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Package: scrapbook
Commit: 80cd6b605a39982b31e368fc45bc172ea1287ee1
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-26 12:45:13 +1000
Commit message:
Commit: 80cd6b605a39982b31e368fc45bc172ea1287ee1
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-26 12:45:13 +1000
Commit message:
Fixed section title for consistency.
Package: scrapbook
Commit: 7eedf6966f01ba717e66f7e0b4c94c8d5c811208
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-26 12:40:31 +1000
Commit message:
Commit: 7eedf6966f01ba717e66f7e0b4c94c8d5c811208
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-26 12:40:31 +1000
Commit message:
Migrated a short nuclei analysis chapter from OSCA.advanced.
Package: IRanges
Commit: 28c9970cca9bcec8eec020bff6390924b0a0e583
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-25 17:29:34 -0700
Commit message:
Commit: 28c9970cca9bcec8eec020bff6390924b0a0e583
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-25 17:29:34 -0700
Commit message:
IRanges 2.47.3: Minor tweaks to as.data.frame.IPosRanges() and as.data.frame.IPos()
Package: S4Vectors
Commit: e4668d7b6cb34e21de42f251764d4a8d13e31824
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-25 17:12:56 -0700
Commit message:
Commit: e4668d7b6cb34e21de42f251764d4a8d13e31824
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-25 17:12:56 -0700
Commit message:
S4Vectors 0.51.8: Various tweaks to as.data.frame.DataFrame() This fixes issue #138.
Package: DuckDBDataFrame
Commit: ddcf2f5d57058deaf061d41f07a43ecf7a6958e3
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-25 16:36:48 -0700
Commit message:
Commit: ddcf2f5d57058deaf061d41f07a43ecf7a6958e3
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-25 16:36:48 -0700
Commit message:
fix: pair the _INCOMPLETE reader check with the directory-wrap fix
Package: DuckDBGRanges
Commit: 94ecf2a80b6b4be8cf50dc9cb0f1739ecbd1b91d
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-25 14:18:11 -0700
Commit message:
Commit: 94ecf2a80b6b4be8cf50dc9cb0f1739ecbd1b91d
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-25 14:18:11 -0700
Commit message:
fix: validate narrow()'s start/end/width request as base does narrow() accepted four requests base refuses, and two of them returned a range wider than the input. A supplied width fixes whichever side was left NA, so exactly one of start/end must be NA; "width only" quietly anchored at the start and supplying all three quietly ignored end. And narrow() may only shrink a range (base solves with allow.nonnarrowing = FALSE), so narrow(x, start=5, end=200) on a 101-wide range returned 104-299 instead of erroring. The widen/invert check is per row, matching base, and costs one aggregate query. The start/end resolution is factored into .narrow_resolve(), used both to build the new columns and to build the validation predicate. Review item R-G3 described this as narrow(width=w) leaving coordinates unchanged while writing an inconsistent width. That does not reproduce: .modify_DuckDBGRanges_datacols() recomputes end as start + width - 1 when only the width changes. The missing validation is the real gap. All solvable forms already matched GenomicRanges and still do.
Package: DuckDBGRanges
Commit: 8adfde28d7d74dea23d8a6a61f84804f84fbf74e
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-25 13:54:57 -0700
Commit message:
Commit: 8adfde28d7d74dea23d8a6a61f84804f84fbf74e
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-25 13:54:57 -0700
Commit message:
fix: correct the remaining element-wise set operations and distance() punion() and pintersect() share .parallel_set_op(), which paired x[i] with y[i] using a bare row_number() over DuckDB's undefined scan order (review item R-G4) and coordinate-sorted its result, so result[i] was not x[i] combined with y[i]. Pairing now goes through the recorded keycol, matching the pgap() and psetdiff() rewrites, and the result keeps the pairing order. Fixing that surfaced the same defect class as R-G1 in both callers, which base treats differently and which was not modelled at all: pintersect() produced a negative width for a non-overlapping pair (unmaterializable) where base returns a zero-width range, and punion() silently spanned a gap where base errors unless fill.gap=TRUE. Neither checked seqname or strand compatibility, so both combined ranges across chromosomes. ignore.strand, strict.strand, and drop.nohit.ranges were all accepted and ignored. Separately, distance() returned a number rather than NA for a pair on different seqnames whenever either strand was '*': the strand OR-chain was not parenthesized inside the AND, so SQL precedence let any '*' strand make the pair valid on its own. Same hazard already documented on pgap(); the existing test never combined a seqname mismatch with a '*' strand. All three operations are now checked against GenomicRanges with and without an explicit keycol; each fix was reverted individually to confirm it is load-bearing.
Package: DuckDBDataFrame
Commit: adfaf4686e19826e596d1b0ad5d93f0328558a35
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-25 13:38:00 -0700
Commit message:
Commit: adfaf4686e19826e596d1b0ad5d93f0328558a35
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-25 13:38:00 -0700
Commit message:
fix: readParquetSchema() leak
Package: DuckDBDataFrame
Commit: 3b3a38e9cca3093d2e9052ec564e5315d92b8742
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-25 13:18:42 -0700
Commit message:
Commit: 3b3a38e9cca3093d2e9052ec564e5315d92b8742
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-25 13:18:42 -0700
Commit message:
fix: release the parquet file handle before renaming or unlinking Follow-up to the mmap fix: removing the memory mapping unblocked the in-place write but not the rename and unlink that splitParquetPart() performs on its source. ParquetFileReader opens the file and has no Close() method, so .findFactorColumns() left a handle live until GC, and Windows refuses to rename or unlink a file that any handle still holds. It now creates its own ReadableFile, passes that to ParquetFileReader, and closes it explicitly; the returned Schema stays valid afterwards. Confirmed by file-descriptor count: the old form leaves one handle open, the new form leaves none. splitParquetPart() also drops its DuckDB temp table before touching the source rather than at function exit, and the "failed to move aside" error now names the Windows cause.
Package: DuckDBDataFrame
Commit: ad1a3e9bb7b8f3d55710c0ec1da325605bec900b
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-25 12:01:26 -0700
Commit message:
Commit: ad1a3e9bb7b8f3d55710c0ec1da325605bec900b
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-25 12:01:26 -0700
Commit message:
fix: unmap parquet reads so in-place rewrites work on Windows The factor-restoration path reads and rewrites each parquet file in place, and arrow's default memory-mapped read leaves a mapping open that Windows refuses to write over, rename, or unlink (error 1224). Staging the write elsewhere and renaming would not help: replacing a mapped file is blocked the same way, so the mapping itself has to go. Fixed at three sites, not just the one in the traceback. .restoreFactorColumns() and .findFactorColumns() both read the source file that splitParquetPart() later renames aside and unlinks, so leaving either mapped would simply have moved the failure downstream into the rollback path. .findFactorColumns() switches from open_dataset(), which cannot opt out of mapping, to ParquetFileReader$create(mmap = FALSE). writeDuckDBTableParquet()'s sample_df read is unmapped for the same reason, though it was not implicated here. The splitParquetPart() half of this is a pre-existing 0.99.22 defect that only surfaced now because that function had no test coverage until this release. Adds a test asserting the files stay renameable and removable after both helpers touch them.
Package: DuckDBGRanges
Commit: a4634eb0dc514478a326e28fc849d8daea18951b
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-25 11:54:59 -0700
Commit message:
Commit: a4634eb0dc514478a326e28fc849d8daea18951b
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-25 11:54:59 -0700
Commit message:
fix: correct psetdiff for non-overlapping, covering, and inside pairs
psetdiff() handled only edge-aligned overlaps, as its header comment
conceded. A non-overlapping pair came back wider than x, and a covering
pair came back with negative width, which is not merely wrong but
unmaterializable ("each range must have a non-negative width"). A y
sitting strictly inside x cannot be expressed as one range and base
refuses it; this returned garbage instead.
Three further defects in the same method: seqname and strand
compatibility were ignored, so ranges were subtracted across
chromosomes; ignore.strand was accepted and never used; and the result
was coordinate-sorted by .build_DuckDBGRanges()'s default ordering, so
result[i] was not x[i] minus y[i].
Pairing also moves from a bare row_number() over DuckDB's undefined scan
order to .add_keycol_indices(), matching the pgap() rewrite. That is
review item R-G4, done here because correct pairing is a precondition
for this method being correct at all; punion/pintersect still need it.
Package: flowViz
Commit: 077ee734b27398a50661e772f281368eeae324d5
Author: Mike Jiang <mike@ozette.com>
Date: 2026-08-25 11:47:51 -0700
Commit message:
Commit: 077ee734b27398a50661e772f281368eeae324d5
Author: Mike Jiang <mike@ozette.com>
Date: 2026-08-25 11:47:51 -0700
Commit message:
Bump version to 1.77.1
Package: flowViz
Commit: 065ecc59d52d978d4ee20af3e2bdd77a18985ce9
Author: Mike Jiang <mike@ozette.com>
Date: 2026-08-25 11:47:37 -0700
Commit message:
Commit: 065ecc59d52d978d4ee20af3e2bdd77a18985ce9
Author: Mike Jiang <mike@ozette.com>
Date: 2026-08-25 11:47:37 -0700
Commit message:
Migrate parallel to parallelplot for lattice >= 0.23
lattice 0.23 removed the long-deprecated parallel() function
(replaced by parallelplot() in 0.20). setGeneric("parallel")
therefore fails at install time with:
must supply a function skeleton for 'parallel'
Rename the generic, methods, exports, and docs to parallelplot.
Package: DuckDBGRanges
Commit: 5a9784db51058d3c90e4127a2c63e129b67f55ef
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-25 11:19:18 -0700
Commit message:
Commit: 5a9784db51058d3c90e4127a2c63e129b67f55ef
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-25 11:19:18 -0700
Commit message:
fix: repair the nearest-neighbour family for row-number-keyed objects Three stacked defects made nearest(), precede(), follow(), and distanceToNearest() unusable on any DuckDBGRanges without an explicit keycol, which is the default for a file-backed object. Every existing test in this family supplies one, so none of it was covered. .add_keycol_indices() treated the keycols slot as literal key values, but a row-number-keyed frame stores set_row_number()'s c(NA, -n) sentinel there; joining against it matched nothing and silently emptied the result. It now derives the position with row_number() instead. window_order() is deliberately avoided: dbplyr keeps that ordering attached and re-emits it after the column has been grouped away. .build_nearest_single_result() subscripted with the SQL-derived index directly, and an integer64 subscript silently yields NA for every position. .nearest_ddb() lacked the is.na(subj_idx) guard .distanceToNearest_ddb() has. DuckDB's greatest() skips NULLs, so a query on a seqname with no subject scored greatest(NULL, NULL, 0) = 0, won its own min-distance filter, and produced a hit to a NULL subject. </pre> </div> Package: scRNAseqApp
Commit: d89bc02109e271b19c586b4c991307869a421ae3
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2026-08-25 13:57:35 -0400
Commit message:
adjust a little bit the css.Package: scRNAseqApp
Commit: 1e32f964f7f3a58664072f5d40a63f784e8ea98d
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2026-08-25 13:27:20 -0400
Commit message:
add splash screen.Package: DuckDBDataFrame
Commit: cfa12fb3e564aed3178e5968a18a10aa06fbd358
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-25 09:49:49 -0700
Commit message:
fix: prevent data loss on two DuckDBTable parquet write paths splitParquetPart() unlinked the source file before copying the split parts into place, discarded file.copy()'s return value, and left overwrite=FALSE. A failed copy destroyed the only copy of the data and returned without error. The source is now moved aside, the copy is checked, and any failure rolls the directory back to its original contents. A read-only target directory previously produced a silent no-op reported as success; it now errors. writeDuckDBTableParquet() never consulted @collevels, so its SQL COPY flattened every factor column to VARCHAR and dropped any level unused in the data. It now re-applies the recorded levels via the same arrow-side fixup splitParquetPart() already used, refactored into a shared .applyFactorLevels() helper, and does so before sample_df is read back so the caller's schema inference sees the factors too.Package: maaslin3
Commit: 4b6855d6a2f8283e1667208ab3c643d71f596426
Author: Will Nickols <willanickols@gmail.com>
Date: 2026-08-25 08:25:03 -0700
Commit message:
Fix random effects handling for multiple crossed random interceptsPackage: IFAA
Commit: 7f243b8d985160cb53bb8c623c6ca91054f893fa
Author: Mingkai Chen <chenm1@ufl.edu>
Date: 2026-08-10 16:03:22 -0400
Commit message:
Internalize HDCI routines to restore package buildPackage: scRNAseqApp
Commit: 6f1778ebb777237397264aa6dd17e557109f3fce
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2026-08-25 09:17:59 -0400
Commit message:
Add gene score vs gene expression modules.Package: scRNAseqApp
Commit: d3ad57d7b80bcc406dbf2f0b488b412cb189810c
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2026-08-14 15:32:02 -0400
Commit message:
fix a typo.Package: scRNAseqApp
Commit: 4a473552eba18c3c3082405140ebb686da40bf85
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2026-08-14 13:23:18 -0400
Commit message:
fix column names for fragments.Package: cytomapper
Commit: 2efbbe1b58492660783b898a3c1cbf87676ecb22
Author: Lasse Meyer <73339780+lassedochreden@users.noreply.github.com>
Date: 2026-08-25 12:29:00 +0200
Commit message:
Merge pull request #102 from BodenmillerGroup/bioc24_buildfix Bioc24 fixPackage: cytomapper
Commit: 65bc5a7969825d303d8caa708c88b01a156494b2
Author: lassedochreden <lasse.meyer@uzh.ch>
Date: 2026-08-25 11:18:24 +0200
Commit message:
Revert "fix runners for shinytest", "update runners" x2 Reverts 6206c47, 67ec23c, f6bc0d8. Back to the bioc24_buildfix branch state as of "bioc24 fix" (064205c), before the GitHub Actions runner/PhantomJS-caching changes.Package: cytomapper
Commit: 6206c4746fd06ac28baac39f0892e8530370f1b5
Author: lassedochreden <lasse.meyer@uzh.ch>
Date: 2026-08-25 10:30:23 +0200
Commit message:
fix runners for shinytestPackage: cytomapper
Commit: 67ec23c4b27b6edc84e44f1babb147e4a1138cf8
Author: lassedochreden <lasse.meyer@uzh.ch>
Date: 2026-08-25 10:06:09 +0200
Commit message:
update runnersPackage: cytomapper
Commit: f6bc0d89a4b6c34cb0363107430483fdcbb98464
Author: lassedochreden <lasse.meyer@uzh.ch>
Date: 2026-08-24 17:14:57 +0200
Commit message:
update runnersPackage: cytomapper
Commit: 064205cfb4f488e62aee5705ef05256194b84a8f
Author: lassedochreden <lasse.meyer@uzh.ch>
Date: 2026-08-24 16:30:33 +0200
Commit message:
bioc24 fixPackage: bluster
Commit: ef34d956f9c1184265beef3fb868bf680ab83d17
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-25 18:29:59 +1000
Commit message:
Cleaned up docstring warnings, bumped version and date.Package: bluster
Commit: 40b38d0eef9fd2b31b728fcc000d18ce87bacd33
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-25 16:58:05 +1000
Commit message:
Switch from scuttle/scran to scrapper for dataset setup.Package: bluster
Commit: 4c7e644f89cce76561341ea6ee7ccf92ca05545d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-25 16:36:33 +1000
Commit message:
Migrated explanatory text from OSCA.advanced's cluster redux chapter. Also switch to scrapper to set up the dataset in the diagnostics.Rmd.Package: bluster
Commit: ce7ac0a3deaf212f86c90c9463bcb515b0ebd657
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-25 15:28:35 +1000
Commit message:
Tidied up pairwiseRand manpage.Package: msa
Commit: 2e9a9e9728455d7c097f7f7f8c9ee66d5429e14f
Author: UBod <ulrich@bodenhofer.com>
Date: 2026-08-25 10:07:18 +0200
Commit message:
