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Package: drugTargetInteractions
Commit: bf6616552e125642ac04d795dec153c00ca63000
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-10-16 19:36:23 -0700
Commit message:
Commit: bf6616552e125642ac04d795dec153c00ca63000
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-10-16 19:36:23 -0700
Commit message:
Add runnable examples to the two hand-written man pages downloadChemblDb.Rd and getUniprotIDs.Rd are among the 15 man pages written by hand rather than generated from roxygen, so the pass that added runnable examples to the other pages never reached them. downloadChemblDb() now shows where the download is cached and that a small sample of the same database ships with the package, which is what the examples of the functions querying it use - so trying those needs no download. That also surfaces the "this is a very large file" warning that was previously only an Rd comment, invisible to readers. getUniprotIDs() shows the shape of its two result tables from the snapshot already shipped in inst/extdata, which is useful on its own given the live UNIREF path depends on UniProt being reachable. The live query stays under \donttest. Exported-object man pages with a runnable example: 57 of 64 (89%), up from 55. The threshold BiocCheck errors below is 80%, so this widens the margin from three pages to five. The remaining seven are REST getters with no local data to demonstrate on.
Package: drugTargetInteractions
Commit: 704b5bb0bdd22a7c0e8a0533edaf3b55a93cd056
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-10-16 16:35:34 -0700
Commit message:
Commit: 704b5bb0bdd22a7c0e8a0533edaf3b55a93cd056
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-10-16 16:35:34 -0700
Commit message:
Give the UniChem cache-lookup tests databases with a real layout .unichemLatestCachedDb() now checks a cached database's tables and columns before returning it, so the two fixtures this test registered - empty files created with file.create(), carrying only the right name - are correctly rejected and the lookup returns NA. Build them as minimal databases with the layout buildUnichemDb() writes, so the test goes back to asserting what it is about: that the most recently added unichem_*.db wins regardless of the date in its name. Added the complementary case while here: a cached database whose layout is two columns short of the current one is skipped rather than returned. Unlike most of this suite these tests touch no network, so they run under R CMD check.
Package: drugTargetInteractions
Commit: 88328aed70775452ccefca69a1a98439bffda973
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-10-16 16:06:43 -0700
Commit message:
Commit: 88328aed70775452ccefca69a1a98439bffda973
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-10-16 16:06:43 -0700
Commit message:
Reuse a cached database only if its layout is the one we build The local-SQLite builds cache a ready-to-query database under a name carrying the upstream release (gtopdb_2026.3.1.db, ttd_.db, ...) and, on rerun = FALSE, return whatever is cached under that name rather than rebuilding. The upstream release alone is not a safe cache key. When this package changes a table's columns, a database built by an older version of the package - same upstream release, so the same cache name - is still sitting there and was returned, after which the query functions failed on columns they expect and cannot find: buildGtoPdbDb(rerun = FALSE) columns returned: ..., selectivity, refIds gtoPdbTargetAnnot(...) Error: undefined columns selected Renaming gtp_interactions' refIds to pubmedId in this release is exactly that case, and it escaped notice only because GtoPdb published 2026.3.1 at the same time, so the stale gtopdb_2026.2.db copies were never consulted. Had GtoPdb not republished, every rerun = FALSE call would have returned a database with the old layout. This is not hypothetical on a build machine: BiocFileCache persists between runs on the Bioconductor builders by design, so such a database outlives an upgrade there and is found first. .dtiCachedDbIfCurrent() reuses a cached database only when every expected table is present with exactly the expected columns; an older layout, or a truncated or half-written file, counts as a cache miss and the caller rebuilds. Wired into the TTD, Repurposing Hub, GtoPdb and UniChem builds through one layout constant per source. Validation rather than a hand-bumped version suffix in the name because it is self-healing, and because its failure mode is fail-safe: a constant that drifts out of date costs an unnecessary rebuild, never a wrong answer. That is what makes it safe to apply to UniChem, whose rebuild takes about an hour. Checked against this machine's real cache - all four layouts are accepted, and the three cheap builds still short-circuit in well under a second. For GtoPdb the constant is now also the single description of the table: the build derives its column selection from it, so builder and validator cannot disagree. UniChem needed a different shape, since .unichemLatestCachedDb() takes the newest unichem_* entry regardless of name: it now walks candidates newest-first and returns the first whose layout matches. Also, buildGtoPdbDb() returned a bfcrpath()-named vector from the fresh-build path and a plain string from the cached-reuse path while documenting character(1), so identical() on two paths naming the same file was FALSE. Unnamed in both now. </pre> </div> Package: drugTargetInteractions
Commit: 1dd8e60ba7ca23b0c99e68bc563d40de54bf9f83
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-10-13 19:45:32 -0700
Commit message:
Bump to 1.21.15; run the r-universe build on every push .github/workflows/r-universe.yml calls the r-universe build workflow with universe: bioc and organization: bioconductor, so a push runs the same build and checks r-universe does rather than waiting for its next scheduled run. ^\.github$ keeps it out of the tarball. Also, from BiocCheck's notes: GeneTarget and Network added to biocViews, and the Description expanded past the 3-sentence minimum, fixing two typos in it along the way.Package: drugTargetInteractions
Commit: cef6e72c36af824e85b20041b3c46bde1aae4c82
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-10-13 19:45:32 -0700
Commit message:
Fix the r-universe build: GtoPdb's REST API now requires an API key r-universe starts from an empty BiocFileCache every run, where BBS keeps its cache between runs. That had been masking a real failure: GtoPdb began requiring a registered API key for every /services/ endpoint, and an unauthenticated request returns HTTP 401 ("API key is missing"), so buildGtoPdbDb() could not run on any machine without a key - including the build machines. The vignette's gtopdb_build chunk was the reported error, as an opaque "bfcadd() failed". GtoPdb still publishes the same data as public bulk downloads needing no registration, so build from those: /DATA/interactions.tsv (the whole ~25,000-row table) joined against GtP_to_HGNC_mapping.tsv as before. Those files carry the same release and more columns than the REST payload did. The authenticated route stays available via downloadGtoPdb(useServices = TRUE, apiKey = ...), defaulting to the GTOPDB_API_KEY environment variable, and a missing or rejected key is now reported as an authentication failure. Two consequences of the flat file's shape: - refIds, GtoPdb's internal reference IDs, has no equivalent there. The file carries the reference's PubMed ID instead, so gtp_interactions and gtoPdbTargetAnnot() now report pubmedId in its place. The REST route cannot populate it. - The affinity string is rebuilt from the file's separate low/median/ high columns: a range where the bounds differ, else the single value, each to one decimal since the file stores single-precision floats. Checked against a cached /services/interactions response - 90.7% exact agreement joining on (targetId, ligandId, type, action), the remainder explained by that key not being unique (up to 23 rows share one) and by the two releases differing. Rows whose Target ID, Target and Target Gene Symbol are all empty carry no target identity and cannot form a (target, drug) edge, so they are dropped at build time. buildGtoPdbDb() gained a paths argument for building from local copies of the two files, writing to a tempfile rather than the cache so a small build can never shadow the real gtopdb_.db. A 12 KB extract of both files now ships in inst/extdata, regenerated byte-for-byte by inst/scripts/generate_gtopdb_example.R. The GtoPdb examples and tests use it, and the vignette falls back to it only if GtoPdb cannot be reached, so the section still demonstrates the real download. Also fixed, found while reproducing the above from an empty cache: A documented field request no longer fails when a source is unreachable. .dtiSelectFields() validated the names passed through 'fields' against the columns the current response happened to carry, so when ChEMBL was intermittently returning HTTP 500 the response came back without its optional columns and documented field names looked like typos: Error in .dtiSelectFields(): Unknown field(s) requested: molecule.molecule_type, target.organism. That alone failed a vignette build. Each source now passes its documented field list, the one listDrugTargetFields() reports; a field on that list which the response does not carry comes back as an NA column, and a name no source documents is still an error. This also covers the case the docs already warned about, where a field appears only for certain record types. BiocCheck's two warnings are gone. getSymEnsUp() loads its EnsDb package namespace instead of attaching it with require(), and says so if the package is missing. The Repurposing Hub's supplemental CA retry no longer sets CURL_CA_BUNDLE for the session - repo-hub.broadinstitute.org still serves its leaf certificate alone, so the workaround is still needed, but the bundle now travels as a per-request curl option. Full chain verification still happens; the bundle only adds the one legitimate InCommon intermediate. BiocCheck's runnable-examples ERROR is gone too. It comments out both \dontrun and \donttest when deciding, so a page whose examples live entirely inside \donttest counts as having none; 18 of 64 pages passed, now 55. Where a function can do real work offline the example does it; for the REST getters the runnable part lists the columns that source returns, which is what the reader needs before choosing 'fields'; for the download and build functions it names the cache directory. The test helpers now download when nothing is cached, rather than erroring, so the suite runs on a cold cache. </pre> </div> Package: SeqArray
Commit: c0e0c0dd2ad9605f71b098fd1f0e4f24ee0a160c
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2026-10-16 21:51:27 -0500
Commit message:
optimize memory usagePackage: spicyR
Commit: 25efbe3f8fa9282781eac22ce634677bd09f13c1
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-17 06:55:25 +1100
Commit message:
1.99.28: images with a missing condition are left out of the unadjusted test The core's excess_test() split image rows with `group == 0 ? g0 : g1`, so a row with a missing condition (R's NA_integer_, Python's -1) was counted in the second condition: the unadjusted test (no adjustment, or the unadjusted_* columns) included those images, while the adjusted design (pair_design_test's keep, .cell_design's keep) left them out. split_groups() now skips negative groups, which fixes excess_test() and excess_tau2() for both front ends (one change in the shared core). availability_test() leaves those rows out too. With more than two conditions, .cell_pair_test_levels() built Zg from NA groups, so every pair failed ("no pair could be tested"); it now fits the unadjusted design on the rows with a condition. informative_units() and no_variation already skipped negative groups. R encodes a missing condition as NA_integer_ (match() - 1L), which reaches the core as INT_MIN, a negative group. The adjusted test is unchanged except where its tau2 is held at the unadjusted value (an added column that varies within patients, e.g. adjustAbundance with several images per patient). The pooled steps that use every image, the allocation side and tau2_image, are not changed. Checks: refs.R 26 of 26, maxt_refs.R 11 of 11 and memref identical() to 1.99.27 (none has a missing condition). Missing-condition cases (scratch/missing_cond_dev/mc_refs.R): with one image per patient the results now equal those with the images removed; R and Python agree to <= 6e-13. testthat: 357 passed, 0 failed (the three new tests fail on 1.99.27). R CMD check: only the src/concaveman.hpp warning. Closes #83 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4Package: SparseArray
Commit: 6614ff6e4a00ec0bfa4605690aa0b3d1d3ad82b2
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-10-16 11:28:14 -0700
Commit message:
small tweak to unit testsPackage: thyroidBRS
Commit: b05a43b5dbe986c9ef2bfeff4eab0b18f5a4b543
Author: Camila Barrios <151900030+camilasauria@users.noreply.github.com>
Date: 2026-10-16 12:00:32 -0600
Commit message:
Merge pull request #4 from camilasauria/bioc-zenodo-badges Add Bioconductor and Zenodo badges, cite the Zenodo DOI (0.99.8)Package: thyroidBRS
Commit: d6195ca72ee933565f2f78f79cf851f4d13dbafc
Author: Hugo Tovar <hatovar@inmegen.gob.mx>
Date: 2026-10-14 23:25:58 -0600
Commit message:
Add Bioconductor and Zenodo badges, cite the Zenodo DOI Badges for the Bioconductor devel build and years in Bioconductor, and the Zenodo concept DOI in the README, which gets a Citation section. inst/CITATION carries the same DOI. Bump to 0.99.8. No code changed. Assisted-by: Claude Haiku 5.5 (Anthropic) Co-Authored-By: Claude Haiku 5.5 <noreply@anthropic.com>Package: StatescopeR
Commit: 0c00f58d630d66adb103364933562895c1b3ec75
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2026-10-16 17:44:54 +0200
Commit message:
same as 1.0.2 but for dev branch actual deprecation warning of aggregrateAcrossCells and fitTrendVar fix & citation update to published manuscriptPackage: ADAPT
Commit: 85b835f558a1d769b8bc7204c356042367e7a165
Author: Mukai Wang <wangmk@umich.edu>
Date: 2026-10-16 11:21:35 -0400
Commit message:
Merge branch 'devel' of github.com:mkbwang/ADAPT into develPackage: ADAPT
Commit: ba9da13f335fa6da96bfd05412b877fbbaca3504
Author: Mukai Wang <wangmk@umich.edu>
Date: 2026-10-16 11:18:49 -0400
Commit message:
Use portable 'strip -S' in Makevars to fix macOS install Apple's strip does not accept the GNU-only --strip-debug flag, which broke installation on Bioconductor macOS builders. -S is accepted by both GNU and Apple strip and is equivalent to --strip-debug in GNU binutils. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>Package: ADAPT
Commit: 78cdfd52fd12bdb67bea1fbb623378a5fdd852ed
Author: Mukai Wang <wangmk@umich.edu>
Date: 2024-08-21 14:55:15 -0400
Commit message:
Merge pull request #21 from mkbwang/debug Address reviewer's requestsPackage: ADAPT
Commit: e2288702a60550c6f917a3e8ba1fbade34325476
Author: Mukai Wang <wangmk@umich.edu>
Date: 2024-07-28 17:13:03 -0400
Commit message:
Merge pull request #20 from mkbwang/debug Two bugs fixed.Package: spicyR
Commit: f197332bf485d7fb4fc16cb70f68b22d65e70c31
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-17 01:55:02 +1100
Commit message:
1.99.27: a radius where a condition has no informative patient is not tested (adjusted_for "none (no_information)") The allocation effect is bounded: an image of an avoiding pair with no `to` cell next to a `from` cell has y = -1 exactly, and one of an attracting pair with every `to` cell next to one +1. When every patient of a condition is at the bound, that condition's CR2 variance is exactly 0, the se rests on the other condition's few informative patients and the Satterthwaite df stay at 9-14 (t of -44 to -63 under relabelling). The core's informative_units() counts, per condition, the units with at least one image row whose (O - E) / n is not exactly -1 or +1 (the omni_calib engine's definition). pair_tests(): allocation, se > 0 and a condition with none -> p and the unadjusted p NaN, with adjustment design 2 "no_information" (no design fitted), and the radius does not enter the davies, maxT or cauchy combination. R's .cell_rows_test() does the same, and .cell_pair_test_levels() (more than two conditions) leaves the pair untested (reason "no_information") when any level has none. The count effect and Kontextual have no bound and are not touched; survival has no condition groups (a response with no variation is already not tested). The printed summary counts the pairs not tested; the vignette's checks count BH calls with na.rm = TRUE. Checks: refs.R 24 of 26 identical() to 1.99.26 (omni_davies_allocation_t40: 156 of 40000 radius tests, all r = 2 on the avoid side, now NA, and the combined p of 131 of 1600 pairs; kontextual$diab/diab_adj: 14 of 193 three-stage pairs no longer tested, the same 14 that the engine's definition finds); maxt_refs.R 11 of 11 identical; memref.R identical except diabetes (the same 14 pairs). Every count result and Kontextual is identical. On the investigation's worst cases (HCC shuffle 14, Metabric 25, Vannan min3 15) and on all 31 labellings of the 12 worst-calibrated real-data analyses, the package's omnibus and single-radius p equal the engine's inf1 p exactly for every pair; any-BH over those 12 falls from 36.1% to 10.8% (omnibus) and from 8.3% to 5.0% (single radius). New tests: a constructed pair with every image of one condition at -1 at r = 4 (not tested, labelled, left out of davies/maxT/cauchy with and without adjustment, count unaffected, three conditions). Tests pass; R CMD check: the src/concaveman.hpp WARNING only. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4Package: exploreSE
Commit: f040a0537d3d18e8e61af9489382b8799aa9ef1b
Author: Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com>
Date: 2026-10-16 16:41:10 +0200
Commit message:
added the adding of context to the app, with testing, vignette changes, etcPackage: BgeeDB
Commit: 00ac7cda111c66cecd316dd8fef900ae723bef05
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2026-10-16 16:41:35 +0200
Commit message:
bump versionPackage: MsBackendParquet
Commit: e24075795b4d9aa3f1fc97642a275a1001de04a0
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2026-10-16 15:02:24 +0100
Commit message:
chore: Update authors list in DESCRIPTIONPackage: BreastSubtypeR
Commit: 962c9e1715fa4c5ae5e0e70bd4436ae52122b0ea
Author: Emmanouil Sifakis <sifakise@gmail.com>
Date: 2026-10-16 10:49:28 +0200
Commit message:
Merge pull request #151 from JohanHartmanGroupBioteam/docs/release-sync-after-1.5.6 Prepare BreastSubtypeR 1.5.7 development maintenance updatePackage: BreastSubtypeR
Commit: 3ff2e032ef74741f370f5193123dfeca02abad0d
Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se>
Date: 2026-10-16 10:33:01 +0200
Commit message:
Clarify regression-test and browser-validation provenancePackage: BreastSubtypeR
Commit: e33928ff045028ff0525abccc4134bdd1968a94f
Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se>
Date: 2026-10-16 10:33:00 +0200
Commit message:
Make installation and distribution-channel documentation durablePackage: BreastSubtypeR
Commit: b90028767a9d15d54f97e773895bc250fa69b146
Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se>
Date: 2026-10-16 10:01:30 +0200
Commit message:
Align roxygen and help pages with validated behaviorPackage: BreastSubtypeR
Commit: 54e487f7b4a9539c7616ffec01a35535b07030f4
Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se>
Date: 2026-10-16 10:01:30 +0200
Commit message:
Synchronize installation and workflow documentationPackage: BreastSubtypeR
Commit: 79634a88ca8a961862c407f2544bd7608512575e
Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se>
Date: 2026-10-16 10:01:29 +0200
Commit message:
Document AIMS and Shiny maintenance corrections in NEWSPackage: BreastSubtypeR
Commit: 06c603bd871ea623f84b24dfbcaab10a31f9b121
Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se>
Date: 2026-10-16 10:01:29 +0200
Commit message:
Prepare version 1.5.7 development maintenance metadataPackage: BreastSubtypeR
Commit: 0ec48ec8f44849588525c48cecb707340ad09c49
Author: Emmanouil Sifakis <sifakise@gmail.com>
