
 
    
  
    

      Package: scConform

      Commit: 966041b236e7f86f1025b431a6e062a39648db3e

      Author:  Matteo Calgaro <mcalgaro93@gmail.com> 

      Date: 2026-06-30 11:18:06 +0200

      Commit message:


	  
		
 Use do.call with dynamic args for pred_fun.
Avoid breaking user-supplied method functions that implement the documented function(lambda, pred, onto) signature.
 
    
  
    

      Package: scConform

      Commit: 6e11964a72a7df305448a807f509610f26c42b00

      Author:  Matteo Calgaro <mcalgaro93@gmail.com> 

      Date: 2026-06-30 01:55:13 +0200

      Commit message:


	  
		
 bump version to 0.99.5
 
    
  
    

      Package: scConform

      Commit: e39097e618d01cef4c50c7525ebdff29856ccf53

      Author:  Matteo Calgaro <mcalgaro93@gmail.com> 

      Date: 2026-06-30 01:54:09 +0200

      Commit message:


	  
		
 Add Matteo Calgaro as contributor and update Roxygen config
 
    
  
    

      Package: scConform

      Commit: fa03e59ab7f5a2b483623a97a7770c5590d5319b

      Author:  Matteo Calgaro <mcalgaro93@gmail.com> 

      Date: 2026-06-30 01:53:44 +0200

      Commit message:


	  
		
 Add onto_cache parameter to plotResult tests and vignette examples
 
    
  
    

      Package: scConform

      Commit: a01d47f5dd2e6244ccda4b366868ca68f3e6b49a

      Author:  Matteo Calgaro <mcalgaro93@gmail.com> 

      Date: 2026-06-30 01:53:14 +0200

      Commit message:


	  
		
 Use precomputed ontology cache to avoid redundant computation
 
    
  
    

      Package: scConform

      Commit: 6c05f7ba1861670430c193e2ee955cb8f44ac93c

      Author:  Matteo Calgaro <mcalgaro93@gmail.com> 

      Date: 2026-06-30 01:50:21 +0200

      Commit message:


	  
		
 Refactor utils functions to use `onto_cache` parameter.

`.getHierarchicalPredSets`: now accepts an `onto_cache` argument and reuses it instead of calling igraph directly inside the loop. The old `.ancestors()` and `.children()` helpers (which made direct igraph calls) are removed;

`.scores()`: computes a node's score as the sum of predicted probabilities for its leaf children, intersected with prediction matrix columns.

`.precomputeCellScores()`: precomputes per-cell ancestor scores in one call (returns the predicted class, ancestors, their scores, and tie-breaking distances from each ancestor to the predicted class.

Updated prediction set functions (`.predSets`, `.predSetsSimple`, `.predSetsStep`, `.predSetsRank`) all now take `onto_cache` and `cell_cache`.
 
    
  
    

      Package: scConform

      Commit: b8408fff8944e06a871ddaf31a65d2069b28bf1a

      Author:  Matteo Calgaro <mcalgaro93@gmail.com> 

      Date: 2026-06-30 01:36:52 +0200

      Commit message:


	  
		
 Add `precomputeOnto` function and documentation.
Builds a named list of precomputed ontology structures (full pairwise distance matrix, leaf children per node, ancestors per node, leaves, root, and all node names.
 
    
  
    

      Package: scConform

      Commit: 77b85d38c7f5f860fb3ca220ef66eb1d0a838c0c

      Author:  Daniela Corbetta <Corbettadaniela@gmail.com> 

      Date: 2026-03-31 18:47:38 +0200

      Commit message:


	  
		
 Update R package manager URL in CI workflow 
    
  
    

      Package: epiregulon

      Commit: 713a0f92059efb465008a97201a03c534ef87613

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2026-07-02 03:53:14 +0000

      Commit message:


	  
		
 handle NA p-values of t-tests resulting from both groups having all zero values
 
    
  
    

      Package: igblastr

      Commit: b3507f9fef3e52377623ffb97973044147aae7b5

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

      Date: 2026-07-01 16:43:48 -0700

      Commit message:


	  
		
 igblastr 1.3.12: 100x speedup or more to percent_mutation()
 
    
  
    

      Package: Rsubread

      Commit: ed1bbb92036d86189b9a7d4c07d611451a758c97

      Author:  Yang Liao (Monash University) <yliao@m3v109.massive.org.au> 

      Date: 2026-07-02 09:12:06 +1000

      Commit message:


	  
		
 added check to filter non-coordinate CB values on HD mode
 
    
  
    

      Package: BiocCheck

      Commit: f81a753913e869c8e56653e6a9be7dcbaee6eacd

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

      Date: 2026-07-01 19:09:46 -0400

      Commit message:


	  
		
 version bump 1.49.25
 
    
  
    

      Package: BiocCheck

      Commit: 4e85cfc4aead6b1ea75ec6348b0e87614ebf92f8

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

      Date: 2026-07-01 19:09:24 -0400

      Commit message:


	  
		
 remove redundant ORCID checks

- person() runs ORCID checks
 
    
  
    

      Package: BiocCheck

      Commit: 1fb76f58321b706a3c851b4d1dc11a7f07de81ac

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

      Date: 2026-07-01 19:05:25 -0400

      Commit message:


	  
		
 update grepl patterns for Authors@R NOTE
 
    
  
    

      Package: gDRutils

      Commit: 62009dfc0f038320f08b187e5376885b6d758363

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

      Date: 2026-07-02 00:45:33 +0200

      Commit message:


	  
		
 Merge pull request #189 from gdrplatform/GDR-3438

perf: optimize curve fitting hot path 
    
  
    

      Package: gDRutils

      Commit: 649bf08a6b92e844ad1c774f4dd529a16a9a03f5

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

      Date: 2026-07-01 17:44:12 +0200

      Commit message:


	  
		
 ci: retrigger build
 
    
  
    

      Package: gDRutils

      Commit: 0e23f749cb826a2628e8c8648cc5ea68c893be68

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

      Date: 2026-07-01 16:51:13 +0200

      Commit message:


	  
		
 ci: retrigger build
 
    
  
    

      Package: gDRutils

      Commit: b747ca70e648403e51455e4d3043e92fdaa40dcc

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

      Date: 2026-07-01 10:15:21 +0200

      Commit message:


	  
		
 fix: move loop docstring next to function, regenerate docs

The roxygen block was separated from the loop function by internal
helpers, causing loop.Rd to be lost. Also removed BiocParallel
references from docs since we now use parallel::parLapply.
 
    
  
    

      Package: gDRutils

      Commit: 700254f285dc997b68dee9f1d4ebf2ce109394c3

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

      Date: 2026-07-01 09:32:00 +0200

      Commit message:


	  
		
 fix: update parallelize docs default, remove unused BiocParallel import
 
    
  
    

      Package: gDRutils

      Commit: 938b10e3040cfc8aa25b1f78978a65e0c5b76ba5

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

      Date: 2026-07-01 09:22:13 +0200

      Commit message:


	  
		
 ci: retrigger build
 
    
  
    

      Package: gDRutils

      Commit: 75d27e278af114263025acb7c5f91f6e602a7a79

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

      Date: 2026-07-01 08:34:13 +0200

      Commit message:


	  
		
 fix: preserve identifier pairing in standardize_se mapping

Use rbindlist+lapply to maintain correct pairing of multi-value
identifiers (e.g. untreated_tag, well_position) when building
the mapping data.table.
 
    
  
    

      Package: gDRutils

      Commit: ebc7e4004e14d719c49a1c65d995153aaa521319

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

      Date: 2026-07-01 08:03:21 +0200

      Commit message:


	  
		
 ci: retrigger build
 
    
  
    

      Package: gDRutils

      Commit: 0e3a88000251007c116584fbc9b33830f7cb28a4

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

      Date: 2026-06-30 15:07:51 +0200

      Commit message:


	  
		
 ci: trigger build
 
    
  
    

      Package: gDRutils

      Commit: 8a11c4696e6c70d5e5c2f17de8e9bd74821e557a

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

      Date: 2026-06-30 13:43:27 +0200

      Commit message:


	  
		
 ci: trigger build
 
    
  
    

      Package: gDRutils

      Commit: 099467abe26f98ea028715693cec74513dc35add

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

      Date: 2026-06-29 14:01:03 +0200

      Commit message:


	  
		
 fix: address PR review comments

- restore comment in predict_efficacy_from_conc
- remove static cache in .metric_output_template (dynamically compute)
- add docstring for .metric_output_template
- handle NA from detectCores()
- restore assert_flag(use_batch) in loop()
- simplify NEWS.md entry
- bump version to 1.11.4
 
    
  
    