updated vignette; version number bumped to 1.45.5Package: MsBackendMetaboLights
Commit: f49c8bc69d49d62c988a85a5a55389a586950592
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-08-25 09:05:17 +0200
Commit message:
Update READMEPackage: MsBackendMetaboLights
Commit: fdfed26db27a8c5b3fb4c9fe4602898c62857eb5
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-08-25 08:39:00 +0200
Commit message:
Fix installation instructions and add 4 second breaks to unit testsPackage: MsBackendMetaboLights
Commit: 798de387ad331d8e097fbedad942367eb77abf5e
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-08-25 08:20:12 +0200
Commit message:
small updates in NEWS and READMEPackage: MsBackendMetaboLights
Commit: bbaddc706e3ee49efd1983e0616578518cc8f164
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-08-24 09:01:32 +0200
Commit message:
Update roxygen versionPackage: scrapper
Commit: 985ad210f9f2b964dcd072ddc4a2bed302d0caef
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-25 11:27:58 +1000
Commit message:
Vignette is now a stub that redirects to the book. No point having a poor man's duplicate of the documentation when we could just point users to the real deal and save ourselves some build time.Package: drugTargetInteractions
Commit: a95ecf0aec40f8aadec98ee09258d4371b359392
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-08-24 21:19:29 -0700
Commit message:
version bumpPackage: drugTargetInteractions
Commit: 93058dc4cc5b0f8350481e46fe2ae40d1b173eea
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-08-24 21:16:28 -0700
Commit message:
Add buildMoaMasterTable(): enumerate the drugs that have a mechanism assembleMoaTable() shapes whatever queryDrugTargets() was asked for, so you have to name the drugs going in. There was no way to ask which drugs have a mechanism at all. A mechanism belongs to the drug, not to a drug-target edge, and the difference is not academic. Measured against the real sources: 1,470 of the Broad Hub's 6,855 drugs with a mechanism name no target gene (21%), as do 329 of ChEMBL's 5,727 (6%). Roughly two thousand annotated drugs are therefore unreachable from buildGenomeWideDrugTargetTable(), which is anchored on genes - "c-Myc inhibitor", "polyamine biosynthesis inhibitor", "Radiotherapy agent" and so on. Sweeps the two sources that can be enumerated: ChEMBL's /mechanism is a pageable collection (7,561 records, ~8 requests) and the Broad Hub is already local SQLite. The whole table is 14,723 rows over 12,582 drugs and 3,263 mechanisms in about a minute. Open Targets carries real MOA too but its GraphQL has no clean enumeration path and its drug annotations derive largely from ChEMBL, so it stays with queryMoa(). Two data details that would otherwise mislead: - The Broad Hub packs up to 6 mechanisms into one "a | b" string, for 493 drugs. Splitting them turns 1,612 apparent mechanisms into 1,294 real terms; without it, 318 of the "distinct MOAs" are combinations. - ChEMBL records "Unknown" as the mechanism for 228 rows. Dropped by default as a placeholder; includeUnknown = TRUE keeps them. Sources are kept side by side, not merged: drug_id is a ChEMBL id on ChEMBL rows and the Hub's own drug name on Broad rows. They also word mechanisms at different granularity - ChEMBL names the isoform ("Carbonic anhydrase VII inhibitor") where Broad names the family ("carbonic anhydrase inhibitor") - so only 7 of 3,263 terms are shared verbatim, and 102 after lower-casing. Documented, since it decides whether grouping the column across sources means anything. Every count reconciles against independent raw measurements of both sources. New .dtiPageAll() for unfiltered collection paging, beside the existing .dtiBatchGET(). Vignette section 7 gains "A Master Table of Mechanisms". test-moaTable.R 57 -> 90 with the network on, the Broad half network-free against a synthetic SQLite.Package: drugTargetInteractions
Commit: 05e656c64d1f073c2c0fb29fd6391de68dbd7c0b
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-08-24 20:48:20 -0700
Commit message:
version bumpPackage: drugTargetInteractions
Commit: 845f69b2a455d6b1885d5f5cc1e17e80e96be3ba
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-08-24 20:45:45 -0700
Commit message:
Reject an unrecognised source or column instead of silently dropping it match.arg(several.ok = TRUE) drops any value it cannot match as long as at least one other value does, and its matching is case-sensitive. So sources = c("chembl", "dgidb", "opentargets", "ttd", "broad", "GtoPdb") built a five-source table with no error, no warning, and no gtopdb element in the result - the mis-cased name simply vanished. Passing gtoPdbDbPath did not help, because the requirement check runs after match.arg has already discarded the name. queryDrugTargets() already validated its own sources with an explicit %in% check; the three match.arg(several.ok = TRUE) call sites were the outliers. All now use .dtiMatchSet(), which errors on anything unrecognised and, when a value differs only in case, says which name was meant - every accepted name is lower-case: 'sources' does not recognise: GtoPdb. Did you mean "gtopdb"? These names are lower-case. Expected any of: chembl, dgidb, opentargets, ttd, broad, gtopdb. Covers buildGenomeWideDrugTargetTable(sources), combineDrugTargets(columns) and mergeDrugTargets(by). Exact matching replaces match.arg's partial matching, which is the same trade queryDrugTargets() already made.Package: RBPEqBind
Commit: e1f34337a3adf282f7e6ccd152753bf194ec2b84
Author: SoonYi <55300935+S00NYI@users.noreply.github.com>
Date: 2026-08-24 22:29:26 -0400
Commit message:
Bump version to 0.99.4 and refine parallel architecturePackage: VDJdive
Commit: 74f33a6f30ed7ba27bf714fa699e020a57a500b5
Author: Kelly Street <street.kelly@gmail.com>
Date: 2026-08-24 16:45:04 -0700
Commit message:
reran Rcpp::compileAttributes()Package: gDRcore
Commit: 0901d750ecc307af97f90cb717aed7a18db4e230
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2026-08-24 13:26:34 +0200
Commit message:
Merge pull request #206 from gdrplatform/GDR-3542 feat: add get_period_timepoints() listing the measurements in each growth-rate windowPackage: gDRcore
Commit: 0c2b2ff294cc0ea4a92d6db8b7db4bc629961e46
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2026-08-20 11:52:04 +0200
Commit message:
refactor: extract .assert_periods() and cover the default lfc_assay pathPackage: gDRcore
Commit: 1e23f5ac51179e9951e1be2df07912aaddfcae15
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2026-08-19 14:18:44 +0200
Commit message:
Merge remote-tracking branch 'origin/main' into GDR-3542 # Conflicts: # DESCRIPTION # NEWS.mdPackage: gDRcore
Commit: 71f2ec036923ebbde7eb22aed7347975c1cd4814
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2026-08-19 12:50:44 +0200
Commit message:
feat: add get_period_timepoints() listing the measurements in each growth-rate windowPackage: lineagespot
Commit: 1c3132ac4f90d93c26f53f0e17c2ee2858ff2545
Author: Theodoros Katzalis <thodkatz@gmail.com>
Date: 2026-08-24 11:04:33 +0300
Commit message:
Remove outdated outbreak api add ci to replicate the bioconductor pipeline and bump versioning to 1.17.1Package: lineagespot
Commit: 13b0d6100e5302342df581c2c290be20032d9bd3
Author: Theodoros Katzalis <thodkatz@gmail.com>
Date: 2026-08-20 15:35:55 +0300
Commit message:
Bump DESCRIPTION to 1.17.1Package: lineagespot
Commit: 3144e41c683375d856d8737a37f795d3a5867e75
Author: Theodoros Katzalis <thodkatz@gmail.com>
Date: 2026-08-20 15:13:56 +0300
Commit message:
remove outdated outbreak.info api we can't get lineages from outbreak api since it has reached end of life, so we have removed it. Lineages currently can be only local - offlinePackage: lineagespot
Commit: 1a04c30d49bbe4828eda3188839103308f58fdc5
Author: Theodoros Katzalis <thodkatz@gmail.com>
Date: 2026-08-20 14:50:03 +0300
Commit message:
use auto-generated bioconductor workflow replaces our custom workflow, and uses the official one, replicating the actual pipeline on bioconductorPackage: lineagespot
Commit: 1da929573143a6b9bcc1089fd0048b8c9126fa69
Author: Theodoros Katzalis <thodkatz@gmail.com>
Date: 2026-08-05 15:58:00 +0300
Commit message:
use dual license file conventionPackage: lineagespot
Commit: 93137be3c7f7d39375c214db7284eccec2dddc3b
Author: Theodoros Katzalis <thodkatz@gmail.com>
Date: 2026-08-05 15:45:01 +0300
Commit message:
add ci to test build in bioconductor containersPackage: methylclockData
Commit: 98e411af857b56ca01ddb539b6b08adb86da71d2
Author: dpelegri <43083225+dpelegri@users.noreply.github.com>
Date: 2026-08-24 09:59:13 +0200
Commit message:
Add the coefGarma resource and bump to 1.21.3 The Garma & Quintela-Fandino (2024) cross-platform age clock needs one new ExperimentHub resource. metadata_v2026_08b.csv (with its make-metadata script) points to the new version of the Zenodo deposit (record 22069904, verified by download); get_coefGarma() joins the accessors, pending its ExperimentHub id. The 28 resources from the previous round are unchanged.Package: MetaboDynamics
Commit: 42de4d6a3457843d3abb624968a3b4ab491de987
Author: Katja Danielzik <katja.danielzik@uni-due.de>
Date: 2026-08-24 09:22:18 +0200
Commit message:
version bumpPackage: MetaboDynamics
Commit: 23a33c72d72db8b100ad015fde911b183b665a11
Author: Katja Danielzik <katja.danielzik@uni-due.de>
Date: 2026-08-24 09:21:56 +0200
Commit message:
bug fix: Guide to prior settingpPackage: scrapper
Commit: dc2904c751ede19a63e91e879a43cbf11e98c6b5
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-24 15:53:08 +1000
Commit message:
Avoid clang errors from alias template class deduction.Package: gDR
Commit: 2fd929fb761bc1f5dfcb55db79dc905dc1fb6824
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2026-08-24 07:48:39 +0200
Commit message:
Merge pull request #61 from gdrplatform/GDR-3530 chore: align DESCRIPTION date with NEWS entryPackage: gDR
Commit: 65f284e0abfa8ebb6b84ea7beb98ff5990e0e596
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-08-18 08:26:51 +0200
Commit message:
chore: align DESCRIPTION date with NEWS entryPackage: drugTargetInteractions
Commit: a93caef2962ddcae9772013ab8c176e07ff1cd89
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-08-23 21:38:38 -0700
Commit message:
Ignore vignette render artifacts rmarkdown::render() leaves a ~1MB html plus a ~1MB knitr cache in vignettes/, so every render ended with a manual cleanup to keep the tree clean. Nothing tracked matches these patterns, so nothing is hidden retroactively. Scoped to vignettes/ rather than a bare *.html on purpose: gh-pages keeps the published page as a root-level index.html and has no .gitignore of its own, so an unscoped rule would silently make the next publish a no-op if this file ever reached that branch.Package: drugTargetInteractions
Commit: cdc5557d74f597a957220cc087d558f1a54c82ce
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-08-23 21:32:13 -0700
Commit message:
Warn about the symbols given, not about the whole HGNC snapshot buildHgncSymbolMap() warned "1268 old symbol(s) map to more than one current symbol" on every call. That count describes the HGNC snapshot - it is the same 1268 whatever you are translating - so every caller got it regardless of relevance. Translating FGFR1 warned about 1268 genes, none of them FGFR1. The vignette showed the cost: four copies of that warning, in chunks querying only genes that are not ambiguous at all. Suppressing it there would have hidden a wrong warning rather than fixed it. normalizeGeneSymbols() now reports the ambiguities the symbols it was given actually run into, names them, and scopes attr(., "ambiguous") to those. A symbol that is already current is passed through untouched and can never be ambiguous, so the common case is silent. addCommonIds() and normalizeGeneSymbols() build their map with warn = FALSE; a direct buildHgncSymbolMap() call still reports the snapshot-wide count, which is meaningful when the map itself is what you asked for. Verified by re-rendering: the vignette now has 0 warnings and 0 errors across all 151 chunks, against 4 before. The full suite is warning-free too (was 2 "expected" warnings), FAIL 0 ERROR 0 SKIP 86 PASS 408.Package: drugTargetInteractions
Commit: c968b7b2e1b4d4947009e759a4d8585f63a44f35
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-08-23 21:13:59 -0700
Commit message:
version bumpPackage: drugTargetInteractions
Commit: e09215a23e80e7663c5bc4c1c67d6c3e1634122f
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-08-23 20:48:39 -0700
Commit message:
Carry gene identity once in mergeDrugTargets, and select columns by concept Two things this function got wrong for a genome-wide build, neither of which changes what placing sources side by side means. The identity block was repeated once per source. A build tags every source's rows with the same gene, so the output carried chembl_symbol, dgidb_symbol, opentargets_symbol and ttd_symbol all reading ADRA1A, and four more columns all reading ENSG00000120907 - 8 of 61 columns spent restating what the key already determines. It is now collapsed like any other column but emitted once, beside the key: 61 columns become 55. Keyed on a gene each cell holds one value; keyed on a compound, symbol holds every gene that drug hits, which is the honest answer rather than an arbitrary winner. Selecting a column meant knowing all six names for it. Reaching FGFR1's drugs took columns = c("Drug_Name", "drug_name", "DrugName", "pert_iname", "ligandName"). `columns` now also accepts a shared name from the mapping table, so "drug_name" selects whatever each source calls it. Source-native names still work unchanged, and the two forms mix. The columns still come back one per source - this view exists to compare what each source says, so it deliberately does not merge them. Also documents a trap the genome-wide data exposed: n_sources counts the sources that returned a row, not the sources that found a drug. A build queries every gene everywhere, so 18,778 of 19,296 genes have a row from all four sources while only 1,025 have a drug in all four, and 14,710 have none anywhere. Test the cells, not n_sources. The hgnc_id clobbering this function also had needed no work here - it routes through addCommonIds(), so the previous fix covered it.Package: drugTargetInteractions
Commit: 2a17f690a972c193eb7da44af363f2283a7a6837
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-08-23 18:27:18 -0700
Commit message:
Add a user-editable column map, and assemble a genome-wide build with it buildGenomeWideDrugTargetTable() returns one table per source, each with that source's own columns. Stacking them needs two things: columns holding the same content under different names aligned onto one column, and columns belonging to one source carried through as their own. combineGenomeWideDrugTargets() does that. The identity block (hgnc_id, symbol, ensembl_gene_id, QueryIDs) is emitted verbatim and never recomputed - see the previous commit for why. Canonical columns are character throughout, since sources sharing a concept do not share a type; each source's own columns keep theirs, since each belongs to exactly one source and nothing has to be reconciled. Which columns hold the same content now lives in a table the user can see and edit. drugTargetColumnMap() returns it as a plain data.frame, and .dtiCuratedColumnMap is the single source of truth: .dtiCombineColMap is derived from it, with a test asserting the derivation reproduces the old hardcoded list exactly, so the map a user edits and the map combineDrugTargets() applies cannot drift apart. Curated groups grow from 3 to 8, each checked against real values first: mechanism (free text naming the target, as against action's bare label - TTD's MOA is a bare label and stays in action), target_uniprot, pubchem_cid, max_phase and indication. max_phase is deliberately lossy and documented as such: ChEMBL a number -1..4, Open Targets PHASE_3, TTD and the Broad Hub Approved. Broad's moa is the one native column feeding two canonical columns, which the map allows on purpose. The map can also be generated from a build, but only as a draft. Matching column names after normalising case and punctuation proposes opentargets:drug_id with ttd:DrugID, which are a ChEMBL identifier and a TTD-internal one - aligning them would fabricate identity. It equally misses groups sharing no name at all, such as approved_symbol/gene_name/ GeneName. So proposals come back inactive and are inert until someone turns them on. Verified on a full 212,827-row build: 212,827 rows out, 41 columns, hgnc_id complete and every value kept as supplied, per-source row counts identical to input, canonical columns identical() to their native source column, and no native column carrying a value outside its own source's rows.Package: drugTargetInteractions