Date: 2026-10-16 09:05:22 +0200
Commit message:
Merge pull request #150 from JohanHartmanGroupBioteam/fix/shiny-state-validation-1.5.6 Prevent stale Shiny downloads and handle invalid inputsPackage: BreastSubtypeR
Commit: a36cd643b695f181c71af4cc923da1e8c9b0bdbd
Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se>
Date: 2026-10-16 08:39:04 +0200
Commit message:
Merge remote-tracking branch 'origin/main' into fix/shiny-state-validation-1.5.6Package: BreastSubtypeR
Commit: dce60984fc73d8b1970defa18f65fc0db77b790d
Author: Emmanouil Sifakis <sifakise@gmail.com>
Date: 2026-10-16 08:38:29 +0200
Commit message:
Merge pull request #149 from JohanHartmanGroupBioteam/fix/aims-single-sample-1.5.6 Fix AIMS single-sample prediction and output documentationPackage: BreastSubtypeR
Commit: c580d5cc57ca58640dea6037beab2d55b496c681
Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se>
Date: 2026-10-15 22:06:05 +0200
Commit message:
Prevent stale Shiny downloads and handle invalid inputsPackage: BreastSubtypeR
Commit: fda1f453c9ef07f17a639768adec32da1a4decd8
Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se>
Date: 2026-10-15 16:45:56 +0200
Commit message:
Fix AIMS single-sample prediction and document output structurePackage: BreastSubtypeR
Commit: 6fbb1fb0c47c899d9159141136c481ac283ba644
Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se>
Date: 2026-10-13 11:32:51 +0200
Commit message:
Merge pull request #146 from JohanHartmanGroupBioteam/maintenance/cihc-itr-1.5.6 Fix cIHC.itr ER balancing and prepare version 1.5.6Package: BreastSubtypeR
Commit: 445b8b86dde41b29a98a7335f02976e63a06fa85
Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se>
Date: 2026-10-12 19:57:14 +0200
Commit message:
Clarify the cohorts affected by the cIHC.itr fix; add an AUTO routing test NEWS.md (1.5.6 entry): the earlier wording limited the affected AUTO runs to ER+ fractions above 0.39, but get_methods() selects cIHC.itr in both branches of the eligible mixed cohort (ten methods when the ER+ fraction is strictly between 0.39 and 0.69, eight methods otherwise). The entry now says that, with the default ratio = 54 / 64, cohorts with an ER-negative majority can be affected, in manual BS_Multi() calls that include cIHC.itr and in AUTO calls that select it under the existing routing and size gates, and that a changed balancing subset need not change every subtype call. The routing code and its thresholds are unchanged. BS_cIHC.itr() roxygen (er_subsample), the regenerated man/BS_cIHC.itr.Rd and the comment above .cihc_itr_plan(): the statement that both modes give the same results when ER+ samples are at least as many as ER- samples is qualified with the default ratio = 54 / 64 and otherwise identical inputs, seed and settings; "larger" rejects a ratio above n_larger / n_smaller, which "target" accepts. tests/testthat/test-auto-cihc-itr-routing.R (new): synthetic phenotype tables only. AUTO selects cIHC.itr in both mixed-cohort branches for 20/80, 39/61, 40/60, 45/55, 50/50, 68/32, 69/31 and 80/20 ER+/ER- with the exact method vectors and strict boundaries; a below-minimum cohort and a HER2+ cohort are not routed to cIHC.itr; the default-ratio plans for 20/80 are 20 : 17 ("larger") and 20 : 24 ("target"). Existing assertions and the retained 1.5.5 fixture are untouched. No executable code changes: the parsed expressions of every R/*.R file are identical to the previous commit.Package: BreastSubtypeR
Commit: 3a4f83d098695564522ab933eddc394dcab12aa8
Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se>
Date: 2026-10-12 19:06:42 +0200
Commit message:
Prepare maintenance version 1.5.6 with the cIHC.itr ER subsampling fix Bump the version to 1.5.6 and document the behaviour-changing cIHC.itr bug fix of the previous commit (db80994) in NEWS.md: target-aware ER balancing, the retained ceiling() rounding convention, the cohorts whose results can change (ER- samples outnumbering ER+ samples), and er_subsample = "larger" for exact reproduction of BreastSubtypeR 1.5.5 and earlier. No code, help-page, README, vignette or test changes in this commit.Package: BreastSubtypeR
Commit: db80994fcf0f630a65f9e85c9c5bb4a016faef2c
Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se>
Date: 2026-10-11 00:45:16 +0200
Commit message:
cIHC.itr: subsample the ER group over-represented relative to the target cIHC.itr subsampled the numerically larger ER group to ceiling(ratio * n_smaller). With the default ratio 54/64 (the ER+ : ER- distribution of the UNC PAM50 reference set) the balancing subset only followed that target when ER+ samples were at least as many as ER- samples; otherwise it was inverted (for example 54 ER+ / 64 ER- was subsampled to 54 : 46). - New default er_subsample = "target": ratio is the ER+ : ER- target; the ER group over-represented relative to it is subsampled without replacement to ceiling(ratio * n_ERneg) ER+ or ceiling(n_ERpos / ratio) ER- samples, the other group is kept in full, and a cohort already at the target is used in full. Any single positive finite ratio is valid. - er_subsample = "larger" keeps the previous rule, sampling order and outputs exactly; it is also exposed through BS_Multi() and affects only cIHC.itr. - Results are identical to 1.5.5 whenever ER+ samples are at least as many as ER- samples (ceiling() rounding is retained for this reason). - Validates ratio (single, finite, positive) and keeps the empty-ER-group error; sizes are computed without integer overflow. - Tests compare both modes with outputs retained from 1.5.5 (commit 0dcc0c8) and check that BS_Multi() changes no other method.Package: BreastSubtypeR
Commit: 0dcc0c8a846290fcca3f266bd79248bff84fb58b
Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se>
Date: 2026-10-09 12:23:42 +0200
Commit message:
Merge pull request #145 from JohanHartmanGroupBioteam/maintenance/bioc-devel-1.5.5 Prepare development maintenance version 1.5.5Package: BreastSubtypeR
Commit: f09b14b99283ab809f9d9d20a5c26ae9e98b0cde
Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se>
Date: 2026-10-09 09:37:53 +0200
Commit message:
Prepare development maintenance version 1.5.5Package: BreastSubtypeR
Commit: ac0f1c20357f4324ee4c9d1e8f2b9fb88d5e3985
Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se>
Date: 2026-10-08 23:00:38 +0200
Commit message:
Merge pull request #144 from JohanHartmanGroupBioteam/ci/bioccheck Add an advisory BiocCheck CI workflow (R 4.6, Bioc 3.24)Package: BreastSubtypeR
Commit: 8201f68a5f68d0b1759567ddfedd4553892ca927
Author: Emmanouil Sifakis <sifakise@gmail.com>
Date: 2026-10-08 22:33:30 +0200
Commit message:
BiocCheck CI: run steps with pipefail and verify it Without a shell setting, GitHub runs Linux steps with "bash -e", so a command piped through tee could fail while its step succeeded. In run 37837213404 BiocCheck exited 1 (one Support Site WARNING) but the step was reported successful; only the summary consistency check failed the job, and the summary table showed the BiocCheck stage as PASS. - Set defaults.run.shell: bash for the BiocCheck job, which GitHub runs as "bash --noprofile --norc -eo pipefail". - The self-test step now checks that pipefail is on in its own (the job's default) shell and that a producer exiting non-zero after writing a clean result fails a "| tee" pipeline in that shell. - Stage status in the job summary is FAIL whenever the recorded result has an ERROR or WARNING, regardless of the step outcome. - Synthetic controls added for the clean-result-then-failure case and for the summary of masked and genuinely failed steps.Package: BreastSubtypeR
Commit: ae0fc7cc7369b06ff9d614404786b2aa06589fcd
Author: Emmanouil Sifakis <sifakise@gmail.com>
Date: 2026-10-08 22:08:00 +0200
Commit message:
Add an advisory BiocCheck CI workflow (R 4.6, Bioc 3.24) New independent workflow with one Linux job, "BiocCheck (R 4.6, Bioc 3.24)". It runs BiocCheckGitClone on the untouched checkout, builds one source tarball, runs R CMD check --no-manual on it and, only if that has no ERROR or WARNING, runs BiocCheck in existing-package mode on the same tarball using the R CMD check installation (install = "check:..."). The job fails on any ERROR or WARNING, on incomplete or malformed results, on an unresolved tarball/installation identity and on missing evidence; NOTEs are listed in the job summary. A synthetic self-test verifies the gate's exit statuses on the runner before the real checks. Evidence is uploaded on every outcome. The existing required R-CMD-check workflow, package sources and dependencies are unchanged; BiocCheck is installed only in the runner library. No secrets are used, so the Bioc-devel subscription check is reported as NOT VERIFIED.Package: BreastSubtypeR
Commit: 2c67e7086b3bc719c8f716496aa1828d86c06b63
Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se>
Date: 2026-10-08 16:51:08 +0200
Commit message:
Merge pull request #143 from JohanHartmanGroupBioteam/fix/citation-bioccheck Fix CITATION reading without package metadataPackage: BreastSubtypeR
Commit: 7d8a4a6e0f4229943d592412c6c6ff13c6b1176e
Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se>
Date: 2026-10-08 14:39:57 +0200
Commit message:
Fix CITATION reading without package metadataPackage: BreastSubtypeR
Commit: f474e6bb5cd5822796836483afa018bfee53b5cc
Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se>
Date: 2026-10-07 11:17:15 +0200
Commit message:
Merge pull request #142 from JohanHartmanGroupBioteam/ci/r-cmd-check Add minimal R CMD check CIPackage: BreastSubtypeR
Commit: b560657ff8553b99fe1899626a6d23ea30131cfe
Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se>
Date: 2026-10-07 10:25:33 +0200
Commit message:
Add minimal R CMD check CIPackage: SpectraStash
Commit: 89ced95d5eb698e4e98233a200a0684e845a9dbe
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2026-10-16 15:39:47 +0200
Commit message:
Merge pull request #15 from rformassspectrometry/jomain feat: add plain text stash format for MsBackendOfflineSqlPackage: SpectraStash
Commit: 208be98ddf654d7b5fce89470f41e9c59f35f9aa
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-10-16 15:14:34 +0200
Commit message:
Address Gabriele's commentsPackage: SpectraStash
Commit: a35c9f821c8f2553e5f9c5735b117d2e9c25fab4
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-10-16 14:47:18 +0200
Commit message:
fix: try to fix Windows path problemsPackage: SpectraStash
Commit: 575d99ac972e5188d7c1e0946c38b22fbf727ef3
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-10-16 12:10:58 +0200
Commit message:
feat: add plain text stash format for MsBackendOfflineSql - Add support for the plain text stash format for the `MsBackendOfflineSql` backend. This backend is defined in the *MsBackendSql* package, but creating yet another stash package (for a single backend) seems not reasonalble. Adding the respective packages to *Suggests* instead of *Imports*.Package: BgeeDB
Commit: da6a0642088daa528d75a385638405791c74862a
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2026-10-16 14:55:23 +0200
Commit message:
check that a download is complete from its last bytes, read the expression calls with fread as character, and keep the calls of Bgee 16 compressedPackage: BindingSiteFinder
Commit: 026576dd29b73ebc725014e7f9d0a05c2ca3b2e2
Author: Mirko Brüggemann <mirko.brueggemann@mail.de>
Date: 2026-10-16 13:44:36 +0200
Commit message:
Add changes to news and bump version numberPackage: BindingSiteFinder
Commit: 2f2e56cb3ff6c4136881c92bbc0e96b89d0ca640
Author: Mirko Brüggemann <mirko.brueggemann@mail.de>
Date: 2026-10-16 13:41:35 +0200
Commit message:
fixed minor ggplot visualsPackage: BindingSiteFinder
Commit: 1dca290f90ab4afe3833fb484d979ad1b7b7647d
Author: Mirko Brüggemann <mirko.brueggemann@mail.de>
Date: 2026-10-16 13:31:14 +0200
Commit message:
bugfix in reproducibilityFilterPackage: BindingSiteFinder
Commit: db6078a32c86f551934fd10656abb08fb2d0beda
Author: Mirko Brüggemann <mirko.brueggemann@mail.de>
Date: 2026-10-16 12:07:46 +0200
Commit message:
Fixed condition variable naming bugPackage: BindingSiteFinder
Commit: 68ca62ba1af50de9a473e2cf0e3cbda2aeae13a3
Author: Mirko Brüggemann <mirko.brueggemann@mail.de>
Date: 2026-10-09 14:51:23 +0200
Commit message:
explicitly call the correct package for the makeTxDbFromGFF functionPackage: BindingSiteFinder
Commit: 27279f5b82b5e94a8a6b3afd98372fc6c0559675
Author: Mirko Brüggemann <mirko.brueggemann@mail.de>
Date: 2026-10-09 14:22:59 +0200
Commit message:
fixed missing colors in the targetGeneSpectrumPlotPackage: BindingSiteFinder
Commit: 9fe0ca285617ede99c1503c12f3e5d4a86373b52
Author: Mirko Brüggemann <mirko.brueggemann@mail.de>
Date: 2026-10-09 13:49:51 +0200
Commit message:
Added a test case to check that meta data is kept after background is addedPackage: BindingSiteFinder
Commit: ea56141c4c8f72b163295854a7f9b9a24313b46b
Author: Mirko Brüggemann <mirko.brueggemann@mail.de>
Date: 2026-10-09 13:49:32 +0200
Commit message:
removed cbind to avoid duplicated meta columnsPackage: BindingSiteFinder
Commit: c8156366c7191c9664e4c6429773187cc23c919f
Author: Mirko Brüggemann <mirko.brueggemann@mail.de>
Date: 2026-10-09 13:48:48 +0200
Commit message:
make explanation of overlap resolve options in assignToTranscriptRegions more clearPackage: BindingSiteFinder
Commit: fff3badcd9d6e12fac06136fcd1000147f5192ca
Author: Mirko Brüggemann <mirko.brueggemann@mail.de>
Date: 2026-10-09 13:48:38 +0200
Commit message:
make explanation of overlap resolve options in assignToTranscriptRegions more clearPackage: BindingSiteFinder
Commit: 1adc8c99231ab052343f1dffce7ff2a27f06fa2e
Author: Mirko Brüggemann <mirko.brueggemann@mail.de>
Date: 2026-10-09 13:47:50 +0200
Commit message:
make explanation of overlap resolve options in assignToTranscriptRegions more clearPackage: gDRcore
Commit: 29d344f530e03d026be9e29abac4c657fd386e75
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2026-10-16 12:06:39 +0200
Commit message:
Merge pull request #212 from gdrplatform/GDR-3637 feat: process time-course data in runDrugResponseProcessingPipeline()Package: gDRcore
Commit: d1393eaa1a583c2a265ca228df756a18f34ce656
Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com>
Date: 2026-10-15 16:01:18 +0200
Commit message:
fix: require three time points before treating a plate as time-course A plate read at time zero and at the end point, or a day 0 plate scanned twice, met the old rule and lost its end-point metrics. Every Incucyte plate processed so far has 16 or more time points, so the stricter rule costs nothing there and keeps such end-point plates on the path they took before.Package: gDRcore
Commit: 688591a31399044952a8b793d942c0a72e450b1b
Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com>
Date: 2026-10-15 12:36:06 +0200
Commit message:
fix: warn about plates read repeatedly without a reading at time zero Such a plate fell back to end-point processing without a word, while data_model() still called the same table time-course. Both now use one helper, identify_data_type() names the plates it sends to the end-point path, and the pipeline documentation states the time-zero requirement. The NEWS entries for the unreleased time-course processing are merged.Package: gDRcore
Commit: 32cdfb8e4eb5b08e874be287aba96f4a71e4c64c
Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com>
Date: 2026-10-14 09:46:56 +0200
Commit message:
refactor: stop time-course data at LogFoldChange in the pipelinePackage: gDRcore
Commit: 12f348a52381e1abc33bfc83e28e238a50fe1260
Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com>
Date: 2026-10-14 09:00:24 +0200
Commit message:
fix: keep the drug order of time-course combinations in split_raw_data()Package: gDRcore
Commit: 320c5d071bbbb81daa8fd59d4387029bd6a3a9c0
Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com>
Date: 2026-10-14 08:14:20 +0200
Commit message:
feat: process time-course data in runDrugResponseProcessingPipeline()Package: miaViz
Commit: 4716552cea29f5c56c1af2a6074bca1d9e849c63
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2026-10-16 13:01:14 +0300
Commit message:
Fix plotBoxplot: duplicated column names (#235)Package: spicyR
Commit: 5bb8e8d239f77207f426d13acba1fdb0fc2de969
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-16 20:48:03 +1100
Commit message:
1.99.26: no adjusted design at a radius with no variation (adjusted_for "none (no_variation)") Where a pair's response has no variation at a radius (no `to` cell has a `from` neighbour, or every one has), the unadjusted test is exactly 0 / 0 and the radius is left out. The adjusted design (adjustAbundance, covariates) turned those zeros into rounding noise (~1e-16), so the radius was kept with t = noise / noise and an arbitrary influence vector, which moved the davies, maxT and cauchy combinations arbitrarily. Now, when the unadjusted test has no variation (!(se > 0)), no design is fitted: adjusted_for "none (no_variation)", p NaN, and nothing of the radius enters the combination (core pair_tests() and R's .cell_rows_test(); Kontextual uses the latter). The core's design_tests() also reports "no_variation" when the weighted residual sum of squares is at most (64 eps n)^2 times the weighted sum of squares of the response (more than two conditions, survival, Hartung-Knapp); survival is adjusted for abundance only where the unadjusted test was done. With several radii, a radius where no pair's design was fitted gets the other radii's effect columns (combining them stopped with an error before). Checks: refs.R (26 cases), maxt_refs.R (11) and memref.R (8) are identical() to 1.99.25's. t04 -> t05 of the 10-type synthetic data (r = 5..125, age, abundance, davies) gives 0.772 (0.967; 0.772 with r = 115, 120 dropped), and with age perturbed by 1e-10 its p no longer moves. The davies_dev perturbation experiments (25 configurations, Jackson, Keren, Schurch and synthetic): no combined p moves by more than 4e-9 (21-28% moved by > 0.01 before on the adjusted real-data runs). New tests: empty and saturated radii give "none (no_variation)" for davies, maxT, cauchy and one radius; the combination equals that without the radius; a perturbed covariate; design_tests() on an exactly fitted response; three conditions and survival. Tests pass; R CMD check: the src/concaveman.hpp WARNING only. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4Package: spicyR
Commit: a2b302ce423df29ab42e00f6a25966f12f2f4531
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-16 19:47:26 +1100
Commit message:
1.99.25: maxT's multivariate normal probability by Genz-Bretz quasi-Monte Carlo (abs. error 1e-4) spicy(combine = "maxT") computes P(max |Z_k| > c) for Z ~ N(0, R) with the quasi-Monte Carlo method of Genz (1992) and Genz & Bretz (2009) in place of recursive Gauss-Legendre quadrature (3.2 million evaluations per pair with six radii). Separation of variables on the Cholesky factor with the Genz-Bretz variable reordering; Korobov lattice rules of growing size (parameters from an exhaustive weighted-P2 search, inst/scripts/korobov_search.cpp), baker's transformation, antithetic points and 12 shifts from a fixed-seed SplitMix64; rules combined by inverse-variance weights until 3.5 standard errors < 1e-4 (at most 100,000 points per shift). Deterministic: the same inputs give the same p on every call and at any number of cores. Written from the publications; no mvtnorm code. Two radii keep the quadrature; it stays in the core as mvn_outside_quadrature() (R: stats_mvn_outside_quadrature(), stats_mvn_outside_qmc()). Validation against mvtnorm::pmvnorm (abseps 1e-6): 100 real 10-type calls, max abs diff 6.1e-5 (0.44% rel. at p < 0.05); 308 random/singular K = 2..6 matrices, max abs 1.0e-4 (4.8% rel. for 0.001 <= p < 0.05). Real calls: 18 ms against 233 ms (pmvnorm at 1e-4: 28 ms). On 4,200 timing pairs 6 p change by > 1e-4 (max 1.4e-4), none crosses 0.05; only p_value, p_adj and unadjusted_p_* change. Non-maxT results identical(): refs.R 18/18 non-maxT cases (the 8 that differ all contain maxT), memref 7/8 (radii is maxT), cores 8 = cores 1. Tests pass (258, 2 skip), with a new test against pmvnorm (mvtnorm in Suggests). R CMD check: only the concaveman.hpp WARNING. Timing, maxT over 6 radii, 50 images x 5,000 cells, 1 core: 80 types 141 s (1,438 s), 40 types 32 s (381 s). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4Package: OMA