      Package: gDRutils

      Commit: 96138a4f6515b746bffa7bfd3d57511eb4bd9610

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

      Date: 2026-06-22 11:30:30 +0200

      Commit message:


	  
		
 ci: retrigger build
 
    
  
    

      Package: gDRutils

      Commit: 9af0511f3f6ebe3bbcc3d021e781506077bc3a52

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

      Date: 2026-06-22 09:39:47 +0200

      Commit message:


	  
		
 ci: trigger build
 
    
  
    

      Package: gDRutils

      Commit: 6416018f2ace440befb26b004e3f277666ff2767

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

      Date: 2026-06-20 08:32:35 +0200

      Commit message:


	  
		
 perf: return invisible from loop() to suppress knitr output for side-effect calls
 
    
  
    

      Package: gDRutils

      Commit: 0ecb31d4fac6d892850caeeb8d4c39e589398bf5

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

      Date: 2026-06-19 12:22:45 +0200

      Commit message:


	  
		
 perf: default parallelize=FALSE in loop(), controlled by GDR_PARALLELIZE env var
 
    
  
    

      Package: gDRutils

      Commit: b88c18427878369235a4fccd57b438c74fc1897c

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

      Date: 2026-06-18 14:19:48 +0200

      Commit message:


	  
		
 fix: export caller environment to PSOCK cluster workers
 
    
  
    

      Package: gDRutils

      Commit: 241b0fcbd4fdf4c84f25b40c2d12bf06522cc533

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

      Date: 2026-06-18 14:16:10 +0200

      Commit message:


	  
		
 perf: use PSOCK cluster for cross-platform parallel support
 
    
  
    

      Package: gDRutils

      Commit: 828e57d81086f44b3ce19b3e0b7ab0406376fd90

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

      Date: 2026-06-18 14:14:27 +0200

      Commit message:


	  
		
 perf: use mclapply on POSIX, parLapply on Windows, enable on macOS
 
    
  
    

      Package: gDRutils

      Commit: dc773451bb94537d356f5ed18d59b3fab12d2775

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

      Date: 2026-06-18 13:53:38 +0200

      Commit message:


	  
		
 fix: disable mclapply fork on macOS (not fork-safe with graphics)
 
    
  
    

      Package: gDRutils

      Commit: 693ec6fbbc506ef9e1d7424bce6991bf2027d714

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

      Date: 2026-06-18 11:25:33 +0200

      Commit message:


	  
		
 perf: replace BiocParallel with parallel::mclapply in loop()
 
    
  
    

      Package: gDRutils

      Commit: 4f460f965474a71a635e165e8a1f6e3aa890a569

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

      Date: 2026-06-18 11:22:03 +0200

      Commit message:


	  
		
 perf: graceful fallback in loop() when BiocParallel unavailable
 
    
  
    

      Package: gDRutils

      Commit: 66a64f837e598957863c0b887bb8145ec2dd2b62

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

      Date: 2026-06-18 08:06:41 +0200

      Commit message:


	  
		
 ci: trigger build
 
    
  
    

      Package: gDRutils

      Commit: 915914f702cbc573d6a1fd3e6dd8f999b22f5764

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

      Date: 2026-06-17 16:51:09 +0200

      Commit message:


	  
		
 ci: trigger build
 
    
  
    

      Package: gDRutils

      Commit: a8827dbbaf8d5620389da8bbca535b0394c757c8

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

      Date: 2026-06-17 16:42:10 +0200

      Commit message:


	  
		
 ci: trigger build
 
    
  
    

      Package: gDRutils

      Commit: d7578b835940c38a307da8caba42bf6c96ad713a

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

      Date: 2026-06-17 13:08:09 +0200

      Commit message:


	  
		
 perf: move batch-only assertions inside use_batch guard in loop()
 
    
  
    

      Package: gDRutils

      Commit: 504300d519091607ab56f230793b4a00008027e5

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

      Date: 2026-06-17 08:14:28 +0200

      Commit message:


	  
		
 perf: vectorize mapping construction and model param extraction
 
    
  
    

      Package: gDRutils

      Commit: 66607a3877586a685a8491b0eaf703d9e0a35496

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

      Date: 2026-06-15 15:21:44 +0200

      Commit message:


	  
		
 ci: trigger build
 
    
  
    

      Package: gDRutils

      Commit: 25009a892968b87e80be757b30d18b0a759cfa6d

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

      Date: 2026-06-15 14:13:09 +0200

      Commit message:


	  
		
 ci: trigger build
 
    
  
    