Commit: bf7d06fe279bbd80bc9dd4af07beb5b43a93764c
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-08-23 18:26:47 -0700
Commit message:
Keep an hgnc_id a caller already established instead of re-deriving it addCommonIds() overwrote hgnc_id unconditionally, which is wrong for any table that already carries one. buildGenomeWideDrugTargetTable() tags every row with the HGNC gene it queried *from*, so that column is complete by construction; recomputing it from the identifiers a source echoes back is strictly worse, and sometimes simply wrong. Measured on a four-source genome-wide build, first 2000 rows per source: re-derivation recovers 497/2000 ChEMBL rows (many UniProt accessions name more than one gene, so NA is the honest answer), 1306/2000 for Open Targets, 1670/2000 for TTD - and moves 98 of TTD's rows to the wrong gene outright. Rows queried as ADRA1A come back as HGNC:280, which is ADRA1D: ADRA1A is also a previous symbol of that gene, and the ambiguity tie-break picks alphabetically. A tie-break that is reasonable when there is nothing better becomes a silent corruption when there is. Now only the gaps are filled. gene_symbol/target_uniprot follow the key that was kept, which incidentally fills ChEMBL's otherwise-NA gene_symbol offline - that previously needed resolveGeneSymbol = TRUE and a network round trip.Package: mobileRNA
Commit: 49137e2b494b71e047939aa0bff147715ee86794
Author: Katie Jeynes-Cupper <katie.jeynescupper@gmail.com>
Date: 2026-08-23 21:26:31 +0100
Commit message:
corrections version control numvering issue lolPackage: mobileRNA
Commit: 2944bf1232044f66c16527eb1e1b3fc158e9af34
Author: Katie Jeynes-Cupper <katie.jeynescupper@gmail.com>
Date: 2026-08-23 21:24:47 +0100
Commit message:
corrections to version controlPackage: mobileRNA
Commit: 41aad760b2851d91878eddeeabd1ebba972f6e15
Author: Katie Jeynes-Cupper <katie.jeynescupper@gmail.com>
Date: 2026-08-23 21:23:25 +0100
Commit message:
Merge branch 'devel' of github.com:KJeynesCupper/mobileRNA into devel # Conflicts: # DESCRIPTION # inst/NEWS.mdPackage: mobileRNA
Commit: dd2a2941eb09ff726deab522dd2c9b7f92a9b709
Author: Katie Jeynes-Cupper <katie.jeynescupper@gmail.com>
Date: 2026-08-23 21:22:48 +0100
Commit message:
version controlPackage: mobileRNA
Commit: 610b846dec780ad644c34a5a34ea35382d520c85
Author: Katie Jeynes-Cupper <katie.jeynescupper@gmail.com>
Date: 2026-08-23 15:31:45 +0100
Commit message:
baymobil integration Integrated baymobil, and removed simDesign (causing loading error).Package: mobileRNA
Commit: 41ab229c9dc6b9d24fcb469641115086afdd1a1b
Author: Katie Jeynes-Cupper <77631989+KJeynesCupper@users.noreply.github.com>
Date: 2026-03-03 20:58:23 -0600
Commit message:
Update README.mdPackage: mobileRNA
Commit: ed1157b28b535adf99642472e0e554e65f6069e3
Author: Katie Jeynes-Cupper <77631989+KJeynesCupper@users.noreply.github.com>
Date: 2026-03-03 12:24:23 -0600
Commit message:
Update R-CMD-check.yamlPackage: mobileRNA
Commit: 3882409fab672a722fea9d53e1e88c71070e0b05
Author: Katie Jeynes-Cupper <77631989+KJeynesCupper@users.noreply.github.com>
Date: 2026-03-03 11:49:28 -0600
Commit message:
Update R-CMD-check.yamlPackage: mobileRNA
Commit: 8b80071012fa6777675cab169280c23963a6b1a3
Author: Katie Jeynes-Cupper <77631989+KJeynesCupper@users.noreply.github.com>
Date: 2026-03-03 11:47:56 -0600
Commit message:
Update README.mdPackage: mobileRNA
Commit: c4bb6f3f3e64f37d2a41232d5b3519a3b646250d
Author: Katie Jeynes-Cupper <77631989+KJeynesCupper@users.noreply.github.com>
Date: 2026-02-27 13:06:42 -0600
Commit message:
Update _pkgdown.ymlPackage: mobileRNA
Commit: 167279072541c6b647c9cf92118ea177b2f8ef6d
Author: KJeynesCupper <kejc@illinois.edu>
Date: 2025-10-23 12:16:01 -0500
Commit message:
version controlPackage: mobileRNA
Commit: dc1d838d8e820f8abbf8f687dd8beb70b434c696
Author: KJeynesCupper <kejc@illinois.edu>
Date: 2026-02-27 12:39:45 -0600
Commit message:
update-version-mkPackage: mobileRNA
Commit: 1a3e4ba750d3ae601405af1deae5352938bd2e8d
Author: KJeynesCupper <kejc@illinois.edu>
Date: 2026-02-27 12:21:13 -0600
Commit message:
mobile_sRNA_import_update Fixed bug that prevent mobile sRNA data being loaded into RPackage: mobileRNA
Commit: a0955c4e64df214396e262e117c728141d8affd8
Author: KJeynesCupper <kejc@illinois.edu>
Date: 2025-11-18 16:48:20 -0600
Commit message:
contact-updatePackage: mobileRNA
Commit: 9f3e7416aa56cb7ea72454f33b72b0620a01d6d1
Author: Katie Jeynes-Cupper <katie.jeynescupper@gmail.com>
Date: 2026-08-23 16:50:07 +0100
Commit message:
Merge branch 'main' into devel # Conflicts: # DESCRIPTION # inst/NEWS.mdPackage: mobileRNA
Commit: 09119fa8de8abe4c004d7d47934140d620204d61
Author: Katie Jeynes-Cupper <katie.jeynescupper@gmail.com>
Date: 2026-08-23 15:31:45 +0100
Commit message:
baymobil integration Integrated baymobil, and removed simDesign (causing loading error).Package: mobileRNA
Commit: 1f721799a7e9b1fe6e255e3d56f9f147182e2b9e
Author: Katie Jeynes-Cupper <77631989+KJeynesCupper@users.noreply.github.com>
Date: 2026-03-03 20:58:23 -0600
Commit message:
Update README.mdPackage: mobileRNA
Commit: f819c5ea875f950077d517b5e4bf98a3eea79051
Author: Katie Jeynes-Cupper <77631989+KJeynesCupper@users.noreply.github.com>
Date: 2026-03-03 12:24:23 -0600
Commit message:
Update R-CMD-check.yamlPackage: mobileRNA
Commit: ad7187067c24187246fef7e0a18a36c7a5231f0c
Author: Katie Jeynes-Cupper <77631989+KJeynesCupper@users.noreply.github.com>
Date: 2026-03-03 11:49:28 -0600
Commit message:
Update R-CMD-check.yamlPackage: mobileRNA
Commit: 6f53c59ded620909b657d3f39061dbf0b7cee378
Author: Katie Jeynes-Cupper <77631989+KJeynesCupper@users.noreply.github.com>
Date: 2026-03-03 11:47:56 -0600
Commit message:
Update README.mdPackage: mobileRNA
Commit: cb4f0aa6e37f2606b677a5baae7201422cb14b2d
Author: Katie Jeynes-Cupper <77631989+KJeynesCupper@users.noreply.github.com>
Date: 2026-02-27 13:06:42 -0600
Commit message:
Update _pkgdown.ymlPackage: mobileRNA
Commit: c5a7a39f8ec1c2ca49fd13b61b48e5f9b5a56623
Author: KJeynesCupper <kejc@illinois.edu>
Date: 2026-02-27 12:39:45 -0600
Commit message:
update-version-mkPackage: mobileRNA
Commit: 8a03e5b40ee534177f0c53f6c6815e82b92fb7ad
Author: KJeynesCupper <kejc@illinois.edu>
Date: 2026-02-27 12:25:59 -0600
Commit message:
Merge branch 'main' of https://github.com/KJeynesCupper/mobileRNAPackage: mobileRNA
Commit: b39d9baa6c2a3c35b631136458d177738e4976af
Author: KJeynesCupper <kejc@illinois.edu>
Date: 2026-02-27 12:21:13 -0600
Commit message:
mobile_sRNA_import_update Fixed bug that prevent mobile sRNA data being loaded into RPackage: mobileRNA
Commit: 9b1f8488950234e5710804e71abac1f55785138d
Author: KJeynesCupper <kejc@illinois.edu>
Date: 2026-01-12 18:40:46 -0600
Commit message:
Bump patch version to 1.6.1Package: mobileRNA
Commit: 13a09409420a76a588153324512830c8acaec074
Author: KJeynesCupper <kejc@illinois.edu>
Date: 2025-11-18 16:50:13 -0600
Commit message:
Merge branch 'devel' of https://github.com/KJeynesCupper/mobileRNA # Conflicts: # DESCRIPTION # inst/NEWS.mdPackage: mobileRNA
Commit: 74c565b943b186dd864f416a210769bb3135cd0f
Author: KJeynesCupper <kejc@illinois.edu>
Date: 2025-11-18 16:48:20 -0600
Commit message:
contact-updatePackage: mobileRNA
Commit: 00bf8fe986a43796f3035cafe734a87fa249541f
Author: KJeynesCupper <kejc@illinois.edu>
Date: 2025-10-23 12:16:01 -0500
Commit message:
version controlPackage: geneslator
Commit: b6ea241cf1c7e90c447d61bc6f918cdbabd04e94
Author: GMicale <gmgmicky@gmail.com>
Date: 2026-08-23 10:49:14 +0200
Commit message:
Fixed queries to KEGG dbPackage: RBPEqBind
Commit: 569d691fd8a79478cf5c43493c90df2dffcf806a
Author: SoonYi <55300935+S00NYI@users.noreply.github.com>
Date: 2026-08-22 19:04:05 -0400
Commit message:
Bump version to 0.99.3 and clean up dependencies for Bioconductor reviewPackage: RBPEqBind
Commit: 0b9c6f4970d63525f52066ee0afd09eb91cca408
Author: SoonYi <55300935+S00NYI@users.noreply.github.com>
Date: 2026-08-22 19:03:59 -0400
Commit message:
Add extdata provenance script, update README BiocManager install, and refine vignettePackage: RBPEqBind
Commit: f3d440379d41d209e02dad76694f603f5c78d5a1
Author: SoonYi <55300935+S00NYI@users.noreply.github.com>
Date: 2026-08-22 19:03:54 -0400
Commit message:
Implement scale-invariant log solver, fix peak edge background, and add invariant testsPackage: RBPEqBind
Commit: f70e67df3777e058c7a09d0fafd80a8c87f1e5e5
Author: SoonYi <55300935+S00NYI@users.noreply.github.com>
Date: 2026-08-22 19:03:45 -0400
Commit message:
Harmonize JSON export, integrate rtracklayer for BED export, and update palettePackage: RBPEqBind
Commit: 02565f7bdce6f602d6c15c1effadbec0298cdf6f
Author: SoonYi <55300935+S00NYI@users.noreply.github.com>
Date: 2026-08-22 19:03:38 -0400
Commit message:
Refactor simulation with future.apply parallelization, add k-mer checks, and regex docsPackage: igvShiny
Commit: d5bca1f423b6607074d33d438e27ed15190361ef
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2026-08-22 20:39:28 +0200
Commit message:
fix: remove a session's track files when the session ends (#173) * fix: remove a session's track files when the session ends Every loader that writes into the served tracks directory left the file behind for the lifetime of the R process. Harmless interactively, where the directory sits under tempdir(), but a deployed app keeps one process across many user sessions, and TRACKS_DIR may point outside tempdir(), where nothing removes them at all. A bam export or a cram copy is gigabytes per load. The six loaders holding a session now name their file through .trackFile(), which collects the paths in session$userData and registers a single onSessionEnded() hook to unlink the set. The bam index rtracklayer writes next to its output is registered the same way. The two write sites without a session in hand - the custom-genome copies in igvShiny() and the GWASTrack constructor - are unchanged. Closes #152 * docs: finish the session parameter description on .stageTrackFile * docs: point agents at a local CLAUDE.md when one is presentPackage: Rarr
Commit: 4a6e9871f491e4e10ba1d8ce72071111ba9207d4
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-22 00:06:19 +0200
Commit message:
Bump versionPackage: Rarr
Commit: 0d0a41e068f8f517b036a56818661d91597118e4
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-22 00:05:49 +0200
Commit message:
Ensure chunk get indexed when out of order with full lengthPackage: Rarr
Commit: 6321417aedb60ff4c301b25bf743844c3060671c
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 14:03:54 +0200
Commit message:
Use RAW_RO() where possiblePackage: Rarr
Commit: 5c33c2a106fe335160064ac0dffcc77ba2844a3f
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-20 19:06:50 +0200
Commit message:
Bump versionPackage: Rarr
Commit: 1811ace32424740077592b0dc4510f6d1e435d48
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-20 22:46:16 +0200
Commit message:
Support scalar case in is.compactPackage: Rarr
Commit: 46d5bfdc269222ee1615fcfe32f97791ad337fa7
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-20 22:56:48 +0200
Commit message:
Restore FIXME commentPackage: Rarr
Commit: abd7a68172103a99df1a6db2e2df3a6ccf72d7f2
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-20 19:30:16 +0200
Commit message:
Factor out + 1LPackage: Rarr
Commit: ff24a58d918965ee436fc02b059256e27c5bcd43
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-20 19:23:29 +0200
Commit message:
Use rapply()Package: Rarr
Commit: 9b565eda08d2dec66bb604df235122fec6cd2ba0
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-20 18:13:40 +0200
Commit message:
Leverage ALTREP on eligible dimensions when reindexingPackage: Rarr
Commit: 9824d062d35421b56aa369ee96988252da675bb0
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-20 17:34:01 +0200
Commit message:
Do not compute quotient and remainder in two separate loopsPackage: Rarr
Commit: 9c8e7385be4b95aba0c91761858658557b1847ec
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-20 16:23:22 +0200
Commit message:
Address identity transpose case earlyPackage: Rarr
Commit: de09cc7e8b2a576895dcbfab8a179b051fc6b5b1
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-20 15:59:49 +0200
Commit message:
Make 1D-like identity case implicit in transpose codecPackage: rhdf5
Commit: 1682d4b493d0ddc9e46cba78a141b780bb8390e8
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 22:25:23 +0200
Commit message:
Bump versionPackage: rhdf5
Commit: ae839a3b4c258cb6919300f28b2bc0b93b5693f7
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 23:34:42 +0200
Commit message:
Make alternative explicit in deprecation warningPackage: rhdf5
Commit: 99f117b166feb0d28879a6b1bc8c7f101403298d
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 22:24:22 +0200
Commit message:
Restore as.na attribute for nowPackage: rhdf5
Commit: 15c5e4237b150d11ccddb9c399d378ff2c491871
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-20 15:26:54 +0200
Commit message:
Set Hugo as autPackage: TSSr
Commit: bba29ddb31aa3bcc5c8e1a4276224de759b5b7ea
Author: JohnnyChen1113 <1020607557@qq.com>
Date: 2026-08-21 15:41:36 -0500
Commit message:
Merge Bioconductor devel history for TSSr 0.99.21Package: TSSr
Commit: 41bc18a8aa1f76ed8e2c1f6ff7699575c7ee9632
Author: JohnnyChen1113 <1020607557@qq.com>
Date: 2026-08-21 14:55:38 -0500
Commit message:
Align vignette text with analysis outputPackage: TSSr
Commit: b2cc5da42adff75ebce8c5cdd358808957b41907
Author: JohnnyChen1113 <1020607557@qq.com>
Date: 2026-08-21 14:19:47 -0500
Commit message:
Revise vignette with end-to-end input workflowPackage: TSSr
Commit: 1fd29d2ec88b7a358683d83e4e0c5c49cfa6f259
Author: JohnnyChen1113 <1020607557@qq.com>
Date: 2026-08-21 12:41:47 -0500
Commit message:
Document pipeline and expose DESeq2 fit typePackage: TSSr
Commit: b90a01f34276ff26b00a54e3b693128d161ca07e
Author: JohnnyChen1113 <1020607557@qq.com>
Date: 2026-08-21 07:57:31 -0500
Commit message:
Close remaining review validation gapsPackage: TSSr
Commit: 876a27e2dab02ee1f4677d2d5c4ba5118c39eb7a
Author: JohnnyChen1113 <1020607557@qq.com>
Date: 2026-08-21 06:40:05 -0500
Commit message:
Expand vignette workflow contextPackage: TSSr
Commit: 4f85fff8b495b0ff48a12834bec3a5bfb2e60804
Author: JohnnyChen1113 <1020607557@qq.com>
Date: 2026-08-21 05:05:05 -0500
Commit message:
Address Bioconductor review feedbackPackage: TSSr
Commit: e2739767956c57b3976dfd69f4eb62ce5577cd42
Author: JohnnyChen1113 <1020607557@qq.com>
Date: 2026-08-05 09:43:18 -0500
Commit message:
Remove automatic GitHub Bioconductor CI Remove the provisional push- and pull-request-triggered GitHub Actions workflow. It was added without being part of the requested validation plan and spent most of its wall time downloading a complete Bioconductor dependency stack into a fresh container. That behavior neither reproduced the pre-installed Single Package Builder environment nor added useful coverage beyond the pinned Linux server checks already used for this submission. Deleting the workflow also prevents routine branch pushes from launching long, network-dependent jobs with little diagnostic value. This commit does not remove or skip any package example, unit test, vignette, R CMD check, or BiocCheck step, and it changes no package implementation. Linux validation continues explicitly in the fixed Bioconductor Docker image recorded in the project reports, while official platform results remain the responsibility of SPB after a Bioconductor repository push.Package: TSSr
Commit: d89aa85ec64b381aeed86f666e7f1ebed43068d4
Author: JohnnyChen1113 <1020607557@qq.com>
Date: 2026-08-04 16:32:15 -0500
Commit message:
Allow cold Bioconductor CI dependency installs Increase only the provisional GitHub Actions job timeout from 45 to 60 minutes. The workflow starts from an ephemeral Bioconductor devel container and must download and install Depends, Imports, and Suggests before package build or check begins; that cold setup exhausted the original job budget before it could provide a package result. This commit changes no package source, dependency declaration, example, test, or R CMD check setting. It is a workflow-infrastructure adjustment intended to separate dependency provisioning time from the package's own check time. The automatic workflow is removed in the following commit after review determined that repeated cold installation did not model the pre-provisioned SPB environment closely enough to justify its time and network cost.Package: TSSr