Commit: e18366ecb4b9b5026ddb09f1436a8519536b55fd
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2026-10-16 08:58:13 +0300
Commit message:
Fix ML chapter build (#903)Package: OMA
Commit: 5cab63b1fd8baedcb165f344c610eb4f9912e4b7
Author: Sadia Zaman <69467219+Sadia12345@users.noreply.github.com>
Date: 2026-10-16 08:35:38 +0300
Commit message:
Change miaverse to OMA in overview, refs #895 (#900) Co-authored-by: Muluh <127390183+0xMuluh@users.noreply.github.com>Package: spicyR
Commit: 9c6becb2ca04ce8627648066c619346cec02616e
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-16 14:37:08 +1100
Commit message:
1.99.24: every pair at every radius in one core call (pair_tests); writeCellStore() region key categorical spicy() (cell method, two conditions) runs the image rows, the image random effect, the frailty test, the adjusted design and the multi-radius combination for all pairs and radii in src/core/src/pairs.cpp (pair_tests, pair_design_test), bound as stats_pair_tests(); R builds each table column-wise. Results identical() to 1.99.23 (26 reference cases, memref 8/8). Omnibus (25 radii, davies) at 80 types: 263 s -> 8.6 s; single radius at 80 types 10.9 s -> 0.6 s; 10M cells unchanged. Rows bindings return data.frames without as.data.frame(). writeCellStore(): the image column always categorical, instance IDs at least uint16, and the "array" encoding on nullable values and masks, so Python's spatialdata and anndata read R stores cleanly. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4Package: Rsubread
Commit: 4337825c3de53b4d57f4b28f2546c7d7ec7e8323
Author: Ubuntu <ubuntu@crispr-screening-webservice.novalocal>
Date: 2026-10-16 03:34:32 +0000
Commit message:
added a missing manual page.Package: SpotSweeper
Commit: 7e6ebf68c205cf0c102d8ed6b363752d5288d179
Author: Michael Totty <mictott@gmail.com>
Date: 2026-10-15 22:22:19 -0400
Commit message:
Fix Windows parallel nearest-neighbor search Select socket workers automatically on Windows in localOutliers and localVariance while preserving the workers interface. Add native and socket parallel regression coverage and bump to 1.9.3. Fixes #27.Package: spicyR
Commit: 99ee1cdf682f6fff878b5182a40c1cc846d34d7d
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-16 12:04:50 +1100
Commit message:
1.99.23: writeCellStore() writes the store in chunks of 2^20 rows, in bounded memory writeCellStore() wrote the cell table with one anndataR call, which writes every array as a single chunk: it failed at 100 million cells on the row index, and reading any slice of its stores decompressed the whole column. The table is now written directly, each column, the row index and obsm "spatial" (float64) in chunks of 2^20 rows compressed with zstd, one chunk at a time. The AnnData layout, data types and attributes are those anndataR wrote; uns region_key/instance_key are now string scalars and the per-image table has the SpatialData table attributes, so Python spatialdata reads the stores. spicy() results are identical to the old stores and to the data.frame (100 million cells: write 81 s, +0.4 GB; spicy(r = 25) from the store 1.8 GB on 1 core, 5.2 GB on 8). anndataR is no longer suggested. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4Package: spicyR
Commit: 0da2feac1f37331027302568ae1401d062b01bfb
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-16 10:23:32 +1100
Commit message:
pkgdown: writeCellStore in the reference index Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4Package: spicyR
Commit: f3c8096829cd8828868c6a118288ff8dd04ba375
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-16 10:13:15 +1100
Commit message:
pkgdown workflow: build against Bioconductor devel (3.24), where spatialdataR and its dependencies are Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4Package: spicyR
Commit: c3dab2361eb86ca297fbd68e4a3cd1017eff53ec
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-16 10:08:18 +1100
Commit message:
1.99.22: images with a missing condition left out of the covariate design (#82); BLAS-thread test skipped where BLAS runs one thread Fixes #82. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4Package: BiocDuckDB
Commit: 8b91a688644e71eafdf979ebecb214d7ad1e9c86
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-10-15 13:53:25 -0700
Commit message:
fix: preserve a matrix label's true extent past an all-zero trailing row/column (0.99.26) writeParquet,ANY only attaches index->label categories (the metadata a reader uses to recover the true axis size) when the array already has dimnames at the point it captures them, before it assigns synthetic seq_len() dimnames for the physical write. A spatialLabels() matrix is normally dimname-less, so no categories were ever recorded for the spatial_label_coord path added above, and .readParquetArray() fell back to inferring the shape from the sparse COO data alone -- undercounting whenever the dropped (all-zero) entries included a whole trailing row or column. Fixed by synthesizing dimnames on the label matrix (the same seq_len() values ANY would assign internally anyway) before writing it, so categories are always attached regardless of what the input happened to have. Added a regression test using a label whose only nonzero entry is at row 1/col 1; the existing round-trip test has a nonzero in both the last row and last column, which masked this gap.Package: Rsubread
Commit: 9c10478e63a557e9285b5d2864b0d745a9c4065e
Author: Ubuntu <ubuntu@crispr-screening-webservice.novalocal>
Date: 2026-10-15 20:04:04 +0000
Commit message:
try fixing slow loading indexPackage: BiocDuckDB
Commit: 8097109a601ed78269d7fc39f268fd79da4370bb
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-10-15 11:52:00 -0700
Commit message:
fix: correct spatial_label_coord write path for matrix-valued labels (0.99.26) The spatial_label_coord write path for a matrix/array-valued spatialLabels() entry (writeParquet,MultiAssaySpatialExperiment-method) was broken and had never been exercised by any test or fixture. The internal .matrixToCoordLabel() built a COO triples data.frame (row, col, value columns) and passed it to DuckDBArray::writeCoordArray() along with row=/col= arguments -- writeCoordArray() has no such parameters (they belong to the unrelated DuckDBMatrix() constructor), so they were silently swallowed by ..., and the COO data.frame itself was passed as the array to write, whose dim() is (nnz, 3) rather than the original matrix's (nrow, ncol). Separately, the resource dict for this layout carried no schema field, unlike every other array writer, so .readParquetArray() could never detect the 2 keycols needed to dispatch to DuckDBMatrix() on read and silently fell back to DuckDBArray() with no datacol or keycols at all. Fixed by writing the label matrix through the existing, already schema-correct writeParquet,ANY-method (the same path used for every other array-like object) instead of a bespoke COO assembly, which fixes both problems by construction. Removed the now-dead .matrixToCoordLabel(). Added a round-trip regression test (writeParquet() + readParquet() a matrix-valued label, asserting it comes back as a DuckDBMatrix with the original values).Package: gDRutils
Commit: 299807bf2a7c45ee414a26c9712d8853f25e907e
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2026-10-15 20:11:54 +0200
Commit message:
Merge pull request #205 from gdrplatform/GDR-3487 feat: record the recipe of each fit in SE metadataPackage: gDRutils
Commit: d34a07be7c38d2673f8b0449335258daef245276
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-10-15 12:48:09 +0200
Commit message:
test: check max_bytes of record_processing_step()Package: gDRutils
Commit: 0228479a6387cbcb17f70b652f8e691f8cb95ff2
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-10-15 12:48:09 +0200
Commit message:
feat: let record_processing_step() store larger settings when askedPackage: gDRutils
Commit: 84c0dc0858246dea88fcdba794278f78721f7576
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-10-14 16:18:25 +0200
Commit message:
test: check that replace drops recipes of other fit sourcesPackage: gDRutils
Commit: 3fb958ad97c271992fd9c48e3cddccb2b6aa55a0
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-10-14 16:18:25 +0200
Commit message:
feat: let record_fit_provenance() drop the recipes of an overwritten assayPackage: gDRutils
Commit: 944e2b66990761b78a997680f037f70c76a75a5e
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-10-14 16:13:24 +0200
Commit message:
chore: mention the provenance recorders in NEWSPackage: gDRutils
Commit: fa4d7a37d8256fa73cbd3b0261c874253d06a5d4
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-10-14 16:13:24 +0200
Commit message:
test: cover recipes of SE-level functions and processing stepsPackage: gDRutils
Commit: 5d624d2d8c4bdf5d68e5ada71aa951bf5df9fafc
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-10-14 16:13:24 +0200
Commit message:
feat: add record_fit_provenance() and record_processing_step() for code outside apply_fit()Package: gDRutils
Commit: 9802efead077c2c49a7e7abde9fc855e1bf0ec42
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-10-14 15:57:21 +0200
Commit message:
test: check that fitting the same data twice gives an identical objectPackage: gDRutils
Commit: 741a3f40f46dfbcefbe13d2ae5abfe77c95729a0
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-10-14 15:57:21 +0200
Commit message:
docs: list the fit provenance functions in the pkgdown referencePackage: gDRutils
Commit: d859c8c2c49c288d467d5bccdba37c7c0a2de842
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-10-14 15:57:21 +0200
Commit message:
fix: leave the run time out of the fit recipe so repeated fits give identical objectsPackage: gDRutils
Commit: 0341febf3dc54139d6d5584130ca525afa5e261c
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-10-13 17:40:54 +0200
Commit message:
chore: bump version to 1.11.18 and update NEWSPackage: gDRutils
Commit: 18c60a8b9a0027c64b59412de6f6cad3332ba241
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-10-13 17:40:48 +0200
Commit message:
test: cover fit provenance and single calls of multi-output functions in apply_fits()Package: gDRutils
Commit: 147ca52691552b03795b05d921ff3b97a3929569
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-10-13 17:39:22 +0200
Commit message:
feat: record the recipe of each fit in metadata(se)$provenancePackage: gDRutils
Commit: d163764559899ff6b480002b19ff4ccd1c703ae8
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-10-13 17:39:13 +0200
Commit message:
fix: stop apply_fits() from writing every row twice for a multi-output functionPackage: quantMSImageR
Commit: d1987f264383c7995d80b8a3679670ddb1d9e366
Author: Matthew Smith <matthew.smith@ki.se>
Date: 2026-10-15 19:12:57 +0200
Commit message:
Version 0.99.10: blocking, per-block ion images, stitch overlap Correct a study for a factor that is not the comparison -- the patient a paired set of treatments came from, the sex of an animal, the slide an acquisition sat on. * `block:` names that factor per sample, beside the `group:` being compared. `parameters: block_centre:` decides what to do about it: `center` divides each feature by the block's own geometric mean, `baseline` by its `baseline_group` arm so a value reads as a fold change against its own control. `off` is the default, so declaring a block changes no number on its own. The correction is multiplicative, so a block's gain goes and the size of its response stays. It reaches the heatmaps and the comparison plots; the ion images stay uncorrected, because an image should show the intensity that was measured. A corrected report says so and gains `blocked` in its filename. `blockCentre()` is exported. * `output: ion_images:` collects the display settings every image in the report shares. `percentile:` is the cap -- previously the animation was fixed at 95, the dropdown computed its own, and the concentration images silently took 99. `scale_within:` gives each block its own colour scale, drawn as one column per block with its groups as rows and replicates across, each column stating the value it is capped at. * `stitchAcquisitions(overlap = )` and `parameters: stitch_overlap:` for pieces of one tissue that share a strip. `error` stays the default. * `fData()` carries `collision_eV` and `cone_V`, so the feature table tells two transitions apart without a trip to the raw data. * A sample's group is given by `group:` rather than `label:`, and `baseline_label:` by `baseline_group:`. Both old names keep working and `validateConfig()` says how many samples still use them. * `heatmap_style: auto` no longer picks the contribution heatmap when the z-score behind it cannot resolve anything: that score is taken within a region, so a region of two rows saturates whatever the data says.Package: dominoSignal
Commit: 80f2f89695bb4a2849b0fc7b53b8fd140aa2014c
Author: kjkrishnan <60410113+kjkrishnan@users.noreply.github.com>
Date: 2026-10-15 12:39:30 -0400
Commit message:
Promote dev to master (v1.7.1) Bioconductor devel release in preparation for 3.24Package: dominoSignal
Commit: e2b463afdfba73352d218733f905467dc39a3a88
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-14 13:03:59 -0400
Commit message:
Logo update with bioconductor templatePackage: dominoSignal
Commit: 2f922f03410a8f7c87ab6d3ebc8524b24df5c9f3
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-14 13:02:23 -0400
Commit message:
Logo update with bioconductor templatePackage: dominoSignal
Commit: 12b3415417fd26dc0f0dc75ebe919017927aeb01
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-12 22:29:37 -0400
Commit message:
Address review comments and add associated testsPackage: dominoSignal
Commit: 609ed42ba3b2b51996caf716859be9d89fcb46f8
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-12 12:00:29 -0400
Commit message:
Stop tracking inst/pkgdown.yml filePackage: dominoSignal
Commit: 6e1ae49a310902de361edb18c25593e128f361da
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-12 11:17:04 -0400
Commit message:
Merge master into dev history for sync (keep dev content, master fixes manually ported to dev already)Package: dominoSignal
Commit: 552034101cffbc3badc913a1621b5a78c4cbf43a
Author: kjkrishnan <60410113+kjkrishnan@users.noreply.github.com>
Date: 2026-10-12 11:01:59 -0400
Commit message:
Merge pull request #200 from FertigLab/sync/compress_data Recompress test dataPackage: dominoSignal
Commit: 9124cfdb16cff27e89e71d43c09fdbea3245f3c0
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-09 21:55:34 -0400
Commit message:
Recompress sysdata with xz instead of bzip2Package: dominoSignal
Commit: 9caf04fc97a0f82adb8001e455ec346df4285b61
Author: kjkrishnan <60410113+kjkrishnan@users.noreply.github.com>
Date: 2026-10-09 20:51:44 -0400
Commit message:
Merge pull request #199 from FertigLab/review/example_data Regenerate example data with newest version, update vignettes and other documentationPackage: dominoSignal
Commit: f9d340eee262d38e8496a44a0c0e2231a7cf930a
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-09 19:48:49 -0400
Commit message:
Update roxygen2 version; fix faviconsPackage: dominoSignal
Commit: 5d46a89e8c4bafa37303bf582d6b6e80f01907b9
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-09 19:23:27 -0400
Commit message:
Update and organize changelog.Package: dominoSignal
Commit: 0182c6601e84dcb23a7104f8862e7a2cb476b4ee
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-09 18:00:18 -0400
Commit message:
Regenerate example data with newest version, update vignettes and documentation for consistent terminology and accuracy, clean up links in vignettes, improve accessibilityPackage: dominoSignal
Commit: f45472fb1850c5ad7304c582ad68e10754f362ae
Author: kjkrishnan <60410113+kjkrishnan@users.noreply.github.com>
Date: 2026-10-08 20:18:07 -0400
Commit message:
Merge pull request #198 from FertigLab/review/tweaks Minor tweaks to documentation, parameters, error handlingPackage: dominoSignal
Commit: d2660717d0edbb3743e39f375becce6e5e2dff98
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-08 19:52:11 -0400
Commit message:
Generate documentation, fix typos, clarify wording.Package: dominoSignal
Commit: 61b356687450a1b1289e4b6bfc409c51fa209acb
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-08 19:39:32 -0400
Commit message:
Update documentation, update function parameters, use log10(x+1) instead of log10(x) in heatmap plots to avoid errors, explicitly handle 0/0 in signaling network, fixed scenic commands + comments in vignettePackage: dominoSignal
Commit: 4e11808b081450e6ae113a075e56dbfa08a41141
Author: kjkrishnan <60410113+kjkrishnan@users.noreply.github.com>
Date: 2026-10-08 18:28:41 -0400
Commit message:
Merge pull request #197 from FertigLab/review/bugfixes Bug fixes and changes to data validation to avoid silent crashes, along with better handling of different inputs, and clearer warning/error/messages to user.Package: dominoSignal
Commit: a4720f9eec38f5ccbea74070e18eb622f410a95e
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-08 18:03:00 -0400
Commit message:
Fix error handling in dom_to_df when complexes miss components (and associated tests).Package: dominoSignal
Commit: f32f40755b5e1b79192875a9bff29e5e94708b9b
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-08 15:42:32 -0400
Commit message:
Fix copilot bugs - error handling in create_domino for missing receptor genes, create_rl_map_cellphonedb gene conversion edge cases, returning appropriate objects even with empty resultsPackage: dominoSignal
Commit: 7c5e68b3a6aa83f21012f2b67bd87d8525331c8a
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-07 18:34:34 -0400
Commit message:
Fix typos, update news, move pull request template and workflow documentation to avoid pkgdown quirkPackage: dominoSignal
Commit: dc2aeae3a0b716239db37fe916c462e0118c3b77
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-07 17:28:02 -0400
Commit message:
Bugfixes for dom_to_df: default parameter for exp_type is counts, empty data frame returned if no signaling is found, handles objects with no complexes (and associated tests).Package: dominoSignal
Commit: 8133b48b7fede4348113409486fc9f681eb3c6f7
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-07 17:03:22 -0400
Commit message:
Bugfixes for create_rl_map_cellphonedb: skip interactions when components lack orthologs, handle missing receptor annotations in protein input, update documentation for gene conversion options (and associated tests).Package: dominoSignal
Commit: 30b49071fc93bfbe5aede6fdaad511b769773f72
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-07 16:07:20 -0400
Commit message:
Bugfix for count_linkage: correctly count subjects when name column is a factor (and associated tests)Package: dominoSignal
Commit: a6df5f84a800435214177b5803a47541d1d224a9
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-07 15:49:31 -0400
Commit message:
Bugfixes for linkage summary functions: update ordering/matching for subject names and metadata, improve error handling, add validity checks to linkage summary object, and associated tests.Package: dominoSignal
Commit: 031a7deefd14fe69024b6f421a088cfe6fb81331
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-07 15:26:16 -0400
Commit message:
Bugfixes for build_domino function: update parameter descriptions, fix error messages, add message for no active TFs, adjust handling of complex ligands, and associated tests.Package: dominoSignal
Commit: 804c5d426d2f23abc3028cbcef404ecacf033e77
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-07 14:15:36 -0400
Commit message:
Bug fixes for create_domino function: improve parameter descriptions, add checks/warnings for invalid inputs, refine handling of rl interactions, and associated tests.Package: dominoSignal
Commit: f767e33bcea4b54f1ad63c60a19acb345afe1af9
Author: kjkrishnan <60410113+kjkrishnan@users.noreply.github.com>
Date: 2026-10-06 18:05:54 -0400
Commit message:
Merge pull request #196 from FertigLab/changes/params Update parameters (and address bugs, validity checks, and documentation), resulting in some breaking changes.Package: dominoSignal
Commit: 5ec98d9e9d206cd65f080333cc9972145b8d69ee
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-06 15:35:32 -0400
Commit message:
Bugfixes: - create_vars stored in domino object in addition to build_vars - cluster networks built in build_domino for all tf selection methods - validity check for object handles empty matrices and unnamed clusters - fix max_tf_pval argument name - Update/add appropriate testsPackage: dominoSignal
Commit: 8bf62febc1914d18df29da05907b7ca4ecb3dba7
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-05 19:16:06 -0400
Commit message:
Update metadata and readme/indexPackage: dominoSignal
Commit: aa844568d1668788333198abe9b31e9682ae5e15
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-05 18:36:07 -0400
Commit message:
Vignette tweaksPackage: dominoSignal
Commit: f60d6ebac3f27d4b82d412748bb9947f73c7a399
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-05 16:43:07 -0400
Commit message:
Regenerate example data with updated package to fix bugsPackage: dominoSignal
Commit: ada1f94fc4c4b1d11aec60493b972ab9dd1bb109
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-05 16:12:44 -0400
Commit message:
Bugfix: align cell inputs by name in create_domino and require matching cell order in domino validity checkPackage: dominoSignal
Commit: 5e6062ee548f654ab2422f169466e477d020cdc2
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-05 15:32:44 -0400
Commit message:
Report package version in print/show and access functionPackage: dominoSignal
Commit: f2fc5a937579c732e96336575be99b24a1fc82c5
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-05 14:33:44 -0400
Commit message:
Add create/build version to domino object and check object validityPackage: dominoSignal
Commit: 41c23409f8d992de952298c0481a4b7593ce4420
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-10-05 14:17:23 -0400
Commit message:
Update default parameters in create_dominoPackage: dominoSignal
Commit: dedead4fbe65904efd979c1bd42629163f75a287
Author: kjkrishnan <60410113+kjkrishnan@users.noreply.github.com>
Date: 2026-09-25 15:37:24 -0400
Commit message:
Merge pull request #195 from FertigLab/documentation/differential_workflow Document differential domino workflowPackage: dominoSignal
Commit: 00f36ffa5677b2b05a20d587a08171748a2d4ae3
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-25 14:54:50 -0400
Commit message:
Update documentationPackage: dominoSignal
Commit: a79eda4dd2e3a7dfcaa5fb29b471bd080c016b5a
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-25 14:52:02 -0400
Commit message:
Spell check, linting, address copilot review notesPackage: dominoSignal
Commit: a6b65f65e17036c4cf61bb9bf28c02a56a6c79bf
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-24 18:45:49 -0400
Commit message:
Merge origin dev into documentation/differential_workflowPackage: dominoSignal
Commit: b97735c4d8b04ecf068bcef1a7a8037df1fc37e7
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-24 18:42:43 -0400
Commit message:
Add example runs to dominoSignal and differential workflow vignettesPackage: dominoSignal
Commit: bd8a53a84e4b60e36a95e3ec74aedea7c37e3fd8
Author: kjkrishnan <60410113+kjkrishnan@users.noreply.github.com>
Date: 2026-09-24 18:19:13 -0400
Commit message:
Merge pull request #193 from FertigLab/bugfix/differential_functions Bug fixes for differential workflowPackage: dominoSignal
Commit: f3dc18aae9ebddca9e9f0927bd9b4f869c672f52
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-24 13:43:41 -0400
Commit message:
Update show-linkage_summary methodPackage: dominoSignal
Commit: abcd2e9b346566a7de617c406406684047f59e71
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-24 13:42:50 -0400
Commit message:
Add linkage_summary object validation, update show/print methods, add testsPackage: dominoSignal
Commit: 1377c9ac779e499d7644e711504128767f1f140c
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-24 11:16:23 -0400
Commit message:
Address linkage_summary subset commentsPackage: dominoSignal
Commit: 9073df4cc5d3afaec1e22cf009b1e070e2e27c76
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-24 10:49:34 -0400
Commit message:
Update link_summary argument in data-raw/ scripts for test/tiny data; remove test_namePackage: dominoSignal
Commit: 84b2bc99f014fdc35ae114023de7a3e9be41953e
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-24 10:41:27 -0400
Commit message:
Update plot_differential_linkages function: - Gradient argument - Allow plotting odds.ratio (check for NA values) - Improved checks for statistic range - Added testsPackage: dominoSignal
Commit: 1a085bab618be5ecaa10660478c56813d32b75c8
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-24 10:36:54 -0400
Commit message:
Add vignette for differential signaling workflowPackage: dominoSignal
Commit: be50b353a7c330d2fa12bdf9ca463df0385e0617
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-22 18:09:27 -0400
Commit message:
update bioc gha with libomp for macPackage: dominoSignal
Commit: 3bed14c4da52a0160deef908a7f609dec8e0d5ed
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-22 18:07:37 -0400
Commit message:
Merge branch 'bugfix/differential_functions' of https://github.com/FertigLab/dominoSignal into bugfix/differential_functionsPackage: dominoSignal
Commit: 2a71b172374998c03dcd022c9b32b6db480e9606
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-22 12:41:10 -0400
Commit message:
Make libomp available in R scripts for bioccheck ghaPackage: dominoSignal
Commit: 16629df797abc74e599fd2b20115c628ad1671b6
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-22 17:50:11 -0400
Commit message:
Make libomp available in R scripts for bioccheck ghaPackage: dominoSignal
Commit: 23edef2a607b6ec2b0d98f9de1e92ea3b800c579
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-22 13:00:53 -0400
Commit message:
Install libomp in bioc GHA /nocachePackage: dominoSignal
Commit: f6fdefd42a5d16da8b514051241c19ea66a295ad
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-22 12:41:10 -0400
Commit message:
Update bioc GHA /nocachePackage: dominoSignal
Commit: 2ac6425d170f338ba569aa9dc511244049f8cd95
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-21 17:39:34 -0400
Commit message:
Update summarize_linkages example documentationPackage: dominoSignal
Commit: 10b9db3e804a5b092ab48d75ff851778d0f16010
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-21 16:43:52 -0400
Commit message:
Add BrE alternative spellings for relevant function namesPackage: dominoSignal
Commit: d96f63add18b07315e1ab8dd947cc2c788a30a81
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-21 16:26:34 -0400
Commit message:
Bug fix: empty linkages in summarise_linkage function no longer return spurious NA <- NA resultsPackage: dominoSignal
Commit: 47a0f1d9e06615ceec68f1feefd1373d6f9431d1
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-21 15:46:13 -0400
Commit message:
Bug fix: implement filtering by subject_names in count_linkage and test_differential_linkagesPackage: dominoSignal
Commit: ee2f20f79b7e47ec61d48068f68316e0412dd29c
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-18 18:56:33 -0400
Commit message:
Merge branch 'dev' of https://github.com/FertigLab/dominoSignal into bugfix/differential_functionsPackage: dominoSignal
Commit: cde785e6f0ac78a66c380b542a6111eba88991a3
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-18 18:56:16 -0400
Commit message:
Add subset method for linkage_summary class (and associated tests)Package: dominoSignal
Commit: 39c5781ec4d2b0645880c24ac66219f5cc8cc60d
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-18 17:41:55 -0400
Commit message:
Fix odds.ratio assignment in test_differential_linkages for more than 2 groups and add test.Package: dominoSignal
Commit: 5e4cda58af4037a41202364a61180a14da521aa2
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-18 17:27:59 -0400
Commit message:
Update count_linkage() argumentPackage: dominoSignal
Commit: c5beca896a4e93dab116caf38df06674bfa9ff2d
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-18 17:09:58 -0400
Commit message:
Update test_differential_linkages argumentsPackage: dominoSignal
Commit: 597cb42a643cb6b4a8a225934c561b2bf346fda0
Author: kjkrishnan <60410113+kjkrishnan@users.noreply.github.com>
Date: 2026-09-18 16:36:49 -0400
Commit message:
Merge pull request #192 Bug fixes (issue #191, silent failures for single ligand/receptor for a cluster)Package: dominoSignal
Commit: 1f7e91636da0a8097ea5bb7bf465e6340f52fab2
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-18 14:44:49 -0400
Commit message:
expect_identical -> expect_equal for object comparison in create_domino testPackage: dominoSignal
Commit: 1e53b5f2411d392028fb02ec3286c7cb9eac19f7
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-17 15:32:08 -0400
Commit message:
Bug fixes: - Fix create_domino to work with custom rl_map without name columns - Fix build_domino silent exclusions for single ligand or receptorPackage: dominoSignal
Commit: 35e84fd1b6cce862d44d6f88ae33af62a6ce78ac
Author: kjkrishnan <60410113+kjkrishnan@users.noreply.github.com>
Date: 2026-09-17 11:08:29 -0400
Commit message:
Update GHAs Update GHAs for documentation, docker build, BiocCheckPackage: dominoSignal
Commit: b257e8bcfb461fe643fa5261498075bc25e83dd5
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-16 15:05:37 -0400
Commit message:
Include testthat in Bioc CheckPackage: dominoSignal
Commit: 4036292ceabe96e656d826ae0fff53dc6a34652d
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-16 14:50:21 -0400
Commit message:
Update roxygen2 version and documentationPackage: dominoSignal
Commit: 74abd9ae022bbfed130d54f3951bdf4c2fb69ad7
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-16 14:10:02 -0400
Commit message:
Remove docs files; fix pkgdown references; update documentation workflowPackage: dominoSignal
Commit: e68ddc4e462f840cd4112dcc897ee21f55cf5c18
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-09-16 11:57:03 -0400
Commit message:
Address copilot reviewsPackage: dominoSignal
Commit: bb01efb10484bcb33142b41e50b7e4871e8d0275
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-06-04 12:52:06 -0400
Commit message:
Update GHAs and admin: - Consolidate .gitignore files - Update Dockerfile - Add bioccheck GHA - Add PR templates and GHA for master branch PR checklist - Change documentation GHA from commit to check - Update page deployment workflow version for pkgdown deployment - Add concurrency checks to avoid duplicate actions simultaneouslyPackage: dominoSignal
Commit: f72df40c4d8d5828fb71d70fdccb9e9e9e4e38af
Author: kjkrishnan <60410113+kjkrishnan@users.noreply.github.com>
Date: 2026-05-26 13:43:19 -0400
Commit message:
Merge pull request #189 from FertigLab/sync/pull_master-dev reconcile master-only changes into dev after bioconductor releasePackage: dominoSignal
Commit: 70540f6c803a6d4927782fe247c61ed7024e5402
Author: kjkrishnan <kjkrishnan@users.noreply.github.com>
Date: 2026-05-18 21:37:56 +0000
Commit message:
Update documentationPackage: dominoSignal
Commit: f39358333dadcf8a672c64fdcafd1058c2c661ba
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-05-18 17:36:13 -0400
Commit message:
documentation fixesPackage: dominoSignal
Commit: f8c24040640da5cbdcdd26903898fb0b49882288
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-05-18 17:22:22 -0400
Commit message:
Add zero protection to link subsetting in gene_network functionPackage: dominoSignal
Commit: 6f6834f319fa50ec114b3cb4582310fe7a0c968c
Author: kjkrishnan <kjkrishnan@users.noreply.github.com>
Date: 2026-05-11 17:43:11 +0000
Commit message:
Update documentationPackage: dominoSignal
Commit: 2f933cb75096d62a65866af0f4947a12da5e2184
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-05-08 15:55:55 -0400
Commit message:
Update vignettes to fix URLsPackage: dominoSignal
Commit: aa6ae2e70600d8ac8da5b6c0bf431d0e6c84d8e9
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-05-06 17:42:38 -0400
Commit message:
Fixes to gene_network() function (see commits b3e8b65 and 0c864dd)Package: dominoSignal
Commit: 688746d3d75d2f6c3905dc3b15d7c916c2d5f320
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-05-06 17:07:20 -0400
Commit message:
Documentation and pkgdown updates - Fix _pkgdown.yml to include accessible colors for dev site version - Update citation in CITATION, README.md, and DESCRIPTION - Change installation information to reflect Bioconductor - Update URLs for links - Update NEWS.md to match stable release versioning - Add workflow notes for bioconductor and github sync - Remove out of date GHAs (pulled from commit 86b9188; syncs changes from commits 069cd9, d5c2e57, 3780907, 9c3c131)Package: dominoSignal
Commit: 9e7da9df315e389078523907af42891131930934
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-05-06 15:16:41 -0400
Commit message:
Documentation updates - Add @family and @seealso to function documentation - Clarified parameters (see commits 0c55514 and b46572c)Package: dominoSignal
Commit: 86b9188b10ac19d264e3329178eeb0521a6a3d2c
Author: kjkrishnan <60410113+kjkrishnan@users.noreply.github.com>
Date: 2026-05-05 14:24:44 -0400
Commit message:
Merge pull request #185 from FertigLab/bioconductor/devel-3.23 Set master branch of repository to mirror devel branch of Bioconductor 3.23 release.Package: dominoSignal
Commit: 7f49e0c8465d95a8778ce65fbcd65d91560d5d42
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-04-17 18:25:51 -0400
Commit message:
Swapped to native R pipe instead of magrittr; added .log for BiocCheck outputs to .gitignorePackage: dominoSignal
Commit: 86ff8e95c34949c201cb849d7a8c3e7f0402705f
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-04-17 18:24:58 -0400
Commit message:
Bug fix for dom_to_df - Fixed bug resulting from rowname assignment in get_ligand_expression helper function - Added message for duplicate clusters - Added filtering for ligand/receptor expression if using counts, tf_auc for both counts and z_scores to be greater than 0 - Implemented tests for duplicated ligand/receptor/complex names - Implemented tests for filtering - Updated existing tests based on changes to intermediate data structures - Added helper functions for to modify domino objects in testing Hopefully resolves #183Package: dominoSignal
Commit: 0c9462b9de1408e9f25ef381b6355b56ffc8daf6
Author: kjkrishnan <60410113+kjkrishnan@users.noreply.github.com>
Date: 2026-03-17 17:20:34 -0400
Commit message:
Merge pull request #140 from branch for issue #138 add test if build_domino fails w/o tf p-values < thd resolves #138: build_domino fails when no TFs have a p-value below the threshold for one or more clusters.Package: dominoSignal
Commit: 00bc7a59b0ff8132ce0ad5454f26c728c835c456
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-17 16:46:56 -0400
Commit message:
update test parameters for new argument checksPackage: dominoSignal
Commit: dd82ff206ec796430bf0177bb79f12794534fa9c
Author: kjkrishnan <60410113+kjkrishnan@users.noreply.github.com>
Date: 2026-03-17 16:00:52 -0400
Commit message:
Merge branch 'dev' into 138-build_domino-fails-when-no-tfs-have-a-p-value-below-the-threshold-for-one-or-more-clustersPackage: dominoSignal
Commit: 14472cd5596bbb2c5f1cb7f5972b799d2a7b57d7
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-17 15:58:54 -0400
Commit message:
move new build_domino test to correct file for merge to devPackage: dominoSignal
Commit: 45ecac27378a52bc49feaac8028b6cd60f158db2
Author: dimalvovs <dlvovs1@jh.edu>
Date: 2026-03-17 13:27:36 -0400
Commit message:
Update tests/testthat/test-processing_fxns.R Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>Package: dominoSignal
Commit: 245efc64fb104cebad9009e9b49a233633d2e4aa
Author: kjkrishnan <60410113+kjkrishnan@users.noreply.github.com>
Date: 2026-03-16 17:38:20 -0400
Commit message:
Merge pull request #175 from FertigLab/feature/dom_to_df Add dom_to_df function, along with helper functions and associated tests.Package: dominoSignal
Commit: 2b815fc8007f339a43128ffcf8df7042b5c7465d
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-16 16:37:03 -0400
Commit message:
copilot fixes avoid direct modification of test fixtures remove NAs when subsetting ligandsPackage: dominoSignal
Commit: 000b8e6c4e1ac426a0e1e995bb07165ccf3b8409
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-13 14:16:13 -0400
Commit message:
Refine tests, fix typosPackage: dominoSignal
Commit: 5161a252a0cf02d18f2a678c491487237bde4260
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-12 19:30:52 -0400
Commit message:
Simplified if statements in get_signaling_info functionPackage: dominoSignal
Commit: 2f0bf6ec45ca06e2b14ad0b53ea85bbcacedc74f
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-12 19:07:19 -0400
Commit message:
Added tests for dom_to_df and related helper functions.Package: dominoSignal
Commit: 9061258c96bc0a8d72f1ef6b40e719c46b937e4c
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-11 19:01:17 -0400
Commit message:
Add dom_to_df function and helper functionsPackage: dominoSignal
Commit: 80085faffd17d36a32d1bc4108b29af212548f56
Author: kjkrishnan <60410113+kjkrishnan@users.noreply.github.com>
Date: 2026-03-11 14:25:54 -0400
Commit message:
Merge fix/plotting bugs Address bugs in gene_network and signaling_network functions. Update testing suite to use testthat v3 (with related testing adjustments).Package: dominoSignal
Commit: ba17c0c403db4fa75889709409b9e9e624f0ed9a
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-11 13:00:14 -0400
Commit message:
address applicable copilot commentsPackage: dominoSignal
Commit: 6848271ff73685d51db303e5572ec0be61c1e5f2
Author: kjkrishnan <kjkrishnan@users.noreply.github.com>
Date: 2026-03-10 19:18:36 +0000
Commit message:
Update documentationPackage: dominoSignal
Commit: 2c03c708691f8931db435743fd140216e9b89107
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-10 15:17:05 -0400
Commit message:
Fix bug in signaling_plot Addresses NA values created by scaling in signaling_plot Changed warning to error if no signaling is found with parameters entered May help to resolve #155 (if the NAs were causing that issue, which is not totally clear)Package: dominoSignal
Commit: 466f9fa6eeadb33721e31b432e330eee71c499dd
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-09 17:51:58 -0400
Commit message:
Pull changes made to dev into branch before any other conflicts arisePackage: dominoSignal
Commit: b2ebea5b0a37102f25975973a7ebe4bef4863043
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-09 17:15:14 -0400
Commit message:
Bugs in gene_network function: Moved cluster naming outside of loop to prevent repeated prefixing. Should resolve issues #166, #157, #156 (also updated testthat to v3 and modified a few tests to address changes)Package: dominoSignal
Commit: 60e3582eefb4049e38f97869a52645f36f2b4563
Author: kjkrishnan <60410113+kjkrishnan@users.noreply.github.com>
Date: 2026-03-09 17:10:36 -0400
Commit message:
Merge from refactor/testing_data to dev Create more comprehensive example and testing dataPackage: dominoSignal
Commit: f5f96e82606da47d34ba08ac445ed0f1f639016c
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-09 16:27:00 -0400
Commit message:
address relevant copilot commentsPackage: dominoSignal
Commit: 32f01bd92fc9ad08076a6601def62b799500225d
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-09 15:35:04 -0400
Commit message:
Set up testing: - Testing file for each file for easier use - Bare minimum test for every function (function runs) - All tests use internal testing dataPackage: dominoSignal
Commit: d2a20c0ecf49bb4fb8e05cb603f374472ef3750f
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-09 14:07:37 -0400
Commit message:
documentation fixesPackage: dominoSignal
Commit: d9b53b7e5ffec48e0bd51f18428bba928a5934f4
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-09 13:02:53 -0400
Commit message:
add test data for linkage functionsPackage: dominoSignal
Commit: b7420f566c319a94db85fac8dd2e17504a2b05f5
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-06 18:17:42 -0500
Commit message:
clean up extra code now that tests/examples are simplerPackage: dominoSignal
Commit: 641bbaae6a488c40a53a96a161f627a7601d9300
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-06 17:58:14 -0500
Commit message:
examples now use toy data instead of relying on other function examplesPackage: dominoSignal
Commit: 16c0e9bd1027016dae8a8b167f96380976f4b7f3
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-06 17:32:28 -0500
Commit message:
simplify tests by reducing internal function callsPackage: dominoSignal
Commit: cdc8124a4ef5bdae0d358b3e47bfd99f23e27b66
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-06 16:53:27 -0500