      Package: gDRutils

      Commit: 4203911710d963dc28a86e19c1dbdd5cfe90eb95

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

      Date: 2026-06-15 12:55:01 +0200

      Commit message:


	  
		
 fix: use approved imperative verb in NEWS.md
 
    
  
    

      Package: gDRutils

      Commit: e7169697b0e894944a0b731194b270a5a1cde8f4

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

      Date: 2026-06-15 12:41:03 +0200

      Commit message:


	  
		
 ci: trigger build
 
    
  
    

      Package: gDRutils

      Commit: 1e1c54e37b81afcd934d1511c9e4f1fbf3e2d3a6

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

      Date: 2026-06-15 12:29:23 +0200

      Commit message:


	  
		
 perf: replace do.call(rbind) with rbindlist in apply_bumpy_function
 
    
  
    

      Package: gDRutils

      Commit: 3cc68a430b4c046d45eee16aa87f54c3648ea9a5

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

      Date: 2026-06-15 12:25:33 +0200

      Commit message:


	  
		
 fix: use data.table instead of data.frame in predict helper
 
    
  
    

      Package: gDRutils

      Commit: 1b6bc0864645c62be1f0f7b13b35d44457070778

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

      Date: 2026-06-15 10:37:56 +0200

      Commit message:


	  
		
 perf: reduce loop() overhead and cache metric output template
 
    
  
    

      Package: gDRutils

      Commit: ae641bfdeede82f7d8d6a7ee91ebcedd04a00d72

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

      Date: 2026-06-11 22:26:41 +0200

      Commit message:


	  
		
 fix: restore assertions in predict_efficacy_from_conc
 
    
  
    

      Package: gDRutils

      Commit: b3b76e67ce54af680a097e022a2545555b388f4c

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

      Date: 2026-06-11 22:12:43 +0200

      Commit message:


	  
		
 perf: optimize curve fitting hot path
 
    
  
    

      Package: gDRcore

      Commit: a627542781b1a2853b767eb4c648e6878826ddb9

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

      Date: 2026-07-02 00:45:07 +0200

      Commit message:


	  
		
 Merge pull request #198 from gdrplatform/GDR-3438

perf: optimize pipeline performance 
    
  
    

      Package: gDRcore

      Commit: 9cf52729683f5a9833a5c368818cd406b2a4a297

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

      Date: 2026-07-01 17:44:13 +0200

      Commit message:


	  
		
 ci: retrigger build
 
    
  
    

      Package: gDRcore

      Commit: fdf821fe6946cb398ee73e278761e30567193c87

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

      Date: 2026-07-01 16:51:15 +0200

      Commit message:


	  
		
 ci: retrigger build
 
    
  
    

      Package: gDRcore

      Commit: 089e7761e2e7864efa74e0a72c31143d5474ebb7

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

      Date: 2026-07-01 10:21:24 +0200

      Commit message:


	  
		
 ci: retrigger build
 
    
  
    

      Package: gDRcore

      Commit: d562ee459b1cbc508b6f28554587c1b95c0f0906

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

      Date: 2026-07-01 09:32:11 +0200

      Commit message:


	  
		
 ci: retrigger build
 
    
  
    

      Package: gDRcore

      Commit: 8900e3b9cf46c0839990cc28f2a86aac0eb5c989

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

      Date: 2026-06-30 15:07:57 +0200

      Commit message:


	  
		
 ci: trigger build
 
    
  
    

      Package: gDRcore

      Commit: 723a6363d4a6d1746d0b8f13703af057a662bbaa

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

      Date: 2026-06-30 13:43:33 +0200

      Commit message:


	  
		
 ci: trigger build
 
    
  
    

      Package: gDRcore

      Commit: c3022d37d7e4b47528a2c98e9c71223f367ce05a

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

      Date: 2026-06-22 11:30:31 +0200

      Commit message:


	  
		
 ci: retrigger build
 
    
  
    

      Package: gDRcore

      Commit: 62fac13901c2f5d20f8d6d081d9eb1836e5b9368

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

      Date: 2026-06-22 09:39:51 +0200

      Commit message:


	  
		
 ci: trigger build
 
    
  
    

      Package: gDRcore

      Commit: 05083a6a796dfe46625c8845761150f48ffa1e41

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

      Date: 2026-06-22 09:39:49 +0200

      Commit message:


	  
		
 ci: trigger build
 
    
  
    