Commit: 5b2c994900eeb31b10f9273e143f3c4f7cb44993
Author: JohnnyChen1113 <1020607557@qq.com>
Date: 2026-08-04 15:54:43 -0500
Commit message:
Reduce SPB runtime and add provisional Linux devel CI Reduce repeated work after the Bioconductor Single Package Builder completed R CMD check in 566 seconds, leaving too little margin below the ten-minute limit. Keep every public function under real execution while replacing unnecessarily repeated full exampleTSSr pipelines with the bundled 100-row, four-sample, two-strand TSStable fixture or with already-computed upstream slots. Each example and test still recomputes the function it is intended to exercise; no skip condition, dontrun block, donttest block, or eval=FALSE path is introduced. Update clusterTSS(), consensusCluster(), shapeCluster(), and exportClustersToBed() examples to construct and run a compact workflow through the public API. Refactor workflow tests to use a balanced 1,000-row subset for clustering, and remove redundant upstream recomputation from downstream analysis tests. Regenerate the affected Rd files and advance the development version to 0.99.20 with a NEWS entry that records the behavioral and timing changes. Add a provisional GitHub Actions workflow based on the Bioconductor devel container to install declared dependencies, build the source tarball, run R CMD check --no-manual --timings, and retain failure artifacts. This workflow was an exploratory local guard and is removed in a later commit after its cold dependency setup proved unrepresentative of SPB. In the pinned Linux Bioconductor container, no example takes more than five seconds and R CMD check --no-vignettes --no-manual decreases from 566 to 421 seconds while all 1,000 test assertions continue to run.Package: TSSr
Commit: 68fc7fabbc55c81aa35657810c0513ab16659661
Author: JohnnyChen1113 <1020607557@qq.com>
Date: 2026-08-04 15:54:33 -0500
Commit message:
Make cluster quantiles deterministic across platforms Fix a cross-platform reproducibility failure in the 10th- and 90th-percentile boundaries used for tag clusters and consensus clusters. The previous strict comparison, cumsum(tags) > fraction * sum(tags), could choose adjacent genomic positions when a cumulative sum landed on the threshold within approximately one double-precision rounding unit. The observed SPB difference changed a discrete cluster boundary by three bases even though the underlying values were mathematically equal. Introduce .firstCumulativeFractionIndex() with a scale-aware tolerance based on machine epsilon, vector length, target magnitude, and cumulative-sum magnitude. Treat a cumulative value equal to the requested fraction within that tolerance as having reached the threshold. Apply the helper consistently to forward and reverse boundaries in tag clustering and in both consensus-cluster execution paths. This implements the documented interval semantics of containing at least 80% of cluster signal and preserves the published macOS-side behavior. Add public-workflow tests for exact-threshold inclusion, invariance under positive signal scaling from 1e-6 to 1e6, and consensus-cluster behavior. Discrete coordinates and table fields remain exact; only aggregate floating tag sums use a 1e-12 comparison tolerance. Regenerate exampleTSSr with the deterministic rule. One control cluster moves its lower boundary from 123531 to 123502 and its interquantile width from 16 to 45, with the corresponding promoter-shape score update. Assigned clusters, enhancers, differential expression, TAG tables, and promoter shifts remain unchanged.Package: ProteinBatcher
Commit: 1c6df35e6b9a0f0f333f23521ff00b7bd5ff508f
Author: Aitor Moruno Cuenca <amoruno@almirall.com>
Date: 2026-08-21 18:59:35 +0200
Commit message:
0.99.7: optional annotation columns, configurable block_var, mzTab dispatch fix, contrast naming fix, DESCRIPTION/NAMESPACE syncPackage: ProteinBatcher
Commit: 0947a727ef1879f022bdc459018091114854098a
Author: Aitor Moruno Cuenca <amoruno@almirall.com>
Date: 2026-07-20 16:04:15 +0200
Commit message:
Update to read .SDRF format for experimental results designPackage: ProteinBatcher
Commit: 7299cde412fb5210b812b7c95de79d2053eda248
Author: Aitor Moruno Cuenca <amoruno@almirall.com>
Date: 2026-07-20 16:03:24 +0200
Commit message:
Incorporating .SDRF format for experimental design matrixPackage: methylclockData
Commit: f0e667d69b4ad6150cc5ce6dc61bee9aa56fb1cb
Author: dpelegri <43083225+dpelegri@users.noreply.github.com>
Date: 2026-08-21 18:25:16 +0200
Commit message:
Fill in the ExperimentHub ids EH10460-EH10487 and bump to 1.21.2 The hubs team loaded the 28 resources into the production database and assigned EH10460-EH10487. Each accessor now carries its id instead of the EH_PENDING placeholder. Metadata updated to the form the hubs team requested: Location_Prefix is https://zenodo.org/ and the rest of the path moved to RDataPath, matching their correction. LICENSE reduced to the YEAR / COPYRIGHT HOLDER template R expects; the full MIT text moves to LICENSE.md, kept out of the build.Package: scrapper
Commit: a31dbc034c8de03f434020ed917f4b37d018bfe8
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-22 02:09:07 +1000
Commit message:
Bumped version and date, rebuilt namespace.Package: scrapper
Commit: bed70e7e72f100a23692c8a36b4c34e05b398299
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-22 00:48:06 +1000
Commit message:
Update C++ bindings for the latest libraries in assorthead. The biggest user-visible change is that the number and ordering of factor levels are now respected in any group= or block= argument. This is possible via the the new num_groups/num_blocks= arguments in the C++ functions. Also added some explicit tests for .transformFactor().Package: biomaRt
Commit: 2b496cbf6d73c2573d2ed57027287e652db0ec4c
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 18:04:10 +0200
Commit message:
Bump versionPackage: biomaRt
Commit: 79aa423c07dcde35f8912dcb377a70b1701514aa
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 18:03:57 +0200
Commit message:
Document setEnsemblSSL() removalPackage: biomaRt
Commit: 4b8b60157f4fbca9575d831043bb52d1f1f89935
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 18:02:58 +0200
Commit message:
Remove SSL modification recommendation from vignettePackage: biomaRt
Commit: 3d8555fac60f64e11f9b15619457e26ce1d4f2af
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 17:13:40 +0200
Commit message:
Prepare deprecation of SSL settings modificationPackage: biomaRt
Commit: 0aeaaa4b73ac0efd96afadb27b0affc9b7dd6ea4
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 16:50:39 +0200
Commit message:
Rename for mock testPackage: biomaRt
Commit: 5f9b4a03001392421d6b7967a14c8964d5c5df7c
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 16:24:29 +0200
Commit message:
Do not eval HTTP 500 chunk for nowPackage: biomaRt
Commit: 0b4f42efacfd0a7f18f84b879613479b439ca2cc
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 16:15:27 +0200
Commit message:
Remove CollatePackage: biomaRt
Commit: b4833d79378afc91af45a9b252a4239272df195d
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 11:27:01 +0200
Commit message:
Leverage dynamic dots in req_url_query()Package: biomaRt
Commit: 67ae68a0e50ffc5c750b638d0e783aa77ab62e61
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 11:11:15 +0200
Commit message:
Factor out guess port utilPackage: biomaRt
Commit: 36a303de4466d11f03fa5d12cb3fe81cdddbfc18
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 10:55:46 +0200
Commit message:
Simplify sep definitionPackage: biomaRt
Commit: 4bbb85a9e2aa8bc4a38f4cdec6527bfcd4b81dba
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 10:51:36 +0200
Commit message:
Run devtools::document()Package: biomaRt
Commit: 25f932f1f1e81928534d8a4ec86a8d7a1a20b9ca
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 10:51:26 +0200
Commit message:
Reduce duplication by moving code to bmRequest()Package: biomaRt
Commit: f4764a53d5b490818291eb18e263aa21d611a370
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 17:06:39 +0200
Commit message:
Silence namespace linterPackage: biomaRt
Commit: 8a34a0a6effe742acb8a9cf41fe081fd0743d50c
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 16:09:51 +0200
Commit message:
Bump versionPackage: biomaRt
Commit: e56b60e3463a645a62e37f1286a6775ec1dd3377
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 16:09:02 +0200
Commit message:
Document all changes in NEWSPackage: biomaRt
Commit: 01240962a41bc72483703d950ca4233a1f083920
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 16:02:56 +0200
Commit message:
Use standard workflowPackage: biomaRt
Commit: c23d02862e906fef32870ae097cd62d4fcd1762e
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 16:01:11 +0200
Commit message:
Run vignettes on CIPackage: biomaRt
Commit: 1fbd4191c9031b7a8791cbae9447863dab5e815d
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 15:20:58 +0200
Commit message:
Small docs tweaksPackage: biomaRt
Commit: 019cda97409249c860985aa2d7853726e8021d89
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 15:18:32 +0200
Commit message:
Run devtools::document()Package: biomaRt
Commit: ad7155beea1a6a1b07caf6afe2ea0bb793e1cfd4
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 15:00:22 +0200
Commit message:
Add dataset to pkgdown reference indexPackage: biomaRt
Commit: 7c354a4bbde40997af8645fff89d35535524f65b
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 14:59:54 +0200
Commit message:
Exclude data-raw/ from lintr configPackage: biomaRt
Commit: 1d9901cce2b6eb2ea3c05d62fc52a88e986bd015
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 14:50:01 +0200
Commit message:
Fix testPackage: biomaRt
Commit: 961d0c4d8d85bc78fe1fef292e7a2df5d4b52dfc
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 14:49:57 +0200
Commit message:
Use local archive cache in .constructEnsemblURL()Package: biomaRt
Commit: b6259f1c9ffc963cdb3559ce96cf97146487c0ce
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 14:45:05 +0200
Commit message:
Add local ensembl_versions to listEnsemblArchives()Package: biomaRt
Commit: 8baaa9168f2185232b765d0bed1c6d536951c803
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 14:28:12 +0200
Commit message:
Add local version <-> release data mapPackage: biomaRt
Commit: 1df52d4328b981838db150d8fce025b28886b04c
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-13 20:03:10 +0200
Commit message:
Simplify mart short name lookupPackage: biomaRt
Commit: 5b5badbce9ffb4a1b31cd6c5f7dc84330528a665
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 11:00:47 +0200
Commit message:
Run devtools::document()Package: biomaRt
Commit: 38bd21d301b562849d460ae67e16797750a53dd1
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 10:15:44 +0200
Commit message:
Default to jun2026 archivePackage: biomaRt
Commit: 42909dfe9cf2596433e80b2f68f19a9bdc9e7e21
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-21 08:34:06 +0200
Commit message:
Avoid redirect from archivePackage: biomaRt
Commit: 0f7b30e60051e3894c95670fd33841bdbc477848
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-20 19:58:50 +0200
Commit message:
Remove unused functionPackage: biomaRt
Commit: 3c563e0ef5b4c2d7626054535b8f84f7048981f4
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-20 22:49:58 +0200
Commit message:
Avoid createHash step is not using cachePackage: biomaRt
Commit: 4725a825bc005fdd137f935aa0aaa4945034576c
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-20 20:03:12 +0200
Commit message:
Do not force redirect to base ensembl sitePackage: carnation
Commit: 1ac0ba123c09a1f207c2e6862c912a9aa14809d1
Author: Apratim Mitra <16709900+mitraak@users.noreply.github.com>
Date: 2026-08-21 11:40:16 -0400
Commit message:
Merge pull request #34 from NICHD-BSPC/v1.1.1 ## minor planned release (v1.1.1): ### various bug fixes - The pca plot was breaking if multiple coloring variables were selected. This was handled by wrapping a condition inside an `if()` statement in `all()`. - For a dataset with multiple pattern analyses, switching between them was refreshing the plot with an incorrect set of clusters. This was because of race conditions - the set of clusters to be shown was not updating in time before the plot was refreshed. The fix was to set a data load flag for initial plotting, and having the plot wait for a `refresh` for subsequent updates. - The scatter plot module was not correctly resetting clicked genes when loading a new dataset. Now the selected genes (and other) cache is correctly reset during data load. - Pattern plot & gene plot x-axis levels (bucket list) were not updating on initial load. This was fixed by updating the reactive values with the initial set of x-axis levels during the initial data load, without depending on an observer cascade. - The visible (plotly) gene plot and downloaded versions were not matching because of different ways of handling boxes and data grouping between `plotly` and `ggplot2`. This is now fixed. ### minor feature updates: - Some gene plot settings are reorganized for better visibility. Specifically, the settings dropdown now has a *sample settings* group which includes `normalization` - relocated from `More options`, and a *plot options* group listing x-axis variable, coloring variable, faceting variable along with `free y axes` - relocated from `y-axis settings`. - The gene plot now has a `box position` input to choose between dodged or overlapping boxes. - The summary table in the `DE analysis` module, now has a `dds_object` column to show which `dds_list` object was used for the contrast.Package: carnation
Commit: ec60c368689e39c126d53ae505b658dda999a071
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-08-21 11:14:42 -0400
Commit message:
bump versionPackage: carnation
Commit: 15d8a9244a5eaa5d74467ccb46e609aedffe4b05
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-08-21 11:13:42 -0400
Commit message:
add action to sync r4.3 w develPackage: carnation
Commit: 3cea3dfdf0c3de2fe228f94245ba65f563cb4b9c
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-31 09:21:33 -0400
Commit message:
mv text aes back to main pltPackage: carnation
Commit: 2975d9ff8ede3f3a7834860311138360bc23dd3a
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-30 16:52:14 -0400
Commit message:
add sample selector to gene pltPackage: carnation
Commit: d1084ff87ecba2b780469851e3ba7787df28448e
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-30 16:52:02 -0400
Commit message:
rm commentPackage: carnation
Commit: a95850ec19ab2cbfe780ebc62b5b919cf82bbc64
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-30 16:49:52 -0400
Commit message:
mv text aesPackage: carnation
Commit: 59f2829dd659d315c1f16acb214087c963e183d6
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-27 16:39:57 -0400
Commit message:
don't run bioccheck & conda actions for develPackage: carnation
Commit: 03f7eb394ea0b91910837ec06bbe7ce4eb7f32c3
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-27 16:11:11 -0400
Commit message:
add any to handle mult facet.cols in gene pltPackage: carnation
Commit: 35572aaa6743bcf8aa8ec562b1b42204ff74fd49
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-24 16:01:36 -0400
Commit message:
grp by color for gene box plotPackage: carnation
Commit: 6d2e2ce6b9e7bc91938d8733edd4f4fb3b298769
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-24 14:01:05 -0400
Commit message:
updt gene plt test to include box_dodge inputPackage: carnation
Commit: 8814e8ea7f1a304bc994cf5bfc0ad0ae942f1743
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-24 13:30:18 -0400
Commit message:
run conda, bioccheck actions on r4.3 branchPackage: carnation
Commit: 90f5aa15557921e8929e1227e46dfed7582b3ae7
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-24 13:04:17 -0400
Commit message:
run actions fr both main, develPackage: carnation
Commit: 646505679eef050440aeea9ae0b178dcd42674ef
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-24 13:02:55 -0400
Commit message:
add check fr data read errorPackage: carnation
Commit: 2e552740429579bf1efb7f288a33368bbfa190b2
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-24 13:02:36 -0400
Commit message:
make type of data dropdown widerPackage: carnation
Commit: 0da37f5fc584ad1bb6faa262b52faca1dc09e957