Commit message:
run scripts and save outputs for exported and internal data. update names of data exports where necessary.Package: dominoSignal
Commit: 9aa125addac64e560975f3b1e80d348558d794be
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-06 16:01:40 -0500
Commit message:
separate creation of exported and internal dataPackage: dominoSignal
Commit: be3a612f122b1ab24789bd7548e6b6541e4e25d7
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-06 15:08:40 -0500
Commit message:
Create multiple domino objects for testingPackage: dominoSignal
Commit: 67e2d4661ae90e0a3bfe34fc3d8880ed01d818a3
Author: kjkrishnan <60410113+kjkrishnan@users.noreply.github.com>
Date: 2026-03-05 19:41:33 -0500
Commit message:
Merge pull request #170 from FertigLab/refactor/check_inputs Add input validation to exported functionsPackage: dominoSignal
Commit: 0cc61260448a3c105df406b37786f23a8ae5841d
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-05 19:29:57 -0500
Commit message:
address copilot review commentsPackage: dominoSignal
Commit: b624ba609388545e610f99a4047312007cb3d8c1
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-05 18:30:48 -0500
Commit message:
more precise input checksPackage: dominoSignal
Commit: 46f6671b482f8f70c90c66ff18c409b1b5e282ad
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-05 18:09:31 -0500
Commit message:
check inputs for linkage functionsPackage: dominoSignal
Commit: 42c67683e5217918372c32fff40c6e2bf4fe8163
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-05 17:59:28 -0500
Commit message:
check inputs for count_linkages, plotsPackage: dominoSignal
Commit: 155533f8df708c893835a1df8ce6fbab7bc55f00
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-05 17:18:47 -0500
Commit message:
check inputs for gene conversion, object modification, circos plots, differential linkage plotsPackage: dominoSignal
Commit: aa4fd2719fa94b06a8a618ee9add223527b69a84
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-04 17:42:40 -0500
Commit message:
More input validation: - cor_scatter - count_linkage - create_regulon_list_scenic - create_rl_map_cellphonedb - expression functionsPackage: dominoSignal
Commit: c31349913bb42bac8f25dd5722898a4f8db28d2e
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-04 16:55:51 -0500
Commit message:
recompress rda file (as recommended in check note)Package: dominoSignal
Commit: 6342444afcb0c9a6e63898adcb6d32215374db26
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-04 16:52:25 -0500
Commit message:
check arguments for build_dominoPackage: dominoSignal
Commit: 5964fe5def07ec7fce0aca6cd6d4533f52e2ff5e
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-04 16:40:21 -0500
Commit message:
add domino object input check to access functionsPackage: dominoSignal
Commit: d046f380264412bfc03bef76b3de4115f2c15904
Author: kjkrishnan <60410113+kjkrishnan@users.noreply.github.com>
Date: 2026-03-04 16:20:31 -0500
Commit message:
Merge refactor/syntax to dev Code changes for clarity, consistency, robustness, based on R best practices. Should not change functionality (except for hopefully handling some edge cases more gracefully).Package: dominoSignal
Commit: 9f7246b6a4462aa0a773516307732e135d52b24f
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-04 16:03:45 -0500
Commit message:
Pull automatically updated documentation.Package: dominoSignal
Commit: 6350b115c3ec5ab28c65c0a1c15d1194c456a1c0
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-04 16:02:36 -0500
Commit message:
bug in rl_map gene name assignment; update show/print for linkage_summaryPackage: dominoSignal
Commit: 9f55e3f281c71d4fc60dab8803efa98ef990d64b
Author: kjkrishnan <kjkrishnan@users.noreply.github.com>
Date: 2026-03-04 19:14:13 +0000
Commit message:
Update documentationPackage: dominoSignal
Commit: 3e93257bd4011bebdff570e53f250d80c9b564f1
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-04 14:12:35 -0500
Commit message:
fix typos, small tweaks from copilot reviewPackage: dominoSignal
Commit: d04d8ac7886a3133e9d6476d4d124d3ca7dc0fdc
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-04 13:42:25 -0500
Commit message:
add create rl_map with gene conversion (ensembl and table options)Package: dominoSignal
Commit: 4d542b06df7db28cde3ed53015cd224b36d4f0f7
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-04 13:06:32 -0500
Commit message:
Merge branch 'dev' of https://github.com/FertigLab/dominoSignal into refactor/syntaxPackage: dominoSignal
Commit: fbe636e3a2edf533ac055ce515b430fc36fa87e8
Author: kjkrishnan <60410113+kjkrishnan@users.noreply.github.com>
Date: 2026-03-04 12:00:49 -0500
Commit message:
Merge pull request #163 from FertigLab/refactor/function_to_file Refactor R source files to split into smaller, more focused files (and updating documentation accordingly). Should cause no functional changes.Package: dominoSignal
Commit: 3c93e07a7e222e5920e0dc77334b0b31f1e69af0
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-03 16:28:00 -0500
Commit message:
Merge branch 'refactor/function_to_file' to refactor/syntax after changes to function_to_file based on copilot reviewPackage: dominoSignal
Commit: cd1fc7e7b5c1eef81a5a185cd94a4bd1a49378e2
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-03 15:27:12 -0500
Commit message:
small fixes from copilot code reviewPackage: dominoSignal
Commit: 8fa54f7cacdd797e3c82738e7f61d649f47f3d23
Author: kjkrishnan <kjkrishnan@users.noreply.github.com>
Date: 2026-03-03 19:44:01 +0000
Commit message:
Update documentationPackage: dominoSignal
Commit: 81a6cefaf840be6331575ae0f4cb0a79bf6e2505
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-03 14:40:49 -0500
Commit message:
Linkage functions: - simplify logical tests - remove unnecessary paste inside warnings - change c() to NULL or typesPackage: dominoSignal
Commit: 26aca2937f062f6cfbffce26c33f6a3c16c58912
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-03 14:12:51 -0500
Commit message:
Plotting functions: - replace nested if/else statements with switch - make sure variables don't overwrite anything - use isTRUE and isFALSE to handle arguments that can be boolean or string - replace c() with NULL or types - &/| -> &&/|| - tried to simplify extra loopsPackage: dominoSignal
Commit: 658e90d57fa389f0f9d218d90b39bb3234d042cf
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-02 17:24:33 -0500
Commit message:
Pull automatic documentation updatesPackage: dominoSignal
Commit: b670fa17f40b4b4745b089f06f95135a66fa7e1f
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-02 17:23:44 -0500
Commit message:
Classes and utility functions: - removed unneeded c() - avoid variable names overwriting things - use inherits for class checks - tried to simplify nested if statements/unnecessary ifelsePackage: dominoSignal
Commit: 2c7b3e34b880d00aeee076343a613bf4776d5a06
Author: kjkrishnan <kjkrishnan@users.noreply.github.com>
Date: 2026-03-02 21:02:09 +0000
Commit message:
Update documentationPackage: dominoSignal
Commit: 50f241f077690428f451d03e279d7ab9753f6117
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-02 16:00:27 -0500
Commit message:
Pull automatic update of documentation and merge into feature branch.Package: dominoSignal
Commit: 9c4e9a8c5ed44c0b7a92ee2dce5938f36c35a429
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-02 15:56:10 -0500
Commit message:
generics for show/print for linkage_summary classPackage: dominoSignal
Commit: f70e2b6799a2949108205778f8058f3384619f21
Author: kjkrishnan <kjkrishnan@users.noreply.github.com>
Date: 2026-03-02 20:38:23 +0000
Commit message:
Update documentationPackage: dominoSignal
Commit: d525c018e1f40bd7b29482b787be7044010d3c28
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-02 15:36:27 -0500
Commit message:
Syntax fixes - domino_class: cat -> message, use of nlevels - expression_functions: seq_len(length) -> seq_along, linting - gene_conversion: import biomart, implement check_arg, update documentationPackage: dominoSignal
Commit: cd8ffebb0f85bdfbbc534dba55db81b9bde9d7d7
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-02 13:51:42 -0500
Commit message:
Regulons/RL Map - create_regulon_list: fixed patterns for string splits, linting - create_rl_map: remove extra c(), && in if, fixed patterns, nzchar for empty strings, lintingPackage: dominoSignal
Commit: a1542fd3e00959cb19f31b4e7fa59809c2bc2950
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-03-02 13:08:29 -0500
Commit message:
Syntax and linting - cor_scatter: linting - count_linkage: ensure variable names aren't overwriting anything, linting - create_domino: update for fixed grep patterns, ensure variable names aren't overwriting things, simplify if statements, lintingPackage: dominoSignal
Commit: 1e37ab8d1f230778f25a6614b339230277578fce
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-02-27 17:42:13 -0500
Commit message:
Build domino: - Added fixed = TRUE to grepl for efficiency - Replaced sapply with vapply with type - Made sure variables don't overwrite anything - Seed empty vectors with types - Linting for legibilityPackage: dominoSignal
Commit: 671d37197274bf76dc1e55da8888399793e24bb0
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-02-27 16:55:01 -0500
Commit message:
Access functions: - Use switch instead of nested if statements - Switch from & to && in if statements - Make sure variables don't overwrite anything - Linting for legibilityPackage: dominoSignal
Commit: 5db80780c62dcdf09d8a3b34de6d5f8d587eb1e2
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-02-26 16:16:33 -0500
Commit message:
Moved functions into separate filesPackage: dominoSignal
Commit: 5f1821daa9e0e025300fef65c2d8cd626cecb0ff
Author: kjkrishnan <60410113+kjkrishnan@users.noreply.github.com>
Date: 2026-02-26 13:06:52 -0500
Commit message:
Merge pull request #162 from FertigLab/fix/pkgdown_build Update documentation and accessibility for pkgdown site.Package: dominoSignal
Commit: d27177732e7218bf481a059436bf5c99bcf861ae
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-02-25 17:24:57 -0500
Commit message:
r-cmd-check badge removedPackage: dominoSignal
Commit: 85475a3cf1f31aae20c767d882823277759e4d9d
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-02-25 16:28:03 -0500
Commit message:
Added alt text to vignette plotsPackage: dominoSignal
Commit: 5911e126fc1750a6307b4c1b2a1eb17226b38c85
Author: kjkrishnan <kkrishnan@som.umaryland.edu>
Date: 2026-02-25 14:56:26 -0500
Commit message:
Update pkgdown documentation - Use keyword internal for circos functions used inside plotting function - Fix logo file path in index.rmd - Update URL in description - Rebuild faviconsPackage: dominoSignal
Commit: 83c35d3737d282b825c7e1d413f53817c1266265
Author: dimalvovs <dmitrijs.lvovs@gmail.com>
Date: 2024-11-13 10:10:52 -0600
Commit message:
add test if build_domino fails w/o tf p-values < thdPackage: Rarr
Commit: a48e22c20c857bd7539e15d88a67547047f5f9a2
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-10-15 15:19:09 +0200
Commit message:
Bump versionPackage: Rarr
Commit: 3201f76088f828523d734b7f9aed785b80efa7ff
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-10-15 15:18:51 +0200
Commit message:
Document update_zarr_array() skipping writesPackage: Rarr
Commit: deb7c785674c130247c0920d293423448189673e
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-10-15 15:17:30 +0200
Commit message:
Add test for empty chunks in update_chunk()Package: Rarr
Commit: 73a21eaa473957a2973974a4a820a6b42b778afd
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-10-15 15:14:49 +0200
Commit message:
Avoid writing or rewriting in update_chunk()Package: Rarr
Commit: 46097aa003176dbcbf927cbf79002fa0f37183e9
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-10-15 15:13:49 +0200
Commit message:
Reimplement is_all_fill in CPackage: Rarr
Commit: 8fea57d1ae388898957e0c1c0497fddbf88d6779
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-10-15 13:57:13 +0200
Commit message:
Implement is_all_fill() helperPackage: Rarr
Commit: 6aa29f1034d24b986e54e229793a82ae30a772db
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-10-14 19:09:41 +0200
Commit message:
Add has_zstd() shortcut for R 4.5Package: spicyR
Commit: c369940dac7ebe8dc3cd69d6b403dcb08dee9f5c
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-16 01:20:56 +1100
Commit message:
1.99.21: the cell method's image-by-image loop in the shared C++ core; imageInfo and tableKey; writeCellStore() and a store example in the vignette - src/core/src/stream.cpp, spicyglm/stream.hpp (new, shared with spicyr): batch_totals(), rows_totals() and stream_totals() run each image in a Dataset of its own, the images handed out to threads in turn; scan_codes(), constant_within(), rows_differing(), rows_of_images() and first_appearance_codes() are the passes over the codes. src/glm_bindings.cpp keeps thin wrappers (cell_block_scan replaces cell_layout). Results identical: 222/236 test expectations, memref 8 of 8 identical(), the 100M store identical() to the data.frame run (1 and 8 cores), 100M and 1B results identical() to 1.99.20. - spicy(): `table` is renamed `tableKey`; new `imageInfo` (data.frame or the name of a table of the store or SpatialData object) for condition, subject, covariates or a Surv outcome missing from the cell table, for data.frames and stores (survival from a store now works). Errors for missing and unknown images. - writeCellStore() (exported) writes cells as a SpatialData store with anndataR; spatialdataR and anndataR in Suggests. Vignette: "Very large data sets: SpatialData stores". Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4Package: spicyR
Commit: 1bfe9a915dd06cea72c9f2f5628c1638e70930de
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-15 21:47:58 +1100
Commit message:
1.99.20: NEWS with the timings from stores of 10M, 100M and 1B cells; spicy.Rd Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4Package: spicyR
Commit: 85d1bdc13cf8808da848e0b3d4b14663e85bb393
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-15 20:51:50 +1100
Commit message:
1.99.20: spicy() takes a SpatialData object (spatialdataR): read from its store, or from its table in memory Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4Package: spicyR
Commit: 22bdadf2022c3b719391670b399c19d4831132a1
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-15 20:48:11 +1100
Commit message:
1.99.20: each image in a Dataset of its own, images handed to threads in turn; batch coordinates read a block of rows at a time Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4Package: spicyR
Commit: 966e64d96e1cb04720cdffe6ce5ace03b417bf39
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-15 20:31:57 +1100
Commit message:
1.99.20: one C++ pass per block of rows; coordinates read once per batch and passed as the matrix; batches capped at 2^26 cells Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4Package: spicyR
Commit: 023a91919f93fe3a93793dbb3f800eea24dd5592
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-15 20:10:30 +1100
Commit message:
1.99.20: spicy() cell method reads a SpatialData / AnnData Zarr store block by block and image batch by image batch (identical results) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4Package: spicyR
Commit: df798054af2705b9f4d0e77eba46af161a86b6c9
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-15 19:02:07 +1100
Commit message:
1.99.19: spicy() cell method reads the cells image by image (identical results; ~1 GB instead of ~17 GB above the data at 100M cells) - cell_stream_totals (R bindings only; src/core untouched): gathers a batch of whole images (about 2^21 cells per thread) from the unsorted columns into its own Dataset and calls the same Dataset functions, so every image's sums are bit-identical to the whole-data Dataset's. - .cell_context: no sorted copies; one C++ pass (cell_layout) gives cells and first row per (image, type); constancy of condition/subject checked in C++ with an exact as.character() fallback; whole-data Dataset only with dataset = TRUE (Kontextual, label-clustering factor, tests). - .format_data(sort = FALSE) for spicy(); character imageID/cellType become factors in one pass when ASCII (first_appearance_factor), else factor() as before. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4Package: spicyR
Commit: 1cb0cafabb73b75ff33ee97e0c76e1a6c98c8b14
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-15 17:51:17 +1100
Commit message:
1.99.18: spicy() cell method uses far less memory and time on large data (identical results) - .format_data(ids = FALSE) for the cell method: no cellID / imageCellID string per cell (unused there). - .cell_context keeps one row per image (ctx$pheno) instead of a reordered copy of the whole cell table, and the cells per image and type (nCells) from its counts instead of tabulating every cell again. 10 million cells: peak 4.3 -> 1.35 GB above the data, 78 -> 24 s. 100 million: about 28 -> 17 GB. All spicy() outputs identical() to 1.99.17 on 8 configurations (fraction, count, kNN, 3 radii, Davies over 10, subject, covariate, diabetesData); 199 tests pass. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4Package: exploreSE
Commit: 6a224d7af43c1ef158a7d3416049828b0d81ee67
Author: Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com>
Date: 2026-10-15 15:38:17 +0200
Commit message:
toggles for various plots, expression, enrichmentPackage: mitology
Commit: be6407d63d13b2a01d5c8c6d601a687f9f90376d
Author: Stefania Pirrotta <s.pirrotta.sp@gmail.com>
Date: 2026-10-15 14:45:29 +0200
Commit message:
Update NEWSPackage: mitology
Commit: 2db59cc1eef28b4f399b1b6349707d48bf01c628
Author: Stefania Pirrotta <s.pirrotta.sp@gmail.com>
Date: 2026-10-15 14:45:05 +0200
Commit message:
Update MitoGenesDB objectPackage: mitology
Commit: 526512090bcd6e9d430101d901b9266268835d84
Author: Stefania Pirrotta <s.pirrotta.sp@gmail.com>
Date: 2026-10-15 14:44:33 +0200
Commit message:
update gseaMito functionPackage: OMA
Commit: 61c23de087f3b21162722e7f87215abefee0b530
Author: Muluh <127390183+0xMuluh@users.noreply.github.com>
Date: 2026-10-15 10:11:40 +0300
Commit message:
Update link to clustering information in community_similarity.qmd (#843) Co-authored-by: Leo Lahti <leo.lahti@iki.fi> Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>Package: OMA
Commit: 4142bdb338375413ccbb8eb895859e515bfa1ab3
Author: Muluh <127390183+0xMuluh@users.noreply.github.com>
Date: 2026-10-15 10:07:29 +0300
Commit message:
Add HuMMANet resource reference (#888) Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>Package: OMA
Commit: bbf4728ec28022b6a791eba2ff6f634367a5f1cd
Author: Muluh <127390183+0xMuluh@users.noreply.github.com>
Date: 2026-10-15 09:51:58 +0300
Commit message:
Remove deprecated workflow telemetry action (#880) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>Package: OMA
Commit: 4db61b951d548484d3c12d6b3f0433724797a075
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2026-10-15 09:47:11 +0300
Commit message:
Fix build (#901)Package: OMA
Commit: 729ef8438e47a1eb899519a79994d0b93e45c426
Author: Muluh <127390183+0xMuluh@users.noreply.github.com>
Date: 2026-10-15 09:40:58 +0300
Commit message:
Document swapping alternative experiments (#884)Package: OMA
Commit: bcc80a289dd91acf16c9876be40b110005108057
Author: Muluh <127390183+0xMuluh@users.noreply.github.com>
Date: 2026-10-15 09:16:36 +0300
Commit message:
[Urgent] Repository-wide whitespace and styling cleanup (#897) (#898) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>Package: OMA
Commit: 25867ad77383fa2764001dc7839ad8a98f68efc9
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date: 2026-10-15 09:04:33 +0300
Commit message:
Bump docker/login-action from 2 to 4 (#893) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Muluh <127390183+0xMuluh@users.noreply.github.com> Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>Package: OMA
Commit: 7a87c1e8df4cce3b8abe1de850f189883e5dba30
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date: 2026-10-15 08:56:15 +0300
Commit message:
Bump JamesIves/github-pages-deploy-action from 4.4.3 to 4.9.0 (#891) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Muluh <127390183+0xMuluh@users.noreply.github.com> Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>Package: OMA
Commit: fa69edce1a81abbb13dd822fd2bdb3bd3ab59c32
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date: 2026-10-15 08:50:35 +0300