      Package: gDRcore

      Commit: b67827875ba8a2f07a4db5d39390f1e48f4fd768

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

      Date: 2026-06-19 12:22:46 +0200

      Commit message:


	  
		
 perf: remove hardcoded parallelize=TRUE from average_SE
 
    
  
    

      Package: gDRcore

      Commit: 1cf65354e8a19676add23cb6efff0ff26df94c53

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

      Date: 2026-06-18 08:06:39 +0200

      Commit message:


	  
		
 ci: trigger build
 
    
  
    

      Package: gDRcore

      Commit: f0f8f437bc6c1797990bc777974f11ec0f94caa6

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

      Date: 2026-06-17 17:43:21 +0200

      Commit message:


	  
		
 ci: trigger build
 
    
  
    

      Package: gDRcore

      Commit: 1a0283a7d930d4091ff88cd505f632fda3adf2b5

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

      Date: 2026-06-17 17:43:18 +0200

      Commit message:


	  
		
 ci: trigger build
 
    
  
    

      Package: gDRcore

      Commit: 149e6b34d6e22a14175b050a4bc5025409605084

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

      Date: 2026-06-17 16:51:08 +0200

      Commit message:


	  
		
 ci: trigger build
 
    
  
    

      Package: gDRcore

      Commit: 417c6d72be134dcda6ec908ceb72c8acc9ef2e54

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

      Date: 2026-06-17 16:41:51 +0200

      Commit message:


	  
		
 ci: trigger build
 
    
  
    

      Package: gDRcore

      Commit: aeaa0ec29607b3e0bbee8525d21ca9f6d517d7aa

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

      Date: 2026-06-17 14:05:15 +0200

      Commit message:


	  
		
 perf: cache aggregate_ref, pre-compute ref mappings, vectorize isobologram smoothing
 
    
  
    

      Package: gDRcore

      Commit: 62140d1077802196196e152ae1d0ecc215f78585

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

      Date: 2026-06-17 08:14:26 +0200

      Commit message:


	  
		
 perf: vectorize drug pair dedup, use data.table merge in combo excess
 
    
  
    

      Package: gDRcore

      Commit: 7a776f52058ed281e1e2ffb37485ea7cc17faf9a

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

      Date: 2026-06-15 15:21:42 +0200

      Commit message:


	  
		
 ci: trigger build
 
    
  
    

      Package: gDRcore

      Commit: 35709057b865c6f51545b0fb3ec176b94cf2ac03

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

      Date: 2026-06-15 14:13:07 +0200

      Commit message:


	  
		
 ci: trigger build
 
    
  
    

      Package: gDRcore

      Commit: f1a7c45cb0737a0d3348f39a9685c23c68e5e560

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

      Date: 2026-06-15 12:54:59 +0200

      Commit message:


	  
		
 fix: use approved imperative verb in NEWS.md
 
    
  
    

      Package: gDRcore

      Commit: 8c2ce3792ecf719276b367c5cc36ad7dc45851e9

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

      Date: 2026-06-15 12:40:56 +0200

      Commit message:


	  
		
 ci: trigger build
 
    
  
    

      Package: gDRcore

      Commit: c10f6e973f0e7f48baf6f2d3f7fb43976c23b592

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

      Date: 2026-06-15 12:29:28 +0200

      Commit message:


	  
		
 perf: rbindlist in isobolograms and rbindParallelList, eliminate redundant id column in normalize
 
    
  
    

      Package: gDRcore

      Commit: 9a4db4f97e0e9665ad40ee2202a005f109a99623

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

      Date: 2026-06-15 10:39:38 +0200

      Commit message:


	  
		
 perf: replace S4Vectors::match with data.table join in combo helpers
 
    
  
    

      Package: gDRcore

      Commit: 898fef5a600ee8b0539a4aa1cf0cb404f1f052b6

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

      Date: 2026-06-11 22:06:40 +0200

      Commit message:


	  
		
 perf: optimize pipeline performance
 
    
  
    

      Package: HuBMAPR

      Commit: d2c1882a185a9b669ac99e5a22cc132392e66cd3

      Author:  christinehou11 <chou11@jh.edu> 

      Date: 2026-07-01 17:35:29 -0500

      Commit message:


	  
		
 version bump in devel
 
    
  
    

      Package: HuBMAPR

      Commit: f95c66dc235a360744aa26bce8e71ea43d523711

      Author:  christinehou11 <chou11@jh.edu> 

      Date: 2026-07-01 17:35:01 -0500

      Commit message:


	  
		
 bug fix
 
    
  
    

      Package: IRanges

      Commit: 7023de1ba34540939a4ebae4d3d284e1c87a051b

      Author:  Michael Chirico <chiricom@google.com> 

      Date: 2026-07-01 14:14:30 -0700

      Commit message:


	  
		
 typo: xlen->x_len (#67) 
    
  
    

      Package: R453Plus1Toolbox

      Commit: c022d307efd1aaf48be38fec2fa70d28db3f95c2

      Author:  huklein <hansulrich.klein@gmail.com> 

      Date: 2026-07-01 15:22:45 -0400

      Commit message:


	  
		
 Replace S4 table() method with breakpointTable() generic
 
    
  
    

      Package: DiffBind

      Commit: a26ef8d38fc02a6865093d58d3636dc531a1fbb8

      Author:  Rory Stark <bioconductor@starkhome.com> 

      Date: 2026-07-01 19:22:37 +0100

      Commit message:


	  
		
 3.23.3: preserve bSubControl set in dba.count()

dba.count(bSubControl=) was recorded on the input object in
pv.counts() but dropped when the counted object was rebuilt by
pv.vectors(), so the returned DBA had $bSubControl = NULL. A
subsequent dba.normalize()/dba.analyze() then fell back to
is.null(greylist), silently subtracting control reads regardless
of the user's choice.

pv.counts() now re-stamps bSubControl onto the reconstructed
object (alongside minCount) and forwards it through the summit
re-centering recursion. Default behavior (no explicit
bSubControl) is unchanged.

Reported by Tomasz Wlodarczyk and Xiaosai Yao.
 
    
  
    

      Package: GSVA

      Commit: ebd04d4105ba60a375e52793b47d237bb8617b0c

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

      Date: 2026-07-01 20:16:41 +0200

      Commit message:


	  
		
 Fixes on code coverage
 
    
  
    

      Package: ClustIRR

      Commit: a562a197b5e9afb57d17d9000be142f0a2a33788

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-07-01 19:47:58 +0200

      Commit message:


	  
		
 merge
 
    
  
    

      Package: ClustIRR

      Commit: 3e4f5ac82b9f0e61d55076b6ed2f64294e74c802

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-07-01 19:46:49 +0200

      Commit message:


	  
		
 bugfix in intro
 
    
  
    

      Package: ClustIRR

      Commit: 9e66a64a524a0b093c8163c118e9aecd7881781c

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-07-01 19:46:32 +0200

      Commit message:


	  
		
 bump
 
    
  
    

      Package: ClustIRR

      Commit: 423dc4a24d3a44c85916de4d4cda53741876a2a5

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-07-01 19:07:43 +0200

      Commit message:


	  
		
 merge
 
    
  
    

      Package: ClustIRR

      Commit: 2d8f2d403e0031eb7558f257aead84ad2c369ebb

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-07-01 19:04:56 +0200

      Commit message:


	  
		
 after Biorxiv
 
    
  
    

      Package: ClustIRR

      Commit: d9cef0a58b1817754a91b1367e0bc13bac7fa914

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-07-01 19:02:11 +0200

      Commit message:


	  
		
 after Biorxiv
 
    
  
    

      Package: ClustIRR

      Commit: b3985778947c576966e006cfcaae16854b1b28bd

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-06-30 11:48:02 +0200

      Commit message:


	  
		
 remove na
 
    
  
    

      Package: ClustIRR

      Commit: 7b67024748bd2a3c6052c98d1f75dd1f87e6736e

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-06-30 11:43:02 +0200

      Commit message:


	  
		
 bump and bugfix in violin
 
    
  
    

      Package: ClustIRR

      Commit: ee75bcc9f76fe8220eb739492473ad285bc63c13

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-06-07 11:46:31 +0200

      Commit message:


	  
		
 Bump
 
    
  
    

      Package: ClustIRR

      Commit: 3fe7c988a977e728e072d059b8e75277aaf4946a

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-06-07 11:46:23 +0200

      Commit message:


	  
		
 efficiency improvement of graph merging
 
    
  
    

      Package: ClustIRR

      Commit: 97cc5974b5506f30c5aafce89bbd68f70d831ea0

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-05-23 11:51:49 +0200

      Commit message:


	  
		
 db creation multicore
 
    
  
    

      Package: ClustIRR

      Commit: 3ffa94c0c57fb9039e5a18092a7ce49e81417da8

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-05-23 11:51:36 +0200

      Commit message:


	  
		
 bump
 
    
  
    

      Package: igvShiny

      Commit: 1a47e71a295bd0563212a4960000cb637de84fef

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

      Date: 2026-07-01 17:59:53 +0200

      Commit message:


	  
		
 Move explore/ dev notes out of git to GDrive (#108)

* Move explore/ dev notes out of git to GDrive

Exploratory scripts and mentoring notes aren't meant to be public;
mirrored to GDrive and symlinked locally instead of tracked in git.