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-24 13:02:03 -0400
Commit message:
adj header spacingPackage: carnation
Commit: 438ab10589eb9338f453e47974804d2eceec7c55
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-24 13:01:27 -0400
Commit message:
decouple sctr plt sel show/reset in tblPackage: carnation
Commit: 5b4020ec2161e7d26446189c62f5390dc70abd6c
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-24 13:00:46 -0400
Commit message:
add validate to wait fr inputsPackage: carnation
Commit: 1f64556051f405a7abaae0dc2b616cfd4c3b7338
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-24 13:00:25 -0400
Commit message:
reset sctr cache on new data loadPackage: carnation
Commit: f979f2358d27271904c5865d274369d6bb7c18be
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-24 12:59:59 -0400
Commit message:
show dds obj fr contrst in summ tblPackage: carnation
Commit: 7edc2c249f5c8868af1567d011eb5ad9f10a827e
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-24 12:59:42 -0400
Commit message:
updt geneplt docs & helpPackage: carnation
Commit: 14e8ab90b744c1ad6ef156e9ac91bed2f1b9608e
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-24 12:04:51 -0400
Commit message:
switch frm name to text fr hover tooltipPackage: carnation
Commit: bf3c14b71606c7f188baed44810eaf0cbd49f3d6
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-24 12:04:11 -0400
Commit message:
handle dodged box plt in plotly pltPackage: carnation
Commit: 9be5177c44628acd6d27a14eac60ab5e3427ef34
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-24 12:03:42 -0400
Commit message:
add gene plt box dodge optionPackage: carnation
Commit: f2194e011f6862648e6bab5f58554402f7a37ff0
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-24 12:02:34 -0400
Commit message:
get x-axis lvls on init load fr bucket listPackage: carnation
Commit: 207f583bef593bb45b48959b78c05db77f8f4010
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-24 12:01:14 -0400
Commit message:
reorg settings for visibility, switch frm checkbox to select inputsPackage: carnation
Commit: c1207308e689f2b9cd465a00d6dcedefca99094d
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-24 09:56:50 -0400
Commit message:
patternplt: set init xaxis lvls fr bucket listPackage: carnation
Commit: 5cd73c34055ff514c20f0901d2e3ad6ba3d62f7e
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-24 09:49:21 -0400
Commit message:
add data load flag to toggle first load & pltPackage: carnation
Commit: a9a16f6a2093e72e9ef8c560a39d80e080d0762e
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-24 09:48:53 -0400
Commit message:
decouple plot data obj from var lvls updtPackage: carnation
Commit: 6476551f0ffe87fe3de75a4652c58872e640770e
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-24 09:48:36 -0400
Commit message:
updt facet var lvls on init loadPackage: carnation
Commit: 8b8d773aec0c774d19d579bfbb64d63b79b190a2
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-24 09:48:01 -0400
Commit message:
mv reset pattern data to funcPackage: carnation
Commit: 28a7af127d46abefc0f1d80c2d2eb817245663f9
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-24 09:18:20 -0400
Commit message:
correctly handle mult color vars in pcaPackage: carnation
Commit: 2043d981c6942911d84e11989bca203e525f75ec
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-07-24 09:17:36 -0400
Commit message:
add check for mult gene cols in resPackage: BiocNeighbors
Commit: 0fc21d1027f138d07837d323f3d7058561e25cee
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-21 11:41:29 +1000
Commit message:
Bumped version to trigger a recompilation.Package: beachmat.tiledb
Commit: ba12275711503607f2b5564656ed1aed75e9c2fa
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-21 11:05:55 +1000
Commit message:
Relax tests for floating-point differences in multi-threaded tatami.sums.Package: beachmat.hdf5
Commit: e65542e20808f5db9e5643f4fe3753f7259b6ff2
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-21 01:55:04 +1000
Commit message:
Updated tests for possible floating-point differences in multi-threaded sums.Package: beachmat
Commit: b91a0d8c7c6859c3ac6995bf67f85604e8cfeb79
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-21 00:42:44 +1000
Commit message:
Updates to the latest roxygen format, bumped version and date.Package: beachmat
Commit: 7612bb47b5397a092caea42caefe0ad902b52679
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-20 23:59:47 +1000
Commit message:
Updates bindings for tatami_stats, tatami_mult functions. - Added num.groups= argument to tatami.sums.by.group(). - Skip creation of a vector of pointers for the dense matrix product.Package: assorthead
Commit: 93b0abde504e0a4ef947d201d38086fe33405f8e
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-22 00:20:23 +1000
Commit message:
Update to the latest versions of all vendored libraries.Package: tidybulk
Commit: 52b69663687da457d23b6d8afcee697dea949a30
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-08-21 23:22:32 +0930
Commit message:
version up with Bioconductor Merge branch 'devel' of git.bioconductor.org:packages/tidybulk # Conflicts: # DESCRIPTIONPackage: tidybulk
Commit: c30d4d29afee8165bfa217ebf8fd8625da1fdedb
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-08-21 21:39:35 +0930
Commit message:
Merge pull request #341 from gaoyingnan-academic/keep_abundant_per_category Keep abundant per category as an alternative filtering methodPackage: tidybulk
Commit: b0b9c4c055fb232a9f112b21383ea245859a5287
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-08-21 21:27:38 +0930
Commit message:
Add unit tests for keep/identify_abundant_per_category Cover threshold filtering, formula_design, CPM override, minimum_category, parameter validation, and force replacement so the PR includes tests as requested in review. Co-authored-by: Cursor <cursoragent@cursor.com>Package: tidybulk
Commit: 0ab6df4c2b24440a9a315ebdc171b3a8bb1ea06c
Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Date: 2026-05-05 08:39:15 +0000
Commit message:
Move category-aware filtering description from README to vignette only Agent-Logs-Url: https://github.com/tidyomics/tidybulk/sessions/35559420-c05c-4207-b057-63d818bca5a4 Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com>Package: tidybulk
Commit: bff851d6672776f0a50e28fe2ae0e2d7d2722d8b
Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Date: 2026-05-05 08:34:22 +0000
Commit message:
Document keep_abundant_per_category and identify_abundant_per_category functions (PR #341) Agent-Logs-Url: https://github.com/tidyomics/tidybulk/sessions/6629bc9d-eb57-4447-8225-94694486a312 Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com>Package: tidybulk
Commit: 75515c2fe2b1c8d0a2b92382ce7929b47f788a28
Author: Yingnan Gao <52718100+gaoyingnan-academic@users.noreply.github.com>
Date: 2026-04-17 15:36:54 +0930
Commit message:
Fix documentation issuesPackage: tidybulk
Commit: a888b8272e5e8299eac6a62c930845c65c6a3d56
Author: Yingnan Gao <52718100+gaoyingnan-academic@users.noreply.github.com>
Date: 2026-04-17 15:16:43 +0930
Commit message:
Update documentation by roxygen2 Automatically generated updates on documentation.Package: tidybulk
Commit: f7b99560004ed62f8eefcf34534c8d03ec35eba3
Author: Yingnan Gao <52718100+gaoyingnan-academic@users.noreply.github.com>
Date: 2026-04-17 15:11:49 +0930
Commit message:
Create keep_identify_abundant_per_category.R Initial commit for experimental filtering functions.Package: tidybulk
Commit: e87cbf7c52957eeb5675e912007123846611cd06
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-08-21 18:33:07 +0930
Commit message:
Merge pull request #344 from jaspitzer/tidybulk_plotting_functions added a plotting function for reduced dimPackage: tidybulk
Commit: 2e7222e33dcf6deaf3fa78fd878581974f146bfe
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-08-21 09:15:25 +0930
Commit message:
Add plot_reduced_dimension examples to vignettes Show the helper after the existing ggplot reduced-dimension plots in introduction and comparison_coding. Co-authored-by: Cursor <cursoragent@cursor.com>Package: tidybulk
Commit: 974bc6eae077fbb30c84cce00fde65c3dce4f019
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-08-21 09:12:35 +0930
Commit message:
Rename plot_reduced_dim to plot_reduced_dimension S4 method Expose plot_reduced_dimension as an S4 generic with SummarizedExperiment and RangedSummarizedExperiment methods, matching other tidybulk APIs. Co-authored-by: Cursor <cursoragent@cursor.com>Package: tidybulk
Commit: cffbe477a21f9249f9dc8c9459dc1848f3e04cda
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-08-21 09:09:26 +0930
Commit message:
Bump version to 2.1.5 Co-authored-by: Cursor <cursoragent@cursor.com>Package: tidybulk
Commit: 28c8c84d8a2f50dc4a02260a3db609c9be49c455
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-08-21 09:06:54 +0930
Commit message:
Skip pkgdown deploy on pull requests Fork PRs cannot push to gh-pages with GITHUB_TOKEN (403), which was failing the Ubuntu rworkflows job. Co-authored-by: Cursor <cursoragent@cursor.com>Package: tidybulk
Commit: af1e5c685704cf80830a3590fedb2ca093ab151f
Author: Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com>
Date: 2026-06-02 10:11:26 +0300
Commit message:
added a plotting function for reduced dimPackage: tidybulk
Commit: 082fa8bd77e91100b990c0677d5cf8bf2bc51fce
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-06-04 16:45:31 +0930
Commit message:
Merge pull request #343 from jaspitzer/master fixed wrong output on PCA variance proportion of reduce_dimensions.RPackage: tidybulk
Commit: 67e0cdb462e6fe4d58656c983a0e6968add55f5b
Author: Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com>
Date: 2026-06-02 14:32:56 +0300
Commit message:
version updatePackage: tidybulk
Commit: 035bb2d244ad1cbada63f6e8bf8808e8f2d95185
Author: Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com>
Date: 2026-06-02 10:00:20 +0300
Commit message:
added test and improved legibilityPackage: tidybulk
Commit: 43e0d69aa475e624ffe2d6c12197e9a36e802bb1
Author: Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com>
Date: 2026-06-01 15:40:30 +0300
Commit message:
fixed wrong output on PCA variance proportion the `.`proportion here calls back to prcomp_obj, thus dividing by that instead of just the standard deviation, leading to a wrong resultPackage: tidybulk
Commit: c78eabb1c8b0181039e314d5285f9b8684b6eea8
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-04-02 20:18:34 +1030
Commit message:
Merge pull request #340 from tidyomics/force_abundance_column_to_reduce_dimensions Force abundance column to reduce dimensionsPackage: tidybulk
Commit: 55cbd99be0cce9f0b672c5ec266c0e29d67f955c
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-04-02 14:23:26 +1030
Commit message:
Revise author and maintainer details Updated author and maintainer information in DESCRIPTION file.Package: tidybulk
Commit: 567906bfd3b4ce6ab4d58592e613705acd4dc2b5
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-04-02 14:19:42 +1030
Commit message:
update the dev script accordinglyPackage: tidybulk
Commit: 01aa7c3a3fb33592531782ce02a77688992f9d51
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-04-02 14:19:16 +1030
Commit message:
Refactor reduce_dimensions to require explicit assay parameter instead of .abundance. Update documentation, examples, and tests accordingly to reflect this breaking change.Package: tidybulk
Commit: 7ef0df3146eab3ae9292a1c748baa6bd3e138d52
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-04-02 13:25:16 +1030
Commit message:
RRequire explicit .abundance parameter for input, and adjust related examples and tests accordingly.Package: betterChromVAR
Commit: 051b3164cc610c6c73b24673e34becc6ee155875
Author: plger <pl.germain@gmail.com>
Date: 2026-08-21 14:02:15 +0200
Commit message:
Fixed bug that some SE-like objects were not recognized as suchPackage: betterChromVAR
Commit: b334887064f7460a89bd52f689d196ae40f83cc3
Author: plger <pl.germain@gmail.com>
Date: 2026-08-14 12:37:06 +0200
Commit message:
updated newsPackage: smartid
Commit: 95826c008bee79bb24d6f591fb0c84257d3572bd
Author: Gene233 <chen_jj97@163.com>
Date: 2026-08-21 18:53:38 +1000
Commit message:
version bumpPackage: smartid
Commit: d3b479c9d12746184f25defbdfb5fa45986d0c34
Author: Gene233 <chen_jj97@163.com>
Date: 2026-08-21 18:43:19 +1000
Commit message:
Optimize transform and scale, improve efficiency.Package: spatialFDA
Commit: 0a191f40c488ed4bd259f81815aa156dfb487389
Author: mjemons <martin.emons@gmail.com>
Date: 2026-08-21 10:38:36 +0200
Commit message:
merged bioc versionPackage: spatialFDA
Commit: 36d4f26fb05087dc2f6064793bd9abbd3901ed81
Author: Martin Emons <55688661+mjemons@users.noreply.github.com>
Date: 2026-08-21 10:04:37 +0200
Commit message:
Fix review (#24) * bug fix in metric plots * implemented proportion covariate plus small fixed * updated intensity adjustement * fixing error when selection is numerical * new defaults for G/F functions for intensity adjustment * bug fix for fixed effects models * bug fix * version bump and adjustements to vignettePackage: smartid
Commit: 16a54b0f6c92415a8ac92f53eb835e368845983a
Author: Gene233 <chen_jj97@163.com>
Date: 2026-08-21 15:28:04 +1000
Commit message:
version bumpPackage: smartid
Commit: 810530d72ee0098aa6e49a01b31cc31287a759d8
Author: Gene233 <chen_jj97@163.com>
Date: 2026-08-21 15:03:47 +1000
Commit message:
Update iae and other functions to allow sparse matrix input and fix some bugs.Package: biocmake
Commit: b1fd350719f1b180706e4efa8ee3e04412315287
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-21 14:15:09 +1000
Commit message:
Upgraded the expected and downloaded versions of Cmake.Package: TADCompare
Commit: f832eb378b46d0bc00c5a5126e722de44acbdb47
Author: Mikhail Dozmorov <mdozmorov@users.noreply.github.com>
Date: 2026-08-20 21:31:34 -0400
Commit message:
Remove residual PRIMME references Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>Package: SpectralTAD
Commit: 6c2c88c8ebb308457144e61a94c72d22091dc29f
Author: Mikhail Dozmorov <mdozmorov@users.noreply.github.com>
Date: 2026-08-20 21:27:44 -0400
Commit message:
Remove stale PRIMME references Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>Package: DelayedArray
Commit: 79633d1afe95e97ad82ff0c52738c0bc5cbd0006
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-20 17:57:29 -0700
Commit message:
add a couple of missing Rd \link{} targets package anchorsPackage: HDF5Array
Commit: 0103beca727b0274d430375bcde685017d2688ab
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-20 17:49:45 -0700
Commit message:
add a few more missing Rd \link{} targets package anchorsPackage: HDF5Array
Commit: a482c3efc636e93ffdd5f4bdc1609c8e06d074a9
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-20 14:28:39 -0700
Commit message:
HDF5Array 1.41.3: Small tweak to writeHDF5Array() and writeTENxMatrix() As per rhdf5's recommendation (starting with version 2.57.10), writeHDF5Array() and writeTENxMatrix() now use a variable-length string dataset instead of a fixed-size string dataset when the array- or matrix-like object to write is of type() character.Package: h5mread
Commit: 6d72e634258051aa7bd2ea303e7418d2810301cf
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-20 16:02:45 -0700
Commit message:
more testing of h5mread() on H5T_STRING datasetsPackage: singIST
Commit: cbb3f3c929898165fe90f9a2e1c158a7430d0941
Author: Aitor Moruno Cuenca <amoruno@almirall.com>
Date: 2026-08-21 00:27:50 +0200
Commit message:
v1.1.2: Reviewer 2 round-2 response (orthology_cache, informative errors, dontrun examples, vignette reproducibility)Package: h5mread
Commit: 87a30349ae714a0d9b974cc14940787eaacbd167
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-20 14:50:32 -0700
Commit message:
no tabs in R codePackage: h5mread
Commit: f9d9e69d09106a8477e4ad6101336668b4a9228d
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-20 14:20:26 -0700
Commit message:
add commentPackage: h5mread
Commit: 2e8c551364e92dc361330c50e44e8571f8af56d0
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-20 13:02:49 -0700
Commit message:
h5mread 1.5.2: Fix h5mread() on H5T_VARIABLE dataset with NULL pointers Starting with rhdf5 2.57.10, NULL pointers in an H5T_VARIABLE dataset are interpreted as NAs. So h5mread() now: - works on an H5T_VARIABLE dataset with NULL pointers (used to crash!); - interprets NULL pointers as NAs like rhdf5::h5read() does. Also, the meaning of HDF5 attribute "rhdf5-NA.OK" is not what I thought it was. In particular, it doesn't seem to have anything to do with how "NA" strings should be treated. So this commit drops all the C code that I added in commit 35698d094f521c9fffcc1377793c1a020e0fc580 to handle this attribute.Package: S4Vectors