Commit message:
Bump actions/checkout from 2 to 7 (#892) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Muluh <127390183+0xMuluh@users.noreply.github.com> Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>Package: OMA
Commit: eca67ae00c93643e15009013233f60c0a47598e7
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date: 2026-10-15 08:45:51 +0300
Commit message:
Bump actions/cache from 3 to 6 (#890) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Muluh <127390183+0xMuluh@users.noreply.github.com>Package: Rsubread
Commit: b289baf7a283685ded7152086b0bacd0a8946e50
Author: Ubuntu <ubuntu@crispr-screening-webservice.novalocal>
Date: 2026-10-15 04:13:17 +0000
Commit message:
removed warnings from makevar and LR mismatchPackage: Rsubread
Commit: 182d84341c0dde9d924175d21877f3bf1a21f5ef
Author: Ubuntu <ubuntu@crispr-screening-webservice.novalocal>
Date: 2026-10-15 03:50:37 +0000
Commit message:
Fixed warnings then bumped version numberPackage: carnation
Commit: f3fb020ede7244bb12ddff1c39a20e90f0cab548
Author: Apratim Mitra <16709900+mitraak@users.noreply.github.com>
Date: 2026-10-14 15:24:06 -0400
Commit message:
Merge pull request #46 from NICHD-BSPC/updt_actions Updt actions - turn off `sync-devel` action - set `bioccheck` and `conda` actions to run on devel - remove reference to `r4.3` branch from READMEPackage: carnation
Commit: 5d6ecc78aa78446f3dd984f0107ab2c093241173
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-10-14 15:22:03 -0400
Commit message:
rm ref to r4.3Package: carnation
Commit: 4a7f9809586bd220a52b8f69a585ad0a692b12ac
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-10-14 15:20:27 -0400
Commit message:
turn off sync-devel, set bioccheck/conda actions to run on develPackage: carnation
Commit: 2c1f20bcefdcd6ff0b8eec25a959d02cedd6d2c1
Author: Apratim Mitra <16709900+mitraak@users.noreply.github.com>
Date: 2026-10-14 15:14:13 -0400
Commit message:
Merge pull request #39 from NICHD-BSPC/v1.2.0rc - volcano plot module (@DaleMcCauley) - various plot updates - MA plot - added aspect ratio and alpha controls - new 'refresh' button for reduced reactivity - Gene plot - add option to show unnormalized counts. This is helpful when the data in the `dds` element is pre-normalized, e.g. in proteomics - scatter plot - raw p-values added as a plotting option - plot/table selection panels now open upon selection - aspect ratio control for PCA & scatter plots - analysis table - updated to show all available datasets - obtain file info (size, mtime) and show in the table - improved selection behavior - misc fixes - correctly reset gene scratchpad when loading data so previously added genes don't show up again. - the gene plot function now sets the 'text' aesthetic to `factor()` to stop warnings about statistical transformation - `fromList.with.names` now uses base R column indexing instead of `dplyr::relocate`.Package: carnation
Commit: 66fcc7c13fddaf59a8a7c90e692a3474cdad00a7
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-10-14 14:55:37 -0400
Commit message:
updt NEWSPackage: carnation
Commit: 716855b50562b64656f9bb8f8cc97a373167bd62
Author: Apratim Mitra <16709900+mitraak@users.noreply.github.com>
Date: 2026-10-14 14:48:42 -0400
Commit message:
Merge pull request #45 from NICHD-BSPC/analysis_tbl version bumpPackage: carnation
Commit: 8e3f0f437fc979427bfdd77b08893d5c1a8d50b6
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-10-14 14:03:59 -0400
Commit message:
version bumpPackage: carnation
Commit: e63104db785e62609462971dc6259697373b310e
Author: Apratim Mitra <16709900+mitraak@users.noreply.github.com>
Date: 2026-10-01 13:39:12 -0400
Commit message:
Merge pull request #44 from NICHD-BSPC/analysis_tbl - analysis table - updated to show all available datasets - obtain file info (size, mtime) and show in the table - improved selection behavior - added aspect ratio control to PCA & scatter plots - scatter plot - raw p-values added as a plotting option - plot/table selection panels now open upon selectionPackage: carnation
Commit: f3c8cd845cfffa463fa89526f408102a430d8c8d
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-10-01 13:25:53 -0400
Commit message:
fix arg in formatStyle callPackage: carnation
Commit: 3e50d6f63c0b1a6f3e96fed678d9a1230fb61330
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-10-01 13:13:24 -0400
Commit message:
add aspect ratio input to pca testPackage: carnation
Commit: 44da44e929798b49b81946fe41f517917bb19520
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-10-01 13:13:12 -0400
Commit message:
clean up commentPackage: carnation
Commit: 6edfc35c12d079a14665e4509071a37c6fe615df
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-10-01 13:12:58 -0400
Commit message:
rm non-existent input frm testPackage: carnation
Commit: dac91507627488d9fd18df7e554bf6cd84ca0bd3
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-10-01 12:15:11 -0400
Commit message:
open plt/tbl sel collapse only after selections & reset on loadPackage: carnation
Commit: ad10455f0a720b81666447cd225ea134cc160f97
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-10-01 12:14:50 -0400
Commit message:
rename log2FoldChange to LFCPackage: carnation
Commit: 20552affc897d127548b4174f746d4315c295ab3
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-10-01 12:13:24 -0400
Commit message:
clean up commented linesPackage: carnation
Commit: abfa31467e6e606b104f5c641531c15105d58f9f
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-10-01 10:54:52 -0400
Commit message:
fmt all columns with numeric vals in scatter tblPackage: carnation
Commit: eceabf7eee8665738531000f7e307cd94c1880f3
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-10-01 10:54:19 -0400
Commit message:
add raw pval option to scatter pltPackage: carnation
Commit: 31b1e4196713bdd96ca263ac7045499cd78833cc
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-10-01 10:53:31 -0400
Commit message:
center scatter plt to handle narrow aspectPackage: carnation
Commit: 65914561ae2b7ea768ca0bc8aef685b1bb840e14
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-10-01 10:52:34 -0400
Commit message:
add aspect ratio ctrl to scatter pltPackage: carnation
Commit: 3d40cdd6172ab4c254da7afc859f8bd503579df6
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-10-01 10:28:34 -0400
Commit message:
simplify grid lines settings for scatterPackage: carnation
Commit: ecd4ec236084a7cc00fbd388f99299e7161c80cf
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-10-01 10:12:27 -0400
Commit message:
clean up commented linesPackage: carnation
Commit: b83e54f1dceb928bc69beeee314f6a285d2194b4
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-10-01 10:09:48 -0400
Commit message:
rm wellPanel, repl w strong plot settings headingPackage: carnation
Commit: c619dd7dbf28dd133dda18eef3227535aded1d86
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-10-01 10:03:52 -0400
Commit message:
mv plt settings out of collapse, deindentPackage: carnation
Commit: 36a69cfd74c97bde810500d0ce3245132341f133
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-10-01 10:02:19 -0400
Commit message:
updt ma plt docsPackage: carnation
Commit: e8ddfafb96bab2226b08212eadc24690e9d37442
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-10-01 10:02:03 -0400
Commit message:
add aspect ratio ctrls to pca plotPackage: carnation
Commit: 77b48dab72da43a046de047e3a9e95fc6f494ecb
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-10-01 09:18:01 -0400
Commit message:
add docs about volcano dashed linePackage: carnation
Commit: f55bdce23dc1f923e18b6185c29b344206a5cf22
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-30 17:32:07 -0400
Commit message:
only updt assay input if differentPackage: carnation
Commit: c2e07ce802c55db2507aad27e4bd60338c6137f4
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-30 17:31:52 -0400
Commit message:
updt analysis tbl based on analysis inputPackage: carnation
Commit: e903fd39334235dade7d466b2953f2f35b3b5654
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-30 17:31:19 -0400
Commit message:
get analysis frm tbl selectionPackage: carnation
Commit: 4454cd9f0dda59e8950057a0c614e45e7cfb1650
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-30 17:30:38 -0400
Commit message:
don't wrap size fieldPackage: carnation
Commit: 397c87006c86cad3385cbd57e89abadbf588e490
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-30 17:30:30 -0400
Commit message:
cache analysis desc dfPackage: carnation
Commit: f064b76b256d87bbab551e2c7bff84936a880f7d
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-30 17:29:26 -0400
Commit message:
show all analysis, handle mult fields in descPackage: carnation
Commit: 4657ca92492660888df3c03b9e61a047097ea49d
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-30 17:27:04 -0400
Commit message:
reorder assay listPackage: carnation
Commit: 5f7960c406dd733de23805be4f33660aa6078978
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-30 17:25:31 -0400
Commit message:
get and cache analysis infoPackage: carnation
Commit: 4e1d37a4965460a861ceeaefe88b97f5d8b5e0ce
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-30 17:24:41 -0400
Commit message:
adj proj/analysis tbl rel widthsPackage: carnation
Commit: e7be5d98114809cbe0a4584c88a435a995274661
Author: Apratim Mitra <16709900+mitraak@users.noreply.github.com>
Date: 2026-09-30 15:32:57 -0400
Commit message:
Merge pull request #43 from NICHD-BSPC/volcano_fixes Volcano fixes - Makes the default y-axis for the volcano plots based on raw p-value, as opposed to adjusted p-value. Also, the ability to switch between them. - Addresses bugs found related to autoscaling. - Addresses bug in coloring of points that are the only one off the plot in a certain direction. - Reduced unnecessary branching for displaying clamped points in the interactive plotting function.Package: carnation
Commit: 851b7217b5531f37441091ee53cb86b0a37bcc7b
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-30 15:15:37 -0400
Commit message:
adjust modal helpPackage: carnation
Commit: 432dd4bf5e35af1e850fd77b606087312858e2a4
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-30 15:15:17 -0400
Commit message:
check res cols fr carnation objPackage: carnation
Commit: 3753aaa1c22773f38a82c82f2c5584215108cbcf
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-30 15:14:54 -0400
Commit message:
add validates fr missing colsPackage: carnation
Commit: 370fdf990f344d2b5d95670c04d5056713007e58
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-30 15:14:00 -0400
Commit message:
don't use withSpinner to avoid plot snapping to left & back to centerPackage: carnation
Commit: 2fa7ba1df42d168dc5ed5dc4d75e02f508107003
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-30 15:13:34 -0400
Commit message:
tweak menu and select shown namesPackage: carnation
Commit: e277fb7a31f99c6e65971ea4959e933d82882ca1
Author: Dale McCauley <dale.mccauley@nih.gov>
Date: 2026-09-29 16:48:11 -0400
Commit message:
Updated and added test coverage for volcano plotPackage: carnation
Commit: 737cc7687b0037759cbcb719e09dfce4324cbc80
Author: Dale McCauley <dale.mccauley@nih.gov>
Date: 2026-09-29 14:56:15 -0400
Commit message:
Reduced unecessary branching in interactive volcano plotting function, and other smaller cleanupsPackage: carnation
Commit: dd6a48de4803d2ec2bc9e11790ffd903a5134d4c
Author: Dale McCauley <dale.mccauley@nih.gov>
Date: 2026-09-29 11:47:18 -0400
Commit message:
Added guards and notification related to having no points on the graph and autoscaling, including if all points have the same y value. Also fixed bug where when a single point was off the top of the plot and clamped to the edge, it would show an incorrect color.Package: carnation
Commit: 1e64f0d91fb58e8634a29692d82d0092588ad350
Author: Dale McCauley <dale.mccauley@nih.gov>
Date: 2026-09-28 16:25:21 -0400
Commit message:
Made capitilization of colors for the volcano plot more consistent. ggplot expects lowercase and plotly expects upper so it is stored as upper and passed to ggplot with tolower()Package: carnation
Commit: 6f299555e00a8b0e6c4eaabd583d1547ca6c1a2c
Author: Dale McCauley <dale.mccauley@nih.gov>
Date: 2026-09-28 15:33:38 -0400
Commit message:
Added correct raw p-value fdr significance line for static volcano plot and added generated docsPackage: carnation
Commit: 5c0b6ccf7da708e4a8b8331c26274cef507a89ba
Author: Dale McCauley <dale.mccauley@nih.gov>
Date: 2026-09-28 14:37:24 -0400
Commit message:
Added raw p-value and adjusted p-value modes for plottingPackage: carnation
Commit: d9c4852e8ccbb2558fa150e0a760db21444acfe3
Author: Apratim Mitra <16709900+mitraak@users.noreply.github.com>
Date: 2026-09-24 14:52:50 -0400
Commit message:
Merge pull request #42 from NICHD-BSPC/geneplt_fixes_v2 Geneplt fixes v2 - revert gene plot to using `nrow` not `ncol` control. A couple of reasons for this: - Fixing `ncol` in `facet_wrap` was making `ggplotly` behave strangely. Some facets were showing up with no data, facets were being labeled wrong - although the static downloaded plot seemed fine. - The solution was to go back to the way this was being handled before and removing the column number control that was implemented. - misc edits: - the gene plot function now sets the 'text' aesthetic to `factor()` to stop warnings about statistical transformation - `fromList.with.names` now uses base R column indexing instead of `dplyr::relocate`.Package: carnation
Commit: fedcccba8677881ef5baa3cdce82ba2475409df5
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-24 14:29:43 -0400
Commit message:
set aes to factor to stop warnings, repl relocate w base indexingPackage: carnation
Commit: 6a7f7201197b4eb32466af2781850aadec2a82ef
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-24 14:29:24 -0400
Commit message:
revert to using nrow fr gene plt, rm ncol cntrlPackage: carnation
Commit: c0e73b123b6a4455714500da60c7b91957e14fbc
Author: Apratim Mitra <16709900+mitraak@users.noreply.github.com>
Date: 2026-09-24 12:00:54 -0400
Commit message:
Merge pull request #41 from NICHD-BSPC/geneplt_fixes various plot updates: - MA plot - added aspect ratio and alpha controls - new 'refresh' button for reduced reactivity - Gene plot - allow users to fix number of columns in faceted plot - add option to show unnormalized counts. This is helpful when the data in the `dds` element is pre-normalized, e.g. in proteomics - misc fixes - correctly reset gene scratchpad when loading data so previously added genes don't show up again.Package: carnation
Commit: a9de2f2706512fa2cb1c1e370e003640d01b9314
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-24 11:46:50 -0400
Commit message:
updt README to point to release biocPackage: carnation
Commit: 9ef0d82aca0c430dacd04563fe7e2f25e9b87b2e
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-24 11:46:40 -0400
Commit message:
updt plotMA.label docsPackage: carnation
Commit: 9579f85b89d3c0e8b0812aebd35ee73d85ad1b24
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-23 13:19:29 -0400
Commit message:
add opt to show raw counts in gene pltPackage: carnation
Commit: b611d2c234c1427c037f674dcf5bb773cc2a9920
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-23 13:19:07 -0400
Commit message:
add reactiveVal for data loadPackage: carnation
Commit: 9aa3cb222740dcd88ec5bea04a19d68e00ed05dc
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-22 19:35:12 -0400
Commit message:
fix indents, wsPackage: carnation
Commit: e8eccee411879fcb692c1f6c25622ad7dd128cff
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-22 19:30:58 -0400
Commit message:
rm withspinner frm uiOutput wrapperPackage: carnation
Commit: 16281e4b0792fae712e327a56426108e382e8784
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-22 19:30:41 -0400
Commit message:
convert ma plot padding to proportionPackage: carnation
Commit: 18c52ddde28b83c9b526bcafe911a1765e53c91a
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-22 19:30:16 -0400
Commit message:
add refresh btn to ma plot to reduce reactivityPackage: carnation
Commit: 6cdb2c04f6e2a970e7ea2cb6eaf94bfdf06c1f5c
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-22 19:29:41 -0400
Commit message:
add aspect ratio ctrl to ma plotPackage: carnation
Commit: ca5fe77582b249aaafab30c20b15ae4e41da36b8
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-22 19:29:09 -0400
Commit message:
add plot settings input groupPackage: carnation
Commit: 1d1938c9ce4d4166ce11847e414ebe170c63582a
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-22 19:27:35 -0400
Commit message:
add alpha controls to ma plot modulePackage: carnation
Commit: 139ab0ad5e0c8f485f9f196599f97cc2020d050d
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-22 19:25:54 -0400
Commit message:
add alpha args to plotma funcsPackage: carnation
Commit: 436458cfe900991a51f8cdd77faa97b80c4c8dcb
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-21 16:41:19 -0400
Commit message:
Merge branch 'v1.2.0rc' into geneplt_fixesPackage: carnation
Commit: 9846fde276794f962f9f31e8d77017c225228677
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-21 16:39:12 -0400
Commit message:
reset gene scratchpad when loading new dataPackage: carnation
Commit: bc42ee102c7bb4721f1a94313b2d674901ccc598
Author: Apratim Mitra <16709900+mitraak@users.noreply.github.com>
Date: 2026-09-21 16:11:02 -0400
Commit message:
Merge pull request #40 from NICHD-BSPC/volcano-addition - This PR adds a new volcano plot module. Modeled after the MA plot module, this provides both static and interactive versions and allows the plot to be colored by either significance or `baseMean` (average expression).Package: carnation
Commit: 065626a63f11dcdf7e59c91999dfef93bb0f5e5c
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-21 15:47:47 -0400
Commit message:
rm R Depends versionPackage: carnation
Commit: 89a6ffdab9628be79b313a898741d45929f3100e
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-21 15:47:28 -0400
Commit message:
tweak author orderPackage: carnation
Commit: 14f5eb45078f107a667f72409a48d64e4d24d3cd
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-21 15:47:01 -0400
Commit message:
updt volcano plt ctrls helpPackage: carnation
Commit: 69f33bb0487d3bbbc7227fe16a6e4c42579309be
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-21 15:45:32 -0400
Commit message:
use refresh btn to reduce some reactivityPackage: carnation
Commit: f2a07c3f6815c5b517a285cd97f03c05e76a4ec4
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-21 15:36:42 -0400
Commit message:
separate colorscale frm fdr/fc thres, save to reactiveValPackage: carnation
Commit: 4bef3a540e7ab02ea8236dd62805a90547510c2c
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-21 15:36:09 -0400
Commit message:
mv axes reset to funcPackage: carnation
Commit: dd92ab9d3ab8dde435627e3423c8a89b91f4e712
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-21 15:33:42 -0400
Commit message:
add aspect ratio controlPackage: carnation
Commit: a3bd19fc62e86673f83594d7e4db875485a0c5d2
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-21 15:32:19 -0400
Commit message:
add visual grouping fr plot settingsPackage: carnation
Commit: 97b6882e21b63ccc21ded28a648fd7ad688029b8
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-21 15:31:35 -0400
Commit message:
convert axis padding to proportionsPackage: carnation
Commit: 13998566b3da5d2ab66f271695cbfd9efc626c0c
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-21 15:31:20 -0400
Commit message:
add legend title to match MA plotPackage: carnation
Commit: 04bd20ca337beaecb3a299000a66f488c5e72811
Author: Dale McCauley <dale.mccauley@nih.gov>
Date: 2026-09-14 17:00:18 -0400
Commit message:
Attached generated docs from previous commitPackage: carnation
Commit: 9113146ca4fcee27b336e4fa33166244fb519fe6
Author: Dale McCauley <dale.mccauley@nih.gov>
Date: 2026-09-14 16:42:13 -0400
Commit message:
Fixed global variable warning, added name to authors listPackage: carnation
Commit: a5beca7ab96c39f09e63e0ad57beaf3a8212dcc4
Author: Dale McCauley <dale.mccauley@nih.gov>
Date: 2026-09-14 14:52:51 -0400
Commit message:
Simplified axis scaling, improved organization, and added module level documentation and examples to volcano-plot.mdPackage: carnation
Commit: 901f5e13b28c62d7e0d150719430a6351e066ff0
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-09-02 17:29:07 -0400
Commit message:
mv ui elements fr volcanoPackage: carnation
Commit: f1797c81a72ef043f254e895636c2923eea7b7c7
Author: Dale McCauley <dale.mccauley@nih.gov>
Date: 2026-08-31 15:48:53 -0400
Commit message:
Improved scaling system to use reactiveVals and have on contrast change rescaling of ymax, improved alpha slider.Package: carnation
Commit: c9bf1fc6a59521b2829f47aa0eccfdf5dae66315
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-08-29 00:03:10 -0400
Commit message:
updt gene plt test-funcsPackage: carnation
Commit: 8ca2da9047a0efa40b8e6c193143b45bfba468be
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-08-29 00:02:57 -0400
Commit message:
updt count plt docsPackage: carnation
Commit: 2d6199e04f50edf3f770ea073e441ca17a564d74
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-08-29 00:02:44 -0400
Commit message:
add default ncol fr gene pltPackage: carnation
Commit: fe66fddda96f0ddc1a41999915ec818095e4f99d
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-08-29 00:02:28 -0400
Commit message:
add column ctrl fr gene pltPackage: carnation
Commit: 4241dce0b7763bb8b6ff0c939fc65bf5063e53d2
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-08-29 00:00:43 -0400
Commit message:
explicitly set group varPackage: carnation
Commit: ff59d806ae2839ac469f9cf6d3628a1a7ee46303
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-08-29 00:00:14 -0400
Commit message:
switch count plt arg to ncol from nrowPackage: carnation
Commit: 6830e97f93ce9a07168e4cb801eb90d98cf68ddf
Author: Dale McCauley <dale.mccauley@nih.gov>
Date: 2026-08-25 09:57:20 -0400
Commit message:
Add tests and bug fixPackage: carnation
Commit: 88f0a702ffe5a62329472f8ef8582b95358ec8bd
Author: Dale McCauley <dale.mccauley@nih.gov>
Date: 2026-08-24 10:04:06 -0400
Commit message:
Removed outdated commentPackage: carnation
Commit: 463542d2ddd893932c19905d0059758ae738b0fe
Author: Apratim Mitra <16709900+mitraak@users.noreply.github.com>
Date: 2026-08-21 14:20:20 -0400
Commit message:
Merge pull request #38 from NICHD-BSPC/devel merge devel into v1.2.0rcPackage: carnation
Commit: 790591a771c14d9b56ae7302977e826e285206d1
Author: Dale McCauley <dale.mccauley@nih.gov>
Date: 2026-08-21 13:20:58 -0400
Commit message:
Adding help files for volcanoplot to gitPackage: carnation
Commit: fa460c32d896a0354d5a93693e5b45ec4399f26c
Author: Dale McCauley <dale.mccauley@nih.gov>
Date: 2026-08-21 12:35:43 -0400
Commit message:
Wired up an alpha slider for the volcano plotsPackage: carnation
Commit: 07f4a2a84f1a2a7a0b29ceca47cc1e0fcf7b432f
Author: Dale McCauley <dale.mccauley@nih.gov>
Date: 2026-08-21 12:08:45 -0400
Commit message:
Fixed a bug in the new trace scheme where scatter wasn't being detectedPackage: carnation
Commit: 9dce4452d61f41d41ece247abb4969b63ec26192
Author: Dale McCauley <dale.mccauley@nih.gov>
Date: 2026-08-21 11:41:30 -0400
Commit message:
Made the significance traces workPackage: carnation
Commit: 90293b5f8a28c053d0b61cbec14b5ad61d4a3c46
Author: Dale McCauley <dale.mccauley@nih.gov>
Date: 2026-08-21 11:23:35 -0400
Commit message:
Checkpoint before changing significance tracesPackage: GSVA
Commit: 428c367041833e51d72911ddbd9fdf98619b9562
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-10-14 21:11:33 +0200
Commit message:
Minor fixes to clean some BiocCheck warnings and one errorPackage: MSstatsBioNet
Commit: bdd0d8042c0eaee5b385f49556e3a04369fed1ca
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-10-14 14:56:42 -0400
Commit message:
fix(ptm): Fix PTM filtering and add function to add global profiling results to network (#134)Package: crisprDesign
Commit: f54cde5da8ddf05e40ec36b96032a847b80d347c
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2026-10-14 11:11:11 -0700
Commit message:
Added 2026 cfd scorePackage: crisprScore
Commit: 66868bcf3d4ec95f7e9013d8e4918d02242ff708
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2026-10-14 10:41:48 -0700
Commit message:
Added cfd 2026Package: crisprScore
Commit: f4de01c84e2229265e48f673173fa103cfc6db7c
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2026-10-14 10:41:16 -0700
Commit message:
Modified CasRxPackage: crisprScore
Commit: 7d9940bd7517e21de19e0fb652459cbb7bf0fc10
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2026-10-14 10:36:13 -0700
Commit message:
2026 cfd scorePackage: Rarr
Commit: c64dae1ec9d5562f071cd6900d27c9e46447bb79
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-10-14 14:35:09 +0200
Commit message:
Bump versionPackage: Rarr
Commit: 86b83a0068624b2e255feddb8788313115504f4c
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-10-14 15:07:05 +0200
Commit message:
Add backport version for has_zstdPackage: Rarr
Commit: 0113c9b95835e7f51cc280968532b015f36f6c89
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-10-14 14:34:48 +0200
Commit message:
Add a class to the zstd warningPackage: ScreenR
Commit: 33390e9609335284da9cf41448ef780eaa83f425
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2026-10-14 16:11:14 +0200
Commit message:
Merge pull request #13 from EmanuelSoda/claude/trusting-ptolemy-bv7bzl Claude/trusting ptolemy bv7bzlPackage: ScreenR
Commit: f19336c0c14fe4a7291b99b4f49df6a4f3587bd7
Author: Claude <noreply@anthropic.com>
Date: 2026-10-14 13:51:55 +0000
Commit message:
Use relative path for pipeline figure in vignette The vignette referenced Pipeline.png by an absolute path on the author's machine, so the image was missing from the built vignette and pkgdown now errors with ENOENT. Point it at ../man/figures/Pipeline.png instead. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Pj7V9rdt9hkgoftdaJDjWuPackage: ScreenR
Commit: c1d689d0e36282ddcbc3035093a9507210903e29
Author: Claude <noreply@anthropic.com>
Date: 2026-10-14 13:49:15 +0000
Commit message:
Address review: raise dplyr/ggplot2 minimums, restore robust z-score test, fix coverage CI - DESCRIPTION: dplyr (>= 1.1.0) since find_zscore_hit() uses reframe(); ggplot2 (>= 3.5.2) since tests use ggplot2::is_ggplot() - tests: re-enable find_robust_zscore_hit test (passes with current deps) - test-coverage workflow: r-lib/actions v1 -> v2 and checkout v4; v1 pulls the retired actions/cache@v2, which GitHub now rejects before any step runs Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Pj7V9rdt9hkgoftdaJDjWuPackage: ScreenR
Commit: 02be4a418b8ddfa536e94f604c00ae315d4655dd
Author: Claude <noreply@anthropic.com>
Date: 2026-10-14 13:35:14 +0000
Commit message:
Merge Bioconductor devel (1.15.0, 5bb5455) and bump to 1.15.1 Brings the Bioconductor devel history into this branch so it holds the most up-to-date code (reframe() in find_zscore_hit, ggplot2::is_ggplot test updates, yearly version bumps) together with the GitHub-only work and the edgeR DPOTRF fix. Conflict resolution: - DESCRIPTION: Version 1.15.1 (devel 1.15.0 + bump for the fix), devel Date - tests/testthat/test-visualization.R, tests/testthat/Rplots.pdf: devel Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Pj7V9rdt9hkgoftdaJDjWuPackage: ScreenR
Commit: ce97559f9a9427a13c13a6f584bbe9d5ec43a9ba
Author: Claude <noreply@anthropic.com>
Date: 2026-10-14 13:12:34 +0000
Commit message:
Fix vignette build failure with new edgeR (DPOTRF error code -4) find_camera_hit() called glmLRT() with coef = all design columns, which leaves a zero-column null design. Recent edgeR passes that to LAPACK DPOTRF, which rejects it with error code -4 and breaks the vignette build on Bioconductor. The LRT result was never used by limma::camera(), so the glmFit/glmLRT/topTags step is removed; CAMERA results are unchanged. Also fix issues surfaced by R CMD check: - remove trailing comma in test-filter.R that caused "unused argument" - restore LICENSE file required by "MIT + file LICENSE" - drop tibble from Suggests (already in Imports) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Pj7V9rdt9hkgoftdaJDjWuPackage: ScreenR
Commit: 05090a72c3c201354135f6d54c6e4ad9f28b79c1
Author: emanuel.soda <emanuel.soda@fht.org>
Date: 2026-02-03 17:10:16 +0100
Commit message:
fixed text errorPackage: ScreenR
Commit: 040f7378bb605f9d7e9e6d5ceeca4af0144c6a81
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2023-09-22 15:24:47 +0200
Commit message:
Merge pull request #10 from EmanuelSoda/EmanuelSoda-patch-1 Update Analysis_Example.RmdPackage: ScreenR
Commit: 26d1024bc5e2bf23e5a26a8c344998fcd28118d4
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2023-09-22 15:24:30 +0200
Commit message:
Update Analysis_Example.RmdPackage: ScreenR
Commit: 98b8a1177d2ad9a4318fd76b8b6593a53adb8ef0
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2023-09-08 15:02:34 +0200
Commit message:
Merge pull request #9 from EmanuelSoda/fix2 Fix2Package: ScreenR
Commit: 99b28c34159abc1e18e5aa454e3dfc79dc92f8e1
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2023-09-08 15:01:37 +0200
Commit message:
oddioPackage: ScreenR
Commit: 870c34e672f56e4387bca9001ab9fa3b3e2c5959
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2023-09-08 14:59:36 +0200
Commit message:
aPackage: ScreenR
Commit: a5c36f6dcd97d95ed604a031b901e4368f46a0c8
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2023-09-08 14:57:54 +0200
Commit message:
maledetto treamentPackage: ScreenR
Commit: 6af95465d7f717af190716554b3fe6f7d8ca7290
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2023-09-08 14:48:59 +0200
Commit message:
Merge pull request #8 from EmanuelSoda/fix modificato ancora filter_slopePackage: ScreenR
Commit: f867f840901a00af48b77a1363909f49fc661cac
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2023-09-08 14:48:28 +0200
Commit message:
modificato ancora filter_slopePackage: ScreenR
Commit: fe36a9c313ecf632a0b860d23e38dac972239002
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2023-09-05 16:46:38 +0200
Commit message:
Merge pull request #7 from EmanuelSoda/fix another quick fixPackage: ScreenR
Commit: ccf23dc27c276102fa36a31509c144d29dedd715
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2023-09-05 16:46:03 +0200
Commit message:
another quick fixPackage: ScreenR
Commit: 92e60cec23bb58da76163f3e95cc081a33ba2524
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2023-09-05 14:26:08 +0200
Commit message:
Merge pull request #6 from EmanuelSoda/fix fixed slope filterPackage: ScreenR
Commit: 574f933416b6990156fa9e32d9f0746c05d8d171
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2023-09-05 14:25:38 +0200
Commit message:
fixed slope filterPackage: ScreenR
Commit: 86f70bf8d0d221cd4efe1c87740dae24f0f78643
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2023-09-05 14:24:09 +0200
Commit message:
fixed slope filter?Package: ScreenR
Commit: bb409df24cf8fcf5bbc4e821a23a0694f39576a4
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2023-09-05 12:41:45 +0200
Commit message:
my bad ihihihPackage: ScreenR
Commit: 307c07bf00bae3ab5f62659ed7f6ea983ee52a1a
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-12-06 09:52:07 +0100
Commit message:
Delete LICENSEPackage: ScreenR
Commit: f0d9a07d8f811cd8c66cca2a745c1b55aab5cf88
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-10-25 11:56:57 +0200
Commit message:
aPackage: ScreenR
Commit: 8ad376ee5e5d3dcbcb121468013e2ac0a042569f
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-10-25 11:39:49 +0200
Commit message:
Update README.mdPackage: ScreenR
Commit: c14646aa3ba009ae503e255dc6c368801db3809e
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-10-25 11:38:45 +0200
Commit message:
Update README.mdPackage: ScreenR
Commit: 147ab1792599b0fec5264dce84b52097ca93ec75
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-10-25 11:38:15 +0200
Commit message:
Update README.mdPackage: ScreenR
Commit: 49880d468588e23fbeb057c1f98f7c0bbb1a9e05
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-10-25 11:37:45 +0200
Commit message:
Update README.mdPackage: ScreenR
Commit: 87fb4c7bd0fc519e63239112d2bbed93bc701cf1
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-10-25 11:36:04 +0200
Commit message:
crete concept for documentationPackage: ScreenR
Commit: bfa7313be6277190cc523ab40ce7a6931f20bf23
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-10-08 18:03:17 +0200
Commit message:
added githubaction pkgdownPackage: ScreenR
Commit: 908bbb42faaab87efbb941062f2aadcbdd3be2b8
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-06-14 09:32:06 +0200
Commit message:
changed error in the markdownPackage: RmzTabM
Commit: 74385bddd7d164ea526f6f2ba4bf40a7405fcbf4
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2026-10-14 15:59:11 +0200
Commit message:
Merge pull request #55 from rformassspectrometry/jomain Small updates and documentation fixesPackage: RmzTabM
Commit: 867a8a066ec8246c8deef38e7fc9da081b607394
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-10-14 15:58:32 +0200
Commit message:
Address Gabriele's commentsPackage: RmzTabM
Commit: e59b09fb3612ebe46c0bae3cf6e6414b914bc956
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-10-14 14:22:01 +0200
Commit message:
Small updates and documentation fixesPackage: RmzTabM
Commit: 709f2d2c9fd25ba24d0684ac5100118b2e3ad51e
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2026-10-14 13:29:47 +0200
Commit message:
Merge pull request #54 from rformassspectrometry/gabri_export feat: add validation of mzTab-M file based on binary validatorPackage: RmzTabM
Commit: c480e3749df2eb7a0daf269427cbf03f444b0e24
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-10-14 11:30:36 +0200
Commit message:
refactor: change from `validation` to `validate`Package: RmzTabM
Commit: 244cd3ea55027faa934ad8dafe3f63cee8bfa0fb
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-10-14 10:20:50 +0200
Commit message:
address johannes commentsPackage: RmzTabM
Commit: f056492dd3c4a18adbf41420da8e79502ce3cdb3
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-10-05 13:23:32 +0200
Commit message:
test: add test download. fix: bug in check force downloadPackage: RmzTabM
Commit: 6c270d0a04b045c9113c562394269c5b7656d618
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-10-05 13:10:52 +0200
Commit message:
minor changesPackage: RmzTabM
Commit: a4ea814b695ec8a41852fa48a5fad1e577a71ee3
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-10-05 12:00:21 +0200
Commit message:
feat: remove file if validation fail during the exportPackage: RmzTabM
Commit: de0e97d18c289cc93c5b1955bddba0f16921561d
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-10-05 11:48:53 +0200
Commit message:
fix: fix check if need to update the validatorPackage: RmzTabM
Commit: 77c65f71e83a29e295a3579d77e20c3ab506bf9b
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-10-05 11:26:12 +0200
Commit message:
fix: fix tests with the validator and update old example filesPackage: RmzTabM
Commit: b45e8a6620b770166ad14c44bf2d7d02fa0a1958
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-10-05 11:25:45 +0200
Commit message:
docs: update documentation for the validatorPackage: RmzTabM
Commit: ae97ab23ef32d25099b76b1960ddd2eb3a13acae
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-10-01 16:40:21 +0200
Commit message:
feat: first version of the function to cache the validator. Fix study_variable_refs missing "s"Package: RmzTabM
Commit: dfac292500eca46dd1213c2ce383334fa4a08fa4
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-10-01 09:57:11 +0200
Commit message:
Merge branch 'main' into gabri_exportPackage: RmzTabM
Commit: e9d1fda4ae0ef522c0ac53037965b31a1699df2b
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-10-01 08:19:03 +0200
Commit message:
Update stickerPackage: RmzTabM
Commit: 406de0f0b6c05788df61e4ef581c86480266eb5d
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-09-30 09:37:30 +0200
Commit message:
Update stickerPackage: RmzTabM
Commit: 92528aa2a7763ca970f07ef13b4901625b6796c0
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-09-29 15:57:17 +0200
Commit message:
Add logoPackage: RmzTabM
Commit: 584ffadece58578a8556efddbf33e18c5d97c325
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-06-26 09:50:02 +0200
Commit message:
Merge branch 'main' into gabri_exportPackage: RmzTabM
Commit: 0aa0adaf29ec27d79be65e1595f43f7d2caaaff0
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-06-17 15:22:37 +0200
Commit message:
docs: update vignette to generate mzTab-M file from SE.Package: RmzTabM
Commit: c4468bdbd682e90ac859f8cf38ccfecf9982f65f
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-06-12 16:36:57 +0200
Commit message:
feat: `readMzTabM()` to create a `MzTabM` objectPackage: RmzTabM
Commit: 44fca67ab68d2122c71f2ac501d227515b9b1406
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-06-12 11:38:45 +0200
Commit message:
docs: update description and newsPackage: RmzTabM
Commit: 266a2ffdc34507745ee0118037f0da6158112004
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-06-12 11:31:46 +0200
Commit message:
feat: support "identifier" for opt columns. Update message validatorPackage: RmzTabM
Commit: 20349072133f28c86b9151c0dbedbe8d1bf79483
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-06-11 17:32:28 +0200
Commit message:
fix: test based on the new updatePackage: RmzTabM
Commit: e822bd70aeca59c40c793b99b1bfe1ce7f788770
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-06-11 17:23:12 +0200
Commit message:
feat: add functionality to export a mzTab-M file from SummarizedExperimentPackage: RmzTabM
Commit: 28907e2ae3d09975af386ab464d50a10aa40391f
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-06-11 11:12:21 +0200
Commit message:
Merge branch 'gabri' into gabri_exportPackage: RmzTabM
Commit: 21e1baf309b036e38bb801153cae3665aed39b34
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-06-08 15:11:31 +0200
Commit message:
Merge branch 'main' into gabri_exportPackage: RmzTabM
Commit: 7a91a4cac404f3ac40f5e888f08d21ee5d224f0d
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-05-18 13:40:07 +0200
Commit message:
Merge branch 'main' into gabri_exportPackage: RmzTabM
Commit: d9fc2241c7992e1e33a76eb4885879531232c7ec
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-05-14 12:44:23 +0200
Commit message:
feat: validator function using Java jar.Package: JASPAR
Commit: c386c49e3014d92819555b93279c7111127a2d08
Author: Damir <dbaranasic1@gmail.com>
Date: 2026-10-14 15:50:16 +0200
Commit message:
Version 0.99.6: state the provenance of the AI-assisted code Add provenance notes (Assisted-by: Claude Code, claude-sonnet-5-5) to the files written or rewritten for 0.99.5, as the Bioconductor policy on AI-generated code asks, and bump the version so that the reopened review (Contributions #3944) gets a new build. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>Package: EWCE
Commit: a4c0110ed5be0a4da7c204905843c289878cf708
Author: Hiranyamaya (Hiru) Dash <16350928+HDash@users.noreply.github.com>
Date: 2026-10-14 12:34:43 +0100
Commit message:
Merge pull request #107 from NathanSkene/fix-delayedarray-cbind Import cbind/rbind from BiocGenerics instead of DelayedArrayPackage: EWCE
Commit: f3c3ef4b283864a62b07230736027c65553ed238
Author: HDash <16350928+HDash@users.noreply.github.com>
Date: 2026-10-14 12:34:16 +0100
Commit message:
Add README badge fallback (#108) to NEWSPackage: EWCE
Commit: 7c9f26c58204e2a93726b90b9dae700bc3eb4523
Author: HDash <16350928+HDash@users.noreply.github.com>
Date: 2026-10-14 10:55:39 +0100
Commit message:
Fall back to badges without Bioc release version in README rvcheck can no longer scrape the version from the redesigned Bioconductor package pages, which made the README render (and rworkflows CI) fail. Fixes #108Package: EWCE
Commit: 3396ab5471cd9165d0a926b20021d9fbe4f164de
Author: HDash <16350928+HDash@users.noreply.github.com>
Date: 2026-10-09 13:56:42 +0100
Commit message:
Ignore .positai and .claude directoriesPackage: EWCE
Commit: a04ff3210eb0a0c1cc9067fb1721d0676ccbc861
Author: HDash <16350928+HDash@users.noreply.github.com>
Date: 2026-10-09 13:56:42 +0100
Commit message:
Rebuild READMEPackage: EWCE
Commit: 712225e9db24a4b903e19f7d5f535ed33ae0d1b1
Author: HDash <16350928+HDash@users.noreply.github.com>
Date: 2026-10-09 13:56:42 +0100
Commit message:
Fix 'Lost braces in \itemize' Rd NOTE Use \describe{} for labelled items in compute_gene_scores and drop_uninformative_genes docs.Package: EWCE
Commit: 19644fa78632cb2c5b4f636613c1398560e8799d
Author: HDash <16350928+HDash@users.noreply.github.com>
Date: 2026-10-09 11:50:37 +0100
Commit message:
Import cbind/rbind from BiocGenerics instead of DelayedArray DelayedArray (Bioc 3.24) no longer re-exports the BiocGenerics cbind/rbind generics, causing EWCE install to fail. Switch the roxygen import and the namespaced calls in merge_sce() to BiocGenerics, add it to Imports, and bump version to 1.21.1. Fixes #106Package: BgeeDB
Commit: 959ea3e9336528a532902453b33f95f9900aec26
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2026-10-14 14:12:26 +0200
Commit message:
bump versionPackage: BgeeDB
Commit: 5a349707f3e297c1ab1d821fdd815b272cb7890b
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2026-10-14 14:05:47 +0200
Commit message:
default the data types of a Bgee object to those of its release, without Affymetrix and EST from Bgee 16Package: BgeeDB
Commit: 1d51299b3c76cb3cd2adb6e7e762cf39832d38a5
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2026-10-14 14:05:47 +0200
Commit message:
document the topAnat changes of Bgee 16, version 2.39.1Package: BgeeDB
Commit: 130b9e52683cf953e235156e1c931e9138340b5b
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2026-10-14 14:05:47 +0200
Commit message:
stop retrying a topAnat download refused by the server, and report its answerPackage: BgeeDB
Commit: 0e1ee8c3c6ec8891a8a57d4394da722700b8fbca
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2026-10-14 14:05:47 +0200
Commit message:
draw the graph of the significant conditions with the new function printTopAnatGraphPackage: BgeeDB
Commit: 0b8e431adb5574613a49c6ec95d022fc0f3def7b
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2026-10-14 14:05:46 +0200
Commit message:
run the classic algorithm of topAnat_galaxy on the propagated calls of Bgee 16Package: BgeeDB
Commit: 2d7bed24c80720fe7b3debcb7504caa7e1dd6ef6
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2026-10-14 14:05:46 +0200
Commit message:
run topGO on the propagated calls without propagating them again, and check the algorithms in runTestPackage: BgeeDB
Commit: 5e9c506bc08af95f97ac4afae6f405aff5f34a80
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2026-10-14 14:05:46 +0200
Commit message:
retrieve the propagated or observed topAnat calls of Bgee 16 with the callFileType argument of loadTopAnatDataPackage: BgeeDB
Commit: afc8db60e8cfd6b21da2b6d1400d9060e6202de3
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2026-10-14 14:05:46 +0200
Commit message:
move the building of the topAnat data to an internal function reading local filesPackage: edgeR
Commit: b5de8d16cef51dcf4316877cddbca13a729edb4e
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2026-10-14 21:52:43 +1100
Commit message:
edgeR 4.99.8 - New function estimateTxExpr(). - Further consolidate concept entries for Rd files. - Add some DOIs for references in Rd files.Package: phenomis
Commit: 0aecc21cecbde2e89506faa0510cf11ebf005f75
Author: Etienne Thevenot <etienne.thevenot@cea.fr>
Date: 2026-10-13 11:30:21 +0200
Commit message:
minor updatesPackage: GSVA
Commit: ee3d26be12be691da68a38434f070cb0df003a5d
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-10-14 10:25:35 +0200
Commit message:
Add winslash="/" to normalizePath() calls to avoid check errors in Windows builders that compare paths using slashes instead of backslashes. Temporary fix in a test to deal with an omp_pause_resource() triggered by SparseArray in Windows buildersPackage: scDblFinder
Commit: e66180a1d84733bbcf63ed8590ae75a4a5329e34
Author: plger <pl.germain@gmail.com>
Date: 2026-10-14 09:53:18 +0200
Commit message:
changed xgboost notePackage: scDblFinder
Commit: f2ddb580fdb24c30718ebc602bdd1f2d7691c36d
Author: plger <pl.germain@gmail.com>
Date: 2026-10-14 09:48:17 +0200
Commit message:
added eval_setPackage: scDblFinder
Commit: 48984adc7211dfdda06c6e6854d04e4561ee1a8b
Author: plger <pl.germain@gmail.com>
Date: 2026-10-14 09:47:26 +0200
Commit message:
renamed filePackage: scDblFinder
Commit: 8f529a08892bbd2c20f1e1a92b63d7ee6eda90ad
Author: plger <pl.germain@gmail.com>
Date: 2026-10-14 09:29:07 +0200
Commit message:
fixed issue with xgboost >=3.4Package: scDblFinder
Commit: b985ff05457b5dfba9971ee5c53a56a28ff405f9
Author: plger <pl.germain@gmail.com>
Date: 2026-10-14 09:08:24 +0200
Commit message:
added breaklinePackage: scDblFinder
Commit: ffcdc04ab6db54be5dc4727cc566bb797311868b
Author: plger <pl.germain@gmail.com>
Date: 2026-10-14 09:07:44 +0200
Commit message:
added warning on failed trainingPackage: simpleSeg
Commit: 5304f331faac14c64f7ede972b0409ba14e555ee
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 17:20:17 +1100
Commit message:
Cell body models on 1,000,000 sampled pixels; no-data pixels keep their value Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y1YeeuxPhptPfm3pWGocSUPackage: simpleSeg
Commit: 0223f658c5c341e502387ec0d3fdae8a7c9a27b6
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 15:46:52 +1100
Commit message:
Tiled segmentation with PCA, cell body models and tissue mask; files opened once per process; band names Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y1YeeuxPhptPfm3pWGocSUPackage: Rsubread
Commit: 30473aa3a541f53e7ddb8d02f3da92204ba5e450
Author: Yang Liao <yang.liao@monash.edu>
Date: 2026-10-14 16:07:20 +1100
Commit message:
fixed an error on MacOS when building index.Package: Rsubread
Commit: dc5b91cdc5fe5a8c616be46f48873a878210c8d4
Author: Yang Liao (Monash University) <yliao@m3-login2.massive.org.au>
Date: 2026-10-14 15:43:26 +1100
Commit message:
removed warnings from Linux buildPackage: SCArray
Commit: 36586cf396f69ba9092ba8633aa7967103586789
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2026-10-13 22:38:03 -0500
Commit message:
bug fixesPackage: simpleSeg
Commit: 4d6380752cae0722b9d567946fb98d9041dc0952
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 14:37:46 +1100
Commit message:
NEWS for reading image files and tiled segmentation Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y1YeeuxPhptPfm3pWGocSUPackage: simpleSeg
Commit: eaf8d1fc20db93d3301d107e9c79af68610658e7
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 14:37:08 +1100
Commit message:
simpleSeg() reads image files and folders, segments large images in tiles, and can return cells as a SpatialExperiment - image can be paths: multi-channel files (OME-TIFF, QPTIFF, multi-page TIFF), folders of single-channel files (one image split by marker) or folders of such folders - output = "masks", "cells" or "none"; maskDir saves masks as TIFF files - images larger than tileSize are segmented tile by tile with the cells and masks of the whole image - Gaussian blur and label sums in C++; position-based tie breaking before the watershed - PCA uses markers that vary over the pixels it is fitted on Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y1YeeuxPhptPfm3pWGocSUPackage: simpleSeg
Commit: ad1f079cebe471eb3c2b2a207845bbcaf92d0d7a
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 13:07:00 +1100
Commit message:
simpleSegFile(): tiled segmentation of large image files; Gaussian blur and label sums in C++ Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y1YeeuxPhptPfm3pWGocSUPackage: simpleSeg
Commit: ccef2435af69edc6c8f128dbb5797b7e5de7098b
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 10:13:41 +1100
Commit message:
Parallel processing with started BiocParallel workers and one BLAS thread per worker Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y1YeeuxPhptPfm3pWGocSUPackage: simpleSeg
Commit: 3c4900c5ddea838f89e987aa3236a9dda8ffa37f
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 09:23:48 +1100
Commit message:
1.15.1: tests for the fixes, NEWS Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y1YeeuxPhptPfm3pWGocSUPackage: simpleSeg
Commit: 17ab5ef2bc4fc8fd6b3d47246f6a945be3392e7a
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 09:18:37 +1100
Commit message:
Merge Bioconductor develPackage: simpleSeg
Commit: 4602ba5cf0a1492d29bea60fdae7a5896b39d243
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 09:18:37 +1100
Commit message:
Fix discModel and marker cell bodies, input checks, faster segmentation and normalizeCells Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y1YeeuxPhptPfm3pWGocSUPackage: simpleSeg
Commit: 2aeb8f2de268d5de0076dde70832cec3779b24af
Author: Ellis Patrick <ellis.patrick@sydney.edu.au>
Date: 2025-07-24 17:49:25 +1000
Commit message:
Fix discModel for multiple images.Package: spicyR
Commit: 6d595e161d909a003d6d38c5c6371dfb7f7f5012
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 13:43:31 +1100
Commit message:
1.99.17: several radii from one neighbour search (identical results; omnibus over 25 radii ~4x faster) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4Package: Statial
Commit: 3d04158568e8a4240edf5b52161ef749c3b5f303
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 12:54:25 +1100
Commit message:
Parallel helper: one thread in already-started workers; eight chunks per socket worker too Workers of a param that was already running set one BLAS and OpenMP thread themselves before their first task (settings changed in this session can't reach them). The eight-chunks-per-worker default now also applies to socket workers. NEWS no longer says all results are unchanged: relabelKontextual()'s relabelled images differ. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y1PuRkfDQ3ApzuNoe5ovxWPackage: Statial
Commit: 3098c7491a69f4cafa50d349b59ea3e652d0ceeb
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 11:19:32 +1100
Commit message:
NEWS: OpenMP threads are limited in workers too Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y1PuRkfDQ3ApzuNoe5ovxWPackage: Statial
Commit: 8c0e0f32299fe3f45821869d896716c4666527eb
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 11:15:25 +1100
Commit message:
Parallel helper: one OpenMP thread in forked workers too Forked workers can hang when the main session has used several OpenMP threads before forking (seen with randomForestSRC in ClassifyR). OpenMP threads are set to one for the call, as BLAS threads are, and restored. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y1PuRkfDQ3ApzuNoe5ovxWPackage: Statial
Commit: f295dbb764c3bba37dd89be35b787ff922ef349e
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 10:48:27 +1100
Commit message:
Parallel helper: leave a single-threaded BLAS alone Restoring several BLAS threads after forking restarts every OpenBLAS thread, and the new threads spin briefly (about 14 CPU-seconds per call with 128 threads). BLAS threads are now changed only when there is more than one. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y1PuRkfDQ3ApzuNoe5ovxWPackage: Statial
Commit: 8e991cfb9a09ee8ab857d1e32d6246505fcda04c
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 10:43:56 +1100
Commit message:
1.15.4: parallel loops forked once per call with one BLAS thread per worker; reproducible relabelKontextual Parallel loops in Kontextual(), relabelKontextual(), getDistances(), getAbundances() and calcStateChanges() go through .par_lapply()/.par_mapply() (the spicyR helper): forked workers start once per call after the task exists and receive only task numbers, tasks go out in about eight chunks per worker, socket workers on Windows, and OpenBLAS runs one thread per worker during the call (RhpcBLASctl, set in the main session). Kontextual() builds point patterns, close pairs and edge correction in one pass over the images and uses one param for both parallel steps. relabelKontextual() seeds its random number streams from the session, so set.seed() makes it reproducible for any number of cores. Other results are identical. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y1PuRkfDQ3ApzuNoe5ovxWPackage: lisaClust
Commit: 3b0cdb0c757008a177d7e336afa1f3f823d4d4b4
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 12:54:23 +1100
Commit message:
Parallel helper: one thread in already-started workers; eight chunks per socket worker too Workers of a param that was already running set one BLAS and OpenMP thread themselves before their first task (settings changed in this session can't reach them). The eight-chunks-per-worker default now also applies to socket workers. lisa() and lisaClust() accept any BiocParallel param (socket params were rejected), and a number of cores gives socket workers on Windows. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y1PuRkfDQ3ApzuNoe5ovxWPackage: lisaClust
Commit: 6f8a7361d0948833025fa560103915f17db123ca
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 11:19:30 +1100
Commit message:
NEWS: OpenMP threads are limited in workers too Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y1PuRkfDQ3ApzuNoe5ovxWPackage: lisaClust
Commit: 5e2d523ccebda439f26d6de57110b6b004cdc6be
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 11:15:25 +1100
Commit message:
Parallel helper: one OpenMP thread in forked workers too Forked workers can hang when the main session has used several OpenMP threads before forking (seen with randomForestSRC in ClassifyR). OpenMP threads are set to one for the call, as BLAS threads are, and restored. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y1PuRkfDQ3ApzuNoe5ovxWPackage: lisaClust
Commit: 12eb54ec5849c74d0608299e14de622703513896
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 10:48:27 +1100
Commit message:
Parallel helper: leave a single-threaded BLAS alone Restoring several BLAS threads after forking restarts every OpenBLAS thread, and the new threads spin briefly (about 14 CPU-seconds per call with 128 threads). BLAS threads are now changed only when there is more than one. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y1PuRkfDQ3ApzuNoe5ovxWPackage: lisaClust
Commit: 960467f56262bf80e378b9d9ed5d3fe94cf10506
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 10:20:37 +1100
Commit message:
Typos: 'BPPARAM' in the argument-check error message; whichParallel default "imageID" Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y1PuRkfDQ3ApzuNoe5ovxWPackage: lisaClust
Commit: b28633336f322cea50e0c5582ddd9783dafe3623
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 10:13:33 +1100
Commit message:
1.21.8: lisa() workers start once per call with one BLAS thread each lisa() runs its images through .par_lapply(), ported from spicyR: forked workers start once (bpstart) after the task and the images are placed in a package environment, receive only task numbers in about eight chunks per worker, and are stopped on exit. BLAS is set to one thread in the main session before the workers start and restored on exit (RhpcBLASctl, now in Imports); socket or already-running workers get OPENBLAS_NUM_THREADS and OMP_NUM_THREADS = 1 instead. Results are identical to the serial run. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y1PuRkfDQ3ApzuNoe5ovxWPackage: spicyR
Commit: 8a6f2032f3e6a07aa3a9ba7b4451e9a00f6c3f44
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 12:54:21 +1100
Commit message:
Parallel helper: one thread in already-started workers; eight chunks per socket worker too Workers of a param that was already running set one BLAS and OpenMP thread themselves before their first task (settings changed in this session can't reach them). The eight-chunks-per-worker default now also applies to socket workers. .par_mapply() rejects zero-length inputs mixed with longer ones with mapply()'s message. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y1PuRkfDQ3ApzuNoe5ovxWPackage: spicyR
Commit: 345a32dd13bc831f67d229f5b945fcd83576e04d
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 11:19:28 +1100
Commit message:
NEWS: OpenMP threads are limited in workers too Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y1PuRkfDQ3ApzuNoe5ovxWPackage: spicyR
Commit: 8eba059b93829f4670e65f3c03c61d785c65c29e
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 11:15:25 +1100
Commit message:
Parallel helper: one OpenMP thread in forked workers too Forked workers can hang when the main session has used several OpenMP threads before forking (seen with randomForestSRC in ClassifyR). OpenMP threads are set to one for the call, as BLAS threads are, and restored. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y1PuRkfDQ3ApzuNoe5ovxWPackage: spicyR
Commit: 5a953d18ff14c36c17ba5225c890e2213e77b3b5
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 10:48:27 +1100
Commit message:
Parallel helper: leave a single-threaded BLAS alone Restoring several BLAS threads after forking restarts every OpenBLAS thread, and the new threads spin briefly (about 14 CPU-seconds per call with 128 threads). BLAS threads are now changed only when there is more than one. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y1PuRkfDQ3ApzuNoe5ovxWPackage: spicyR
Commit: 7f2c703b465188dc1c1cac5980acbafe22095e69
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 10:20:37 +1100
Commit message:
Typo: 'BPPARAM' in the argument-check error message Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y1PuRkfDQ3ApzuNoe5ovxWPackage: spicyR
Commit: e9fbcd5dd054ec0ad6c42b2dab4cb25138351212
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 09:39:30 +1100
Commit message:
1.99.16: R-level parallel loops on BiocParallel, workers forked once per call, one BLAS thread per worker parallel::mclapply is replaced by BiocParallel (Bioconductor guideline). Forked workers start once per call after the data exist and receive only task numbers; tasks go out in about eight chunks per worker; socket workers on Windows. OpenBLAS threads are set to one in the main session before forking and restored after (RhpcBLASctl), since OpenBLAS otherwise starts one thread per core in every worker. Results are identical. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y1PuRkfDQ3ApzuNoe5ovxWPackage: spicyR
Commit: 5b8fbb1efa6577b8e615315fbc44e0edf300245f
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-14 13:05:14 +1100
Commit message:
1.99.15: combine = "davies" for many radii (Davies' bound for the maximum over radii); maxT stops beyond six radii Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4Package: systemPipeShiny
Commit: 300471e416849e42fce812f210982df85d2ffb31
Author: Le Zhang <35240440+lz100@users.noreply.github.com>
Date: 2026-10-13 18:45:27 -0700
Commit message:
Merge pull request #108 from systemPipeR/fix/bioc Fix BiocCheck ERROR and WARNINGs (r-universe Bioconductor check)Package: systemPipeShiny
Commit: 3e100f59e614ce5de03c06b127188082c99e33aa
Author: Le Zhang <35240440+lz100@users.noreply.github.com>
Date: 2026-10-13 18:44:45 -0700
Commit message:
chore: bump version to 1.23.1; add NEWS entry for BiocCheck fixes Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>Package: systemPipeShiny
Commit: 63b26b223b5c571b7ccf4d1cc02b501ec888e571
Author: Le Zhang <35240440+lz100@users.noreply.github.com>
Date: 2026-10-13 18:44:45 -0700
Commit message:
docs: add BiocCheck hosting-platform invariant to spec; correct version-bump rule in AGENTS.md Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>Package: systemPipeShiny
Commit: 13e330bc183b32d82909e53273be92f0a51784f3
Author: Le Zhang <35240440+lz100@users.noreply.github.com>
Date: 2026-10-13 18:44:41 -0700
Commit message:
fix: resolve BiocCheck ERROR and WARNINGs - Avoid references to external hosting platforms (ERROR): the About tab reads the installed NEWS.md via system.file() instead of raw.githubusercontent.com, and the RNAseq/workflow tabs use the bundled img/spr.png logo. - Vignette no longer sets a global eval=FALSE (duplicate opts_chunk$set arg); every chunk already sets eval explicitly, so output is unchanged. - Add @return to the spsDb, spsEncryption and spsAccount R6 classes. - Regenerate docs with roxygen2 8.1.1 (NAMESPACE reformatted, Rd package anchors added, RoxygenNote -> Config/roxygen2/version). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>Package: systemPipeShiny
Commit: 6c1c95f9807b18354e9fc47a4849c41f03ab2b3d
Author: Le Zhang <35240440+lz100@users.noreply.github.com>
Date: 2026-10-13 18:22:51 -0700
Commit message:
feat: add AGENTS.md and spec.md for AI guidance and product specifications; update .gitignore and .RbuildignorePackage: bedbaser
Commit: 701b3d2f00d095f4d446f561742bc51406227bd1
Author: A Wokaty <awokaty@users.noreply.github.com>
Date: 2026-10-13 19:54:55 -0400
Commit message:
Bump version to 1.5.2Package: bedbaser
Commit: 4123c0973ccabcea79b7cd00977d981134f8b05e
Author: A Wokaty <awokaty@users.noreply.github.com>
Date: 2026-10-13 19:54:39 -0400
Commit message:
Update path
</div> </div>