* Ignore build_log.txt

Leftover 20MB log from local Containerfile builds, never meant to be tracked. 
    
  
    

      Package: ENmix

      Commit: 183c7b51ee9a9c6e1f0ee71aa38d3c7e5815efba

      Author:  xuz1 <xuz@niehs.nih.gov> 

      Date: 2026-07-01 11:06:24 -0400

      Commit message:


	  
		
 bugfix

Signed-off-by: xuz1 <xuz@niehs.nih.gov>
 
    
  
    

      Package: biomaRt

      Commit: 7b0e998d83c1081b4677bf03e5f80f702b480893

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-01 14:05:59 +0200

      Commit message:


	  
		
 Document more return values
 
    
  
    

      Package: Rsubread

      Commit: f18fa230c6569895f53c8bda8ce4068cf4d4ee8a

      Author:  Yang Liao (Monash University) <yliao@m3-login2.massive.org.au> 

      Date: 2026-07-01 18:10:18 +1000

      Commit message:


	  
		
 support "sb" tag from new Space Ranger for 2um spot coordinates.
 
    
  
    

      Package: GSVA

      Commit: 4a660b70edd6f1b764e64e9e8541982caa970e65

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

      Date: 2026-07-01 09:39:21 +0200

      Commit message:


	  
		
 Cosmetic changes in the code, harmonizing indentation, etc.
 
    
  
    

      Package: CoSIA

      Commit: b1c2605a9c98d99fd2d85e07498ef4a0b78c2e10

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-06-30 15:31:05 -0500

      Commit message:


	  
		
 Version bump in devel
 
    
  
    

      Package: CoSIA

      Commit: 80e78d18cd81976b72ef9693e7bd5dd0449ab8ac

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-06-30 15:28:41 -0500

      Commit message:


	  
		
 Merge branch 'devel' of github.com:lasseignelab/CoSIA into devel
 
    
  
    

      Package: CoSIA

      Commit: e4399809fb4dd8784c96fd15842de8dd9aafe5d8

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-06-30 15:27:48 -0500

      Commit message:


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

      Package: CoSIA

      Commit: 86d4a398ae006b87aad8280f262545ffab80aae9

      Author:  Tonie <148514625+toniecrumley@users.noreply.github.com> 

      Date: 2026-06-30 14:25:37 -0500

      Commit message:


	  
		
 Merge pull request #75 from lasseignelab/fix-tidyr

Fix tidyr::separate_rows issue with plots 
    
  
    

      Package: CoSIA

      Commit: 3dd54c5d8a5511ee5f50e3d3fc6259a471ae8bf6

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-06-16 15:09:14 -0500

      Commit message:


	  
		
 Fix path issue in test suite
 
    
  
    

      Package: CoSIA

      Commit: 17cfea694a4e57df6b43a45e4a0309cefc26464f

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-06-12 14:13:51 -0500

      Commit message:


	  
		
 Change validation container to lasseignelab account
 
    
  
    

      Package: CoSIA

      Commit: 836471979807b179e9639edc379614ffaf01f660

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-06-12 13:25:39 -0500

      Commit message:


	  
		
 Clean up trailing white space
 
    
  
    

      Package: CoSIA

      Commit: cbe79eda315d93215d0b68e6b9b04282b749f01b

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-06-12 13:25:14 -0500

      Commit message:


	  
		
 Fix warnings for violin plots
 
    
  
    

      Package: CoSIA

      Commit: 3bf6976e18639f4e004ec598565f1adcd4f7d41b

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-06-12 13:08:19 -0500

      Commit message:


	  
		
 Add validation for gene expression plot error
 
    
  
    

      Package: CoSIA

      Commit: d7e15374ea403bb8f1c4ae88bd7477854a346176

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-06-12 13:05:51 -0500

      Commit message:


	  
		
 Add docker file
 
    
  
    