Commit: fc819a547a51d682f7788ae16a42c26840b1ed2f
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-20 11:08:32 -0700
Commit message:
S4Vectors 0.51.7: C level utility _new_CHARACTER_from_CharAEAE() now handles NAsPackage: bsseq
Commit: 449fdcbff7f0c551534faa34e0318c46ee21bc8e
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2026-08-20 13:59:49 -0400
Commit message:
documentation fixesPackage: bsseq
Commit: bebb72aa57fd12510d93abf1c0467ccaa6504e68
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2026-08-20 10:05:33 -0400
Commit message:
Merging from Github into Bioconductor devel; bumping version to 1.49.1Package: bsseq
Commit: 62693020723f4842624eee8a796ca2c895b949e1
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2026-08-18 14:38:03 -0400
Commit message:
Merge pull request #156 from SrenBlikdal/devel Add user guide and test data focusing on import and filtering of longread data.Package: bsseq
Commit: 6205c89830b2cc52fccf8797c83f4b35e43651bf
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2026-08-18 11:09:17 +0200
Commit message:
minor edits to the longread user guidePackage: bsseq
Commit: 81156dc97da09826f78be9af09838207df8e6cb9
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2026-08-17 16:24:05 +0200
Commit message:
Add tidyverse to DESCRIPTION for longread user guidePackage: bsseq
Commit: b17064b1884277c6c560d0f9af9f4151736662ed
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2026-08-17 15:46:18 +0200
Commit message:
Add bsseq:: to combine function in vignettes/bsseq.Rmd to avoid dplyr linked errorPackage: bsseq
Commit: 0376b523557ed023c786c45ab304eb2caf62b190
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2026-08-17 14:29:06 +0200
Commit message:
Addition to add hdf5 chunk to user guide add both data and guidePackage: bsseq
Commit: 9d32d8398ca2ffa377ff8f80f491ef70ad1d007e
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2026-08-17 14:27:01 +0200
Commit message:
add hdf5 chunk to user guidePackage: bsseq
Commit: aef733fe4f83fe2b72e64538083238ba0c983044
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2026-08-17 14:15:28 +0200
Commit message:
Bump version to 1.47.7Package: bsseq
Commit: 1dbde36b694640f35622e210c43af7ddc4c1610e
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2026-08-17 14:14:34 +0200
Commit message:
Add user guide and test data for long-read methylation analysisPackage: bsseq
Commit: b5f6a00a42268468474d8547dff9da3b3b91a0db
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2026-02-06 17:02:52 -0500
Commit message:
Update DESCRIPTION Fixed version numberingPackage: bsseq
Commit: aef3c641f439c5aa1181a8f4ace8dc1e84d033f9
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2026-02-06 16:59:57 -0500
Commit message:
Merge pull request #155 from SrenBlikdal/devel Update read.bedMethyl() and alpha version of implementation for working with 5hmC and 5mC in bsseq()Package: bsseq
Commit: 575074234cd955fac90796b96e3eedd4d24fe886
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2026-02-04 13:40:28 +0100
Commit message:
Fix small typo in bsseq.bibPackage: bsseq
Commit: 00d786e274454a8f80748372e2053d7ae0949f06
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2026-02-03 09:14:20 +0100
Commit message:
Merge remote-tracking branch 'upstream/devel' into develPackage: bsseq
Commit: 924aadf1ca2dedee884d596e949776448d1b989e
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2026-02-03 08:57:27 +0100
Commit message:
add MethylCount as input option from BSseq constuctor function and include modtype in the print info of the classPackage: bsseq
Commit: b6708547e4e0750f53e7cd9fcc78411a36a0fd59
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2026-01-30 12:53:10 -0500
Commit message:
fixing typoPackage: bsseq
Commit: 2c0011b1c8a2c0461f3539dc33eccd8936f4d307
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2026-01-30 11:29:16 -0500
Commit message:
update to local.correctPackage: bsseq
Commit: dca8ac24a8079fa98b2f21c516d8d2f15c070b6c
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2026-01-30 09:06:32 +0100
Commit message:
add vingnettes with references to folder and add MethylCount as input for BSseq constructor functionPackage: bsseq
Commit: 7ca8dfb23d2b2c07919841a25d78bf081ff6118b
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2026-01-20 16:05:16 +0100
Commit message:
quick fix bug caused Cov being DelayedMatrix object when MethylCount is read as hdf5Package: bsseq
Commit: 2885cb6ff9d99e8ce71272dce5209eca0da45b3c
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2026-01-20 11:16:38 +0100
Commit message:
remove rmZeroCov from read.bedMethyl and update documentationPackage: bsseq
Commit: 16025c765f134759f5f7cafcf128e5979778c94b
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2026-01-19 15:26:10 +0100
Commit message:
add #inline annotation to read.bedMethylPackage: bsseq
Commit: ee751e0c497d46b9957584fe459d01e00e23e82e
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2026-01-13 16:28:42 +0100
Commit message:
include check of bedMethylfiles in read.bedMethyl and small improvements of the man files.Package: bsseq
Commit: 69ab7250dd91b0de26021c302a102cb6b6caf229
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2026-01-13 13:07:49 +0100
Commit message:
Add function (check_bedMethyl) to validate input for read.bedMethyl(). Adjust text in MethylCounts-class.Rd to fit the imported matrixes. nd version bumbPackage: bsseq
Commit: 1e2ec767b2a3f0dc25f5177147d0096d7aef7749
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2026-01-06 12:57:58 +0100
Commit message:
Update functions and manuals to use MethylCounts object, shift the positions in the object by 1 but double check if it is inline with GRranges formatPackage: bsseq
Commit: e8148fcbfd082ca3097f95c62dc883ea9985f483
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2026-01-14 16:26:37 -0500
Commit message:
small fix to previous commitPackage: bsseq
Commit: fb13ec654d1765819f59043fc9d21f60e50d4536
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2026-01-14 16:19:39 -0500
Commit message:
small fix to previous commitPackage: bsseq
Commit: 6e9c305014f649172b842440ad95c0fbe6fac853
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2026-01-14 16:11:56 -0500
Commit message:
fixing an issue with local.correct=TRUE reported by Luke MorinaPackage: bsseq
Commit: 57e4072ec537b1960b47fa8133b3dfbb435cff50
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2025-11-19 15:19:56 -0500
Commit message:
Adding the MethylCounts-class man pagePackage: bsseq
Commit: 62223153c3ac408c61d61d25e747c8e98f1024c4
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2025-11-19 15:02:44 -0500
Commit message:
adding documentation to MethylCounts and friendsPackage: bsseq
Commit: 67ad2e8786e71ca05c90f9777affee159d838ae3
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2025-11-19 09:53:20 -0500
Commit message:
Merge pull request #154 from SrenBlikdal/devel Adapt likelihood functions to MethylCounts and update test, manuals, and examples (alpha version).Package: bsseq
Commit: dc9f3a3d53df54372e6de363e73a6ae059265a42
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2025-11-10 10:51:20 +0100
Commit message:
Merge branch 'devel' of https://github.com/hansenlab/bsseq into devel Merge Kaspers update to workflows with Srens updates to likelihood functionsPackage: bsseq
Commit: 0deb59a534fea197eb921c1540eba67dcb375c80
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2025-11-10 10:34:29 +0100
Commit message:
Update examples in likelihood man files to use MethylCounts instead of bsseqPackage: bsseq
Commit: 72bbcf01309551fc5e4ad4afb258cdc3111aea5c
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2025-11-07 17:04:29 -0500
Commit message:
updating github actions for develPackage: bsseq
Commit: 3dbb6e161a943ede0205d1f3bf3bb3b1b092da92
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2025-11-07 16:19:27 -0500
Commit message:
updating github actionsPackage: bsseq
Commit: f44291786ae21b09be9f0d2ef67e31e4028fc5e7
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2025-11-07 11:19:04 +0100
Commit message:
add test for likelihood_function for MethylCountsPackage: bsseq
Commit: a81676aaca3aa2d711b53d4769725b015a669961
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2025-11-07 11:05:27 +0100
Commit message:
increase the number of tests for read.bedMethyl and test MethylCount output. fix typoPackage: bsseq
Commit: ff7c1031fd1ad5aa40973c2356c82cfc5ba9d539
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2025-11-07 11:02:49 +0100
Commit message:
increase the number of tests for read.bedMethyl and test MethylCount output.Package: bsseq
Commit: b300f257b17983b3e20d597f3243e6cb61e135b7
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2025-11-06 15:45:34 +0100
Commit message:
merge changes from hansen lab into forkPackage: bsseq
Commit: cdd2786fc32ee1dcf0db4276d8545075a5222794
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2025-11-06 15:34:34 +0100
Commit message:
Add type=Cov to getMethylCounts and adjust likelihood functions to U for unmethylatedPackage: bsseq
Commit: afe12e5ec780a012313bed565495338a708a1c89
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2025-11-04 15:00:56 -0500
Commit message:
Merge pull request #153 from SrenBlikdal/devel Fix read.bedMethyl when strandCollapse=F and add alpha version of read.bedMethyl for output="MethylCounts"Package: bsseq
Commit: c734a5cc949ad72d3c3047f1cbbef1d950001657
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2025-11-04 15:13:21 +0100
Commit message:
Fix MethylCount/MethylCounts typoPackage: bsseq
Commit: 3d20b1ebc01fc3ae2636e8f95a71edb70bf6e055
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2025-11-04 14:17:04 +0100
Commit message:
version bumpPackage: bsseq
Commit: 3a0c50260d9f01814e44c6a226eb7eacc8aedb6d
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2025-11-04 14:08:17 +0100
Commit message:
add alpha version of read.bedMethyl which can output MethylCount object. Default is still a BSseq object and is not modified in this commitPackage: bsseq
Commit: e6f80196cdfd971c7c65199c1dfb5e05960841ed
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2025-11-04 11:49:36 +0100
Commit message:
Change C for canonincal to U for unmethylated in R/read.bedMethylPackage: bsseq
Commit: 4c0d982a82b16669e43b69299803f26ed246b345
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2025-11-04 11:37:13 +0100
Commit message:
Update R/read.bedMethyl.R from SrenBlikdal/MOD-lik-update to fix strandCollapse = F bugPackage: bsseq
Commit: 1fd8a4663d795de9dfe5f4f6f7664c0739e14c85
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2025-10-31 11:32:22 -0400
Commit message:
adding alpha version of MethylCountsPackage: bsseq
Commit: 07bb0bbdc83498fd3883d067fc2f108b79ad5b00
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2025-10-31 11:05:10 -0400
Commit message:
merghing methylcountPackage: bsseq
Commit: dedca66cb8df350a99b616b774338c0800037d1a
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2025-10-31 09:57:36 -0400
Commit message:
Making strancCollapse compatible with MethylCountsPackage: bsseq
Commit: 4400127dd8b7c492509b028b180022690600c423
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2025-10-28 21:58:00 -0400
Commit message:
initial run of MethylCountsPackage: bsseq
Commit: 35e23db4535ce3dad674f3f5abd7d5aa9ba7a900
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2025-10-22 16:51:45 -0400
Commit message:
initial work on MethylCountsPackage: Hiiragi2013
Commit: c989baa870904021f0f66b3e031dcd465aab1c9b
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-20 14:02:40 +0200
Commit message:
Bump versionPackage: Hiiragi2013
Commit: 540f1e05bd2fcc35fdd569b946726fc0cba6fdac
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-20 14:02:24 +0200
Commit message:
Remove dependency on RColorBrewerPackage: HD2013SGI
Commit: 8f64c179a4f236b8474dd11237809d22c133d654
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-20 14:01:04 +0200
Commit message:
Bump versionPackage: HD2013SGI
Commit: 59c81daa15f617f139c7cc479a02062f47c7dd34
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-20 14:00:52 +0200
Commit message:
Remove dependency on RColorBrewerPackage: splots
Commit: d360638bfc667dcba5997c0715fe951dbfef6af9
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-20 13:54:54 +0200
Commit message:
Bump versionPackage: splots
Commit: d49b11207d2bd09b585deed5626a688de6f68453
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-20 13:54:29 +0200
Commit message:
Remove dependency on RColorBrewerPackage: splots
Commit: 22f0b3b41531b0b23e91ad639fb9f6ae53451f64
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-07-01 14:12:13 +0200
Commit message:
Bump versionPackage: splots
Commit: 2d3b6bb7e9e94a38dcaf15935c0ed9559dc5480c
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-20 12:54:01 +0200
Commit message:
Take into account data removal in HD2013SGIPackage: splots
Commit: 8466a13f50c4a3234231096f07c706b0a3dba026
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-07-01 14:12:01 +0200
Commit message:
Switch to Authors@RPackage: HD2013SGI
Commit: cb6725409dba3587cfce625764194553754e704c
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-20 12:49:33 +0200
Commit message:
Bump versionPackage: HD2013SGI
Commit: 91948df6c27a9ccf0e1058896301a0e0ec65e80f
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-20 12:49:00 +0200
Commit message:
Update maintainerPackage: rhdf5
Commit: 7b58a7efee52e51efed6146189e78f8e9988f58f
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-19 20:14:35 +0200
Commit message:
Reverse if / elsePackage: rhdf5
Commit: 92f2f18251a1c8ac7adf58365a96ec9e05a7e3ca
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-19 19:56:44 +0200
Commit message:
Bump versionPackage: rhdf5
Commit: e7eaa83a422b0c8cb8039308c32295bf727c9f94
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-19 19:56:21 +0200
Commit message:
Mention new ignored argument warning in NEWSPackage: rhdf5
Commit: 5d30005c19a46156f4a888e5c355f05a5d9b1318
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-19 19:34:04 +0200
Commit message:
Add warning for ignored arguments when dataset already existsPackage: rhdf5
Commit: c7f942325c9bfe8ded9d140c936bc3d98d6f0c08
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-19 19:33:37 +0200
Commit message:
Emit warning even if dataset was created beforehandPackage: rhdf5
Commit: ba5eaa600d814c1b31332ff2fef6f30fe5c32c76
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-19 19:22:59 +0200
Commit message:
Add test for NA_character_ in fixed-length strings created through h5createDataset()Package: Rsubread
Commit: 89ba7feab4b160979d79d70167f3d2af7e09046c
Author: Yang Liao <yang.liao@onjcri.org.au>
Date: 2026-08-20 16:07:54 +1000
Commit message:
Skip overlapping transcript exon junctionsPackage: tidySummarizedExperiment
Commit: 86922f96fe4733393e3775e8aeb94195eaa139ef
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-08-20 13:04:38 +0930
Commit message:
update docsPackage: tidySummarizedExperiment
Commit: 8e7d11846711dc4de37c09d947158fbad7831b07
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-08-20 13:03:09 +0930
Commit message:
Merge pull request #121 from tidyomics/use-tidyprint Use tidyprintPackage: tidySummarizedExperiment
Commit: 60d4471e33099bcca4379e034805187da7bed5b9
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-08-20 12:41:25 +0930
Commit message:
Merge branch 'use-tidyprint' of https://github.com/tidyomics/tidySummarizedExperiment into use-tidyprintPackage: tidySummarizedExperiment
Commit: 4108149f95e2820075fb1eab89b7edbb6bbbd48c
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-17 13:52:51 +1030
Commit message:
Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>Package: tidySummarizedExperiment
Commit: c751d78232cf1c0b8cfdc36e72243572277e5025
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-17 13:51:59 +1030
Commit message:
Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>Package: tidySummarizedExperiment
Commit: 06561fd11b53590d7c75cf92555bb3d447c4cd2e
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-17 13:51:25 +1030
Commit message:
Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>Package: tidySummarizedExperiment
Commit: 7b1f1e9a96f38641ff0c798a502982c16e86c546
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-17 13:51:16 +1030
Commit message:
Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>Package: tidySummarizedExperiment
Commit: 7956bd5558854a55acf31a45da55a10f1d8c42f9
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-13 17:05:47 +1030
Commit message:
Enhance introduction vignette with tidyomics context and detailed tidy print options. Update GitHub installation link and add new references for the tidyomics ecosystem.Package: tidySummarizedExperiment
Commit: 5dacc2a6ed7e6aea7eaf97aac149c10eae248eaf
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-12 14:27:19 +1030
Commit message:
Add tidy_print_off to vignette to prevent display issues with pasilla datasetPackage: tidySummarizedExperiment
Commit: d41f3cc56c91cd8a763e2151770d75576580029d
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-12 13:51:44 +1030
Commit message:
Add tidy print functionality for SummarizedExperiment This commit introduces three new functions: tidy_print_on, tidy_print_off, and tidy_print_enabled, which allow users to enable or disable tidy printing for SummarizedExperiment objects. The NAMESPACE and documentation have been updated accordingly. Additionally, the tidy_warning and tidy_stop functions have been modified to utilize tidyprint for consistent message formatting.Package: tidySummarizedExperiment
Commit: 1cacb81d9d91f1c5ab58d4f48499b94d127882a8
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-11 17:54:31 +1030
Commit message:
Update version to 1.20.4, add tidyprint dependency, and replace messages with tidy_message for improved consistency in user feedback. Enhance error handling in various functions to provide clearer guidance on usage and potential issues.Package: tidySummarizedExperiment
Commit: 278b6703cf119ada5c36b47a53d0549bc897a1ea
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-08-20 12:15:25 +0930
Commit message:
Merge pull request #125 from tidyomics/copilot/fix-deprecated-when-warning Remove deprecated `when()` usage from dplyr methodsPackage: tidySummarizedExperiment
Commit: 4ab4127a2be2f95b6b2880bcdb3223f01990c379
Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Date: 2026-08-20 02:07:10 +0000
Commit message:
Remove deprecated when usage Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com>Package: tidySummarizedExperiment
Commit: 88983babc7e0037301d812a97b2b306fd94f89ac
Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Date: 2026-08-20 02:03:42 +0000
Commit message:
Initial planPackage: tidySummarizedExperiment
Commit: e05294334cbcb40e807753530ba4b091418478d8
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-17 13:52:51 +1030
Commit message:
Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>Package: tidySummarizedExperiment
Commit: 4d71d40779796ceceffbaca036f9e3b7c71de129
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-17 13:51:59 +1030
Commit message:
Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>Package: tidySummarizedExperiment
Commit: f82f4bc7cc6824b3112d7167d5f9f99fe6c87596
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-17 13:51:25 +1030
Commit message:
Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>Package: tidySummarizedExperiment
Commit: 0335cabae7f83a928b7d78177a229e5f1fb726a4
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-17 13:51:16 +1030
Commit message:
Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>Package: tidySummarizedExperiment
Commit: 7d0f133f64e7f06450c50551559ff7ba7b82de1e
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-13 17:05:47 +1030
Commit message:
Enhance introduction vignette with tidyomics context and detailed tidy print options. Update GitHub installation link and add new references for the tidyomics ecosystem.Package: tidySummarizedExperiment
Commit: de3e4045ced7f0b3842e01450f1a0aba03071c29
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-12 14:27:19 +1030
Commit message:
Add tidy_print_off to vignette to prevent display issues with pasilla datasetPackage: tidySummarizedExperiment
Commit: ca22843c0c2514f054e79bbdf4f1ec73f06bae21
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-12 13:51:44 +1030
Commit message:
Add tidy print functionality for SummarizedExperiment This commit introduces three new functions: tidy_print_on, tidy_print_off, and tidy_print_enabled, which allow users to enable or disable tidy printing for SummarizedExperiment objects. The NAMESPACE and documentation have been updated accordingly. Additionally, the tidy_warning and tidy_stop functions have been modified to utilize tidyprint for consistent message formatting.Package: tidySummarizedExperiment
Commit: d0aa78879a24679cd4d4ba8093a40d94adaae360
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-11 17:54:31 +1030
Commit message:
Update version to 1.20.4, add tidyprint dependency, and replace messages with tidy_message for improved consistency in user feedback. Enhance error handling in various functions to provide clearer guidance on usage and potential issues.Package: tidySummarizedExperiment
Commit: de9e00cec08848ec70417d856189f7cc370062af
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-08-20 11:39:50 +0930
Commit message:
version UPPackage: tidySummarizedExperiment
Commit: 92b39bb4378a04b0d08ed6e7fd783be7328254fc
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-08-20 11:39:05 +0930
Commit message:
version up to Bioc devel Merge branch 'devel' of git.bioconductor.org:packages/tidySummarizedExperiment # Conflicts: # DESCRIPTIONPackage: tidySummarizedExperiment
Commit: 1f15a3abe12b03939cd32a6a82131195dabf96d5
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-08-20 11:37:20 +0930
Commit message:
update docsPackage: tidySummarizedExperiment
Commit: 0a030eeb51b838af9747b00effd84ff03a7c400a
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-11 17:01:53 +1030
Commit message:
Merge pull request #119 from tidyomics/drop-when-function Refactor usage of `when` to `if` for improved readability and perform…Package: tidySummarizedExperiment
Commit: 12a9e592790dbd29c3b09e2a86ae902cfd96411d
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-11 16:16:13 +1030
Commit message:
Merge branch 'drop-when-function' of https://github.com/tidyomics/tidySummarizedExperiment into drop-when-functionPackage: tidySummarizedExperiment
Commit: 4b655a301f86608adc854dadb3b4b69238220fa7
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-11 13:36:11 +1030
Commit message:
Refactor usage of `when` to `if` for improved readability and performance in various functions. Remove deprecated imports and enhance documentation for clarity. Update `NAMESPACE` to reflect changes in imported functions.Package: tidySummarizedExperiment
Commit: 7b1a04cab35c842d925bf4ff2d1129e745fd8d59
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-11 16:14:41 +1030
Commit message:
Merge pull request #120 from tidyomics/fix-mutate-using-special-columns Fix mutate using special columnsPackage: tidySummarizedExperiment
Commit: 70c00f6a217fa0f0345c8fa3639c1789d1dba541
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-11 15:06:19 +1030
Commit message:
Update DESCRIPTION to include microbenchmark as an additional package suggestion.Package: tidySummarizedExperiment
Commit: 3f81d7c6c55fecde399681f95ea02df780fd74b7
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-11 14:35:45 +1030
Commit message:
Update DESCRIPTION to include additional package suggestions: AnnotationDbi and org.Hs.eg.db.Package: tidySummarizedExperiment
Commit: 1959be5fc9468ff757338a73ca84d74cff098f83
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-11 14:23:24 +1030
Commit message:
version UPPackage: tidySummarizedExperiment
Commit: cd76e8273691a9fe238bdf9560625cdc646eefd5
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-11 14:21:39 +1030
Commit message:
Rename pivot.R to subset_data.R Made-with: CursorPackage: tidySummarizedExperiment
Commit: b0fe76c17c5379f13dca4f8620e60cb37cca6077
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-11 14:21:10 +1030
Commit message:
change function namePackage: tidySummarizedExperiment
Commit: a037c222bbf0a035a47cdb42f496bb34bc80b2e5
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-11 14:09:08 +1030
Commit message:
Add pivot_transcript and pivot_sample methods for SummarizedExperiment Introduce new methods to extract transcript-wise and sample-wise information from SummarizedExperiment objects. These methods facilitate downstream analysis by returning tibbles with relevant data. Update modify_features and modify_samples functions to utilize these new methods for improved data handling. Add tests to ensure correct functionality of analyze_query_scope_mutate with various scenarios.Package: tidySummarizedExperiment
Commit: a19c245790a3b889a677887f5ffa1575f0d3e659
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-11 13:36:11 +1030
Commit message:
Refactor usage of `when` to `if` for improved readability and performance in various functions. Remove deprecated imports and enhance documentation for clarity. Update `NAMESPACE` to reflect changes in imported functions.Package: tidySummarizedExperiment
Commit: 5627f7f5d56f47266df55d68fc27cdfc6a8c249d
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-12-22 12:32:22 +1030
Commit message:
Enhance dimnames consistency checks in check_se_dimnames, and add performance benchmarks for distinct function. Improve documentation and ensure proper handling of duplicated names in SummarizedExperiment.Package: tidySummarizedExperiment
Commit: 13c3ed3025e04c08a6519bdad8666e5eba4603d2
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-12-22 10:16:16 +1030
Commit message:
test mutate special columnsPackage: tidySummarizedExperiment
Commit: 4590c4ecc8340514f1c8c4df2b6a06545ebffb93
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-12-22 10:14:01 +1030
Commit message:
trigger GitHub actionsPackage: tidySummarizedExperiment
Commit: 6626935fb9a79ae087b7a5b244fd11b65ce52782
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-11-10 09:45:31 +1030
Commit message:
Merge branch 'RELEASE_3_22' of git.bioconductor.org:packages/tidySummarizedExperimentPackage: tidySummarizedExperiment
Commit: b2213baa29d93f2034d43715fba8d64addda1e6d
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-11-10 09:43:45 +1030
Commit message:
Merge pull request #114 from tidyomics/improve-startup-message-tidyprint Update startup message in zzz.R to use cli for improved formatting an…Package: tidySummarizedExperiment
Commit: 42832c71a88fd9ea949d05a3b49b8bf058a6dea4
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-11-07 16:57:37 +1030
Commit message:
Update startup message in zzz.R to use cli for improved formatting and clarity.Package: tidySummarizedExperiment
Commit: ef6f9cb3d77ec11dc79808aaf8cf4d680a45453e
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-29 22:53:30 +1030
Commit message:
Merge pull request #112 from tidyomics/use-tidy-generics rely on generics tidyPackage: tidySummarizedExperiment
Commit: a19b80c58cbe14856e7d468727728bf7c70be6a2
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-29 22:40:28 +1030
Commit message:
Remove 'object' parameter from documentation for tidy function to enhance clarity and maintain consistency with updated parameter naming.Package: tidySummarizedExperiment
Commit: 95cf53539927609697324865fcebfecbd7656ec5
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-29 22:36:17 +1030
Commit message:
Refactor tidy_ function parameters from 'object' to 'x' for consistency and clarity; update documentation accordingly.Package: tidySummarizedExperiment
Commit: 7d0366061950abe2cefe564f535c37d11cf48a7f
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-29 21:39:08 +1030
Commit message:
Merge pull request #111 from tidyomics/fix-slice Fix slicePackage: tidySummarizedExperiment
Commit: 289e1ada088dd2090e8215f552e9606c25b34db7
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-29 17:46:21 +1030
Commit message:
rely on generics tidyPackage: tidySummarizedExperiment
Commit: cd62829b8289b53c69be684c2b83d1e9b278c3fa
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-25 16:37:29 +1030
Commit message:
Apply suggestion from @Copilot Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>Package: tidySummarizedExperiment
Commit: 59ad0686202f85d8efe75977252387314cf229fb
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-25 16:37:19 +1030
Commit message:
Apply suggestion from @Copilot Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>Package: tidySummarizedExperiment
Commit: b54102956844cf615e01accb64766dbd0b516370
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-25 16:22:20 +1030
Commit message:
Update R/utilities.R Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>Package: tidySummarizedExperiment
Commit: 8d74d74aff4bfefdefb4c043a2f78b22d5ae4e01
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-25 16:22:13 +1030
Commit message:
Update R/utilities.R Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>Package: tidySummarizedExperiment
Commit: 35be04b30393d83851611f4d2b4b314c0175cf9b
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-25 16:20:12 +1030
Commit message:
fixed tests Refactor is_range_slice_ungrouped_detected function to accept .data as the first argument for improved clarity. Update corresponding tests to reflect argument order change and ensure correct functionality with various input scenarios.Package: tidySummarizedExperiment
Commit: ecb1bf9eafac7df791dde456426442afdf1bc11f
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-25 15:57:05 +1030
Commit message:
Update error message in slice_optimised function to clarify usage of .by parameter for range slices on ungrouped data.Package: tidySummarizedExperiment
Commit: cda0453494a55e704bfd519edb37d83b21bd462e
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-25 15:53:14 +1030
Commit message:
version UPPackage: tidySummarizedExperiment
Commit: c3c18c3325286f4f500653750b4a87ef7979e1a9
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-25 15:52:52 +1030
Commit message:
Enhance slice functionality in SummarizedExperiment by adding .by parameter for grouping. Implement is_range_slice_ungrouped_detected to handle range slices on ungrouped data, with corresponding tests to ensure correct behavior. issue: https://github.com/tidyomics/tidySummarizedExperiment/issues/53Package: DuckDBGRanges
Commit: 8b434a94cc4ff5b46d2c66efbe786f7c00ef6fb3
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-19 18:35:08 -0700
Commit message:
feat: Add coverage() for DuckDBGRanges DuckDBGRanges had no coverage() method, so it inherited GenomicRanges's, which crashed with a C stack overflow via split(ranges(x), seqnames(x)) on a DuckDBDataFrame. Implement a real, lazy coverage() using the same delta-event/cumsum sweep-line pattern as disjoin()/gaps(), collecting only the compact breakpoint table and reconstructing a SimpleRleList. Supports shift/width; weight is scalar-only for now (mcols-column or per-range weights would need row-order alignment against a lazy table, left out rather than risk getting it wrong silently).Package: nullranges
Commit: 5ac484cfca1ae0c4b2a87f737ae32b6c9cb99553
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-08-19 14:49:39 -0400
Commit message:
version bumpPackage: nullranges
Commit: 370c2131edbcfe0aae2cc84d1ab42e8563b62bfe
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-08-19 14:49:24 -0400
Commit message:
Merge branch 'devel' of git.bioconductor.org:packages/nullranges into develPackage: nullranges
Commit: d7ff3bb8ef50397a9df54ad89853e7db539b5f0a
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-08-06 10:45:06 -0400
Commit message:
fix in devel for new exclude resources Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>Package: nullranges
Commit: 129e1bee8b63cd1e164d0015e18e326e8a198074
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-08-06 10:27:25 -0400
Commit message:
try devel on GHAPackage: DelayedArray
Commit: 6850cefe66b6d953b15c79da830d3296a09d0e45
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-19 11:42:38 -0700
Commit message:
DelayedArray 0.39.6: Fix code/documentation mismatch warning from 'R CMD check'Package: rigvf
Commit: 21f794573b8730897cdd0bf1b249998b021e13c6
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-08-19 14:40:27 -0400
Commit message:
push to bioc, version bumpPackage: rigvf
Commit: 4dfd40419d316ea7af52e4ff202d0528656d8c7d
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-08-17 11:14:39 -0400
Commit message:
dealing with breaking changes from APIPackage: rigvf
Commit: ae45d4a0e71d17cc776404073ae51f50a02955a7