      Package: CoSIA

      Commit: c0d131facdcffbe7bc341a21b0bb5ca13887d613

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-06-09 15:56:18 -0500

      Commit message:


	  
		
 Add validation script for tidyr fix
 
    
  
    

      Package: CoSIA

      Commit: adb1a0ea595d5f877463f7734300f0e5ab7b439e

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-06-04 12:45:20 -0500

      Commit message:


	  
		
 Add plot tests and fix VST unnesting in plotSpeciesGEx/plotTissueGEx

Replace tidyr::separate_rows with tidyr::unnest for the VST list column
in both plot methods. separate_rows no longer handles list columns in
current tidyr, causing all VST values to become NA and breaking violin
rendering.

Add offline tests (test-plots.R) using mock CoSIAn objects with list-column
VST data. Tests fail with separate_rows and pass with unnest.

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

      Package: CoSIA

      Commit: 7ad5a900f76218d78b4cf7c1afba849728795080

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-06-04 11:43:48 -0500

      Commit message:


	  
		
 Fix VST parsing in plotSpeciesGEx and plotTissueGEx

Replace deprecated tidyr::separate_rows with tidyr::unnest for the VST
list column. separate_rows no longer handles list columns correctly in
current tidyr, causing all VST values to become NA and breaking violin
plot rendering.

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

      Package: IRanges

      Commit: 603b16caf90d5933e1e89a2bd58920fb13d9151f

      Author:  Michael Chirico <chiricom@google.com> 

      Date: 2026-06-30 10:59:09 -0700

      Commit message:


	  
		
 Use '::' for exported name (#61) 
    
  
    

      Package: AnnotationHub

      Commit: b406e89030efd8e164f2c00f6ece5ec98ee4301d

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

      Date: 2026-06-30 13:36:56 -0400

      Commit message:


	  
		
 Version bump to fix windows testing error
 
    
  
    

      Package: AnnotationHub

      Commit: 4a01132d347f2a09dcaaf250f0e162036dd07aee

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

      Date: 2026-06-30 11:35:15 -0400

      Commit message:


	  
		
 fix unit test to work on windows paths when user name is abbreviated
 
    
  
    

      Package: IRanges

      Commit: cdf31628a9129d58adbb4e3d471ef640eaeed566

      Author:  Michael Chirico <chiricom@google.com> 

      Date: 2026-06-30 10:19:33 -0700

      Commit message:


	  
		
 Don't memcpy a 0-length vector (#66) 
    
  
    

      Package: GenomicRanges

      Commit: 8d860039ee1e770b34ae51fc8680add91c49e56a

      Author:  Michael Chirico <michaelchirico4@gmail.com> 

      Date: 2026-06-30 10:05:13 -0700

      Commit message:


	  
		
 Add XVector to Suggests (#99) 
    
  
    

      Package: IRanges

      Commit: 3cf54e23328ba683659e3a556cd81c7ee77a6150

      Author:  Hervé Pagès <hpages@users.noreply.github.com> 

      Date: 2026-06-30 08:35:05 -0700

      Commit message:


	  
		
 Merge pull request #65 from MichaelChirico/patch-3

Remove '...' which is not in \usage 
    
  
    

      Package: IRanges

      Commit: e1b82c5df7e30b16baae80771b52308147a1b8ce

      Author:  Michael Chirico <chiricom@google.com> 

      Date: 2026-06-11 14:11:51 -0700

      Commit message:


	  
		
 Remove '...' which is not in \usage 
    
  
    

      Package: GSVA

      Commit: bd50e7e4335c18f96bb90c43f7eb2c3e289176f7

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

      Date: 2026-06-30 16:47:48 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: GSVA

      Commit: bef33d261d927ce9f9397c557ca55be474df8ba3

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

      Date: 2026-06-30 16:46:52 +0200

      Commit message:


	  
		
 Merge pull request #271 from rcastelo/270-mapreduce-layer

Map-Reduce layer 
    
  
    

      Package: GSVA

      Commit: 5124264a5299a4b79f313ecf4cfd9e90f8ef58c6

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

      Date: 2026-06-30 16:16:23 +0200

      Commit message:


	  
		
 Add batchtools to suggests
 
    
  
    

      Package: GSVA

      Commit: f5d985aae7fdf4594022e381d8d5de7ac8546a9d

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

      Date: 2026-06-30 13:59:21 +0200

      Commit message:


	  
		
 Fixes addressing issues raised by the Copilot review
 
    
  
  


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