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-08-17 10:22:33 -0400
Commit message:
attempt fixPackage: rigvf
Commit: e292774dad9825a1c3636fd337416bbba698a04e
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-08-14 10:52:45 -0400
Commit message:
version bumpPackage: rigvf
Commit: 02a9e7adb27f1be76fe0e8286e0dfe126c55c272
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-08-14 10:52:14 -0400
Commit message:
Merge branch 'devel' of git.bioconductor.org:packages/rigvf into develPackage: rigvf
Commit: bbcc8a16dfd4a0c5de97b84dd290a41d6b74c68c
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-08-04 13:02:44 -0400
Commit message:
update pkgdownPackage: rigvf
Commit: 62a8adc18eb12a4ac62f2d2953681032392e7531
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-08-04 13:00:31 -0400
Commit message:
font sizesPackage: rigvf
Commit: b6b5952345ce387ab0f9dff55a7d43784c9818d5
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-08-03 22:30:41 -0400
Commit message:
working on CLS lookupPackage: rigvf
Commit: a1d5ad23cb1c5f9787725b6e22a5a9abdac21e2f
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-08-03 21:03:11 -0400
Commit message:
working on data portal scriptPackage: rigvf
Commit: 3b86a14931120b6378b1640f5b4161642ee04490
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-06-24 14:48:18 -0400
Commit message:
script to query the portalPackage: rigvf
Commit: 9e5c0a19d7c273db50d939366d5a3d2608a34f67
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-06-24 13:29:09 -0400
Commit message:
add portal_files() to query IGVF Data Portal files by content typePackage: ZarrArray
Commit: 3b97f7e9783e90bad2f8af15fe4f672cdbf8f3c3
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-19 11:39:11 -0700
Commit message:
ZarrArray 1.1.7: Fix code/documentation mismatch warning from 'R CMD check'Package: ZarrArray
Commit: b00bd04af558c8fa2aae31ac1b8389b08ca02704
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-19 19:34:31 +0200
Commit message:
Add support for bfloat and enable more Rarr test cases (#13)Package: HDF5Array
Commit: 83a904923ea5a72781e334d75ddcee963f92d11d
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-19 11:36:46 -0700
Commit message:
Address a couple of 'R CMD check' warnings/notesPackage: HD2013SGI
Commit: f97f05ee84bfb229cb3b0819c6a1341d3fec7929
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-19 10:35:15 +0200
Commit message:
Update documentationPackage: HD2013SGI
Commit: d20bc809810b89af3eae6bcaebf94fc00dd65638
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-19 09:57:09 +0200
Commit message:
Update data loading instructions in vignettesPackage: HD2013SGI
Commit: d997b4c183efa7a48102990b6c1a5628899cc8a4
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-19 08:38:42 +0200
Commit message:
Add deprecation warnings to data filesPackage: HD2013SGI
Commit: 6246306cb87b647f18845aea02d8d7f1ecf6db1c
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-18 22:16:01 +0200
Commit message:
Improve performance a bitPackage: HD2013SGI
Commit: f52bde4864e239235a93b72ab2cae29afaef64a5
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-18 22:15:48 +0200
Commit message:
Convert data files to functions fetching data from zenodoPackage: HD2013SGI
Commit: 2ae24a143b1b448c7ef9aa781099ba1c82265323
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2026-04-28 08:25:33 -0400
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_23 branchPackage: HD2013SGI
Commit: 1e584be794dfa577eb8a1f0e4b8e7da3a883379b
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2026-04-28 08:25:33 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_23 branchPackage: HD2013SGI
Commit: 33e92c0ab30c3bcb688b8c46569cdb6b21d8808b
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-29 09:53:07 -0400
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_22 branchPackage: HD2013SGI
Commit: 9e0ba9aa7e7ea099a6c4c2c7be8f15f9528298de
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-29 09:53:07 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_22 branchPackage: HD2013SGI
Commit: 722c5d464ee2eda4cefce52b93fe5dfdd84b1d06
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-04-15 09:22:13 -0400
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_21 branchPackage: HD2013SGI
Commit: e01a5979898f299d9eec5895f93c183f8a706b14
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-04-15 09:22:13 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_21 branchPackage: HD2013SGI
Commit: def2e846ee2fdbac737122a554d8b6200ad1d02f
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2024-10-29 09:36:14 -0400
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_20 branchPackage: HD2013SGI
Commit: e30cf69addac4af4837295990420bb276e7c9a13
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2024-10-29 09:36:14 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_20 branchPackage: HD2013SGI
Commit: bd4eaea04f31da79b2839e3d1eac80c333fa26b2
Author: Mike Smith <grimbough@gmail.com>
Date: 2024-06-29 02:13:50 +0200
Commit message:
Fix issues with colours in vignettePackage: HD2013SGI
Commit: b00a26cf3be0f8040af891de0a9b4dc9817a9e8a
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-30 10:38:57 -0400
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_19 branchPackage: HD2013SGI
Commit: f7eabe5aeda4a3eb34a944e0ca676bc0c07a7357
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-30 10:38:57 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_19 branchPackage: HD2013SGI
Commit: 7121d585a34ebf417212a1836703b845a346dae3
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2023-10-24 09:05:17 -0400
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_18 branchPackage: HD2013SGI
Commit: cc326b5fa700c43d12373ad8b80245ccb1a8bc0c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2023-10-24 09:05:17 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_18 branchPackage: HD2013SGI
Commit: 2200ac765429963025a648d8a7a7149afd50dd7a
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2023-04-25 10:32:41 -0400
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_17 branchPackage: HD2013SGI
Commit: c36858fdb4f1226c4914785d6a494485531cd61f
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2023-04-25 10:32:41 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_17 branchPackage: HD2013SGI
Commit: 9d6b3881cd2c7d05b410e280a89d3d2e97f671aa
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2022-11-01 10:54:00 -0400
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_16 branchPackage: HD2013SGI
Commit: b6114949bd78b0a1ef271cc326e135557ae6d31e
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2022-11-01 10:54:00 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_16 branchPackage: HD2013SGI
Commit: 1d0e54838bf23e7a06c30e5478936bf3b4b28586
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2022-04-26 17:07:56 +0000
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_15 branchPackage: HD2013SGI
Commit: b56ac16093d23063c2aa9d73333296d0c69e928f
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2022-04-26 17:07:56 +0000
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_15 branchPackage: HD2013SGI
Commit: e1ce458833c021563d37aba9ec112993d87a4958
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2021-10-26 11:59:06 -0400
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_14 branchPackage: HD2013SGI
Commit: 6fc6418fd4d9c1fe3338113d68407b69f8288a87
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2021-10-26 11:59:06 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_14 branchPackage: HD2013SGI
Commit: a24e87a49acd655d248878e240e5d2477afc629b
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2021-05-19 11:39:44 -0400
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_13 branchPackage: HD2013SGI
Commit: 6bec64df896ab107d793c9967681b9061aa38c42
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2021-05-19 11:39:44 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_13 branchPackage: HD2013SGI
Commit: 2426d986b2aeff18897d5d74c073bfc4ea6cdf93
Author: Mike Smith <grimbough@gmail.com>
Date: 2021-05-06 16:38:03 +0200
Commit message:
update maintainer emailPackage: HD2013SGI
Commit: 91593aae2bc91aa2fd518ce6e9b8d4851be827da
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2020-10-27 10:01:22 -0400
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_12 branchPackage: HD2013SGI
Commit: 961027d30b33f1e140f1e8b21ac8c2bcd4a3454e
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2020-10-27 10:01:22 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_12 branchPackage: HD2013SGI
Commit: af9968a7ed0046dcab1f08a48f52758634e03c16
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-04-27 15:17:22 -0400
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_11 branchPackage: HD2013SGI
Commit: d87f44b799e77078f8361fec786a89b2b45d0f76
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-04-27 15:17:22 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_11 branchPackage: HD2013SGI
Commit: d8043f11773c3716dc699cc901268aa787993613
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-10-29 13:37:01 -0400
Commit message:
bump x.y.z version to odd y after creation of RELEASE_3_10 branchPackage: HD2013SGI
Commit: 8fce63585245a00214c4cb1a08124f351e92820d
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-10-29 13:29:40 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_10 branchPackage: HD2013SGI
Commit: 3c49a50a4dab57543964e798e4097a114eab5f54
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-05-02 12:06:18 -0400
Commit message:
bump x.y.z versions to odd y after creation of RELEASE_3_9 branchPackage: HD2013SGI
Commit: 8d9e1abf37a2e1f8373cbf0a261f3db1bdf79e1b
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-05-02 11:56:32 -0400
Commit message:
bump x.y.z versions to even y prior to creation of RELEASE_3_9 branchPackage: HD2013SGI
Commit: 6cbe9bff4829c6d934105516e743a42e03946981
Author: nturaga <nitesh.turaga@gmail.com>
Date: 2018-10-30 11:38:33 -0400
Commit message:
bump x.y.z versions to odd y after creation of RELEASE_3_8 branchPackage: HD2013SGI
Commit: 5cc0804cbd8b8d55efc76732334fac3da157b682
Author: nturaga <nitesh.turaga@gmail.com>
Date: 2018-10-30 11:36:22 -0400
Commit message:
bump x.y.z versions to even y prior to creation of RELEASE_3_8 branchPackage: HD2013SGI
Commit: 6cef6f084560bc61d61188d4ad4ea19be5a860a7
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2018-08-31 18:01:03 +0000
Commit message:
replace BiocInstaller biocLite mentions with BiocManagerPackage: HD2013SGI
Commit: 0ad66b97688a51e6d8641282ae843fd1d7ef4e61
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2018-04-30 10:34:47 -0400
Commit message:
bump x.y.z versions to odd y after creation of RELEASE_3_7 branchPackage: HD2013SGI
Commit: cb7abe997dbee0dc6da6dc73868c6cb26bb891fb
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2018-04-30 10:31:27 -0400
Commit message:
bump x.y.z versions to even y prior to creation of RELEASE_3_7 branchPackage: HD2013SGI
Commit: 024cb0004101ec08bde1f0c12d653ad66cf2b505
Author: vobencha <valerie.obenchain@roswellpark.org>
Date: 2017-10-30 12:09:07 -0400
Commit message:
bump x.y.z versions to odd y after creation of RELEASE_3_6 branchPackage: HD2013SGI
Commit: 470c4eb3486607dbf348bd982f4c741f662a07af
Author: vobencha <valerie.obenchain@roswellpark.org>
Date: 2017-10-30 11:58:25 -0400
Commit message:
bump x.y.z versions to even y prior to creation of RELEASE_3_6 branchPackage: davidTiling
Commit: c2d32bbb7c099dc50f5103c2967735d09cadbbd2
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-17 15:24:08 +0200
Commit message:
Bump versionPackage: davidTiling
Commit: 17ac26a806e4877795bceac8457744b6a84d6308
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-18 22:17:04 +0200
Commit message:
Bump minimum required R versionPackage: davidTiling
Commit: ff2baff1791467b09b71ac2df180bd0a7be8ffa4
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-17 15:26:10 +0200
Commit message:
Convert Author & Maintainer fields to Authors@R with updated emailPackage: davidTiling
Commit: dd36c5db2f3b8b0b8e0cdcfadea0c5a4889b0338
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-17 15:23:47 +0200
Commit message:
Document data removal in NEWSPackage: davidTiling
Commit: a674f5ae4a577423fc955b58b2b8ff15646d305b
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-17 16:27:52 +0200
Commit message:
Run devtools::document()Package: davidTiling
Commit: 46b6a21a56bc46523ce8342d17316ddfa7e6117f
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-17 16:12:57 +0200
Commit message:
Add BuildResaveData: to avoid triggering promisePackage: davidTiling
Commit: a054d7bdd5574da1929ce43ef28af30eaf5f5a4f
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-17 15:32:40 +0200
Commit message:
Add deprecation error in data("davidTiling")Package: davidTiling
Commit: fa0daf27b898e71502af052830b5012a36d074a1
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-14 17:21:19 +0200
Commit message:
Convert dataTiling dataset to an R scriptPackage: davidTiling
Commit: 96545153662b19cece691f8f95f8b1cb931109f7
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2026-04-28 08:21:38 -0400
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_23 branchPackage: davidTiling
Commit: 34b3c4ee510d3e98bdbdd2c75ce5cd14864ce583
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2026-04-28 08:21:38 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_23 branchPackage: davidTiling
Commit: 1ffa0bf79cbea2e3709883af928ac14cf1a1fd64
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-29 09:23:27 -0400
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_22 branchPackage: davidTiling
Commit: 77d0ffe299d549af0390a27b6236476f7e034e57
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-29 09:23:27 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_22 branchPackage: davidTiling
Commit: c46e46722b09bdf097aa6348d044e883bdf42b0d
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-04-15 09:13:24 -0400
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_21 branchPackage: davidTiling
Commit: 60cf608086614c1b1f50ee3f17fbda926a926cc1
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-04-15 09:13:24 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_21 branchPackage: davidTiling
Commit: 5dc4c86d99f87535ae2b2778e3828de9e91b3e25
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2024-10-29 09:25:04 -0400
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_20 branchPackage: davidTiling
Commit: ac286e063a4154b2d2693661f16f42b299e92946
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2024-10-29 09:25:04 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_20 branchPackage: davidTiling
Commit: f633422c87e7917d857652e558c9729305a787b8
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-30 10:26:40 -0400
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_19 branchPackage: davidTiling
Commit: e40314b88aa9e2bff883cf73908186830ad28562
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-30 10:26:40 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_19 branchPackage: davidTiling
Commit: 594f17a54fc8c45fafd2584941fcaf15b7e6634d
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2023-10-24 08:53:28 -0400
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_18 branchPackage: davidTiling
Commit: 0afc895fc6b3dbe1076d1226880cfb1a0deb8d3d
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2023-10-24 08:53:28 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_18 branchPackage: davidTiling
Commit: dac8bbe1ef5eba01af5a10cf1b6d8a6c2b47405d
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2023-04-25 09:49:15 -0400
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_17 branchPackage: davidTiling
Commit: b8a489d6aa3c3e5e5842e91ae39dc0e574066d2c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2023-04-25 09:49:15 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_17 branchPackage: davidTiling
Commit: 8ec3ea647593a2ab31232d483b38cd2f105fb165
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2022-11-01 10:38:19 -0400
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_16 branchPackage: davidTiling
Commit: 9bd1bc35429026bce7090764996efee299c2d89c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2022-11-01 10:38:19 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_16 branchPackage: davidTiling
Commit: 9e3343f31a7a9906b21f0fe067246acbc96c839f
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2022-04-26 16:54:48 +0000
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_15 branchPackage: davidTiling
Commit: 129e3bfe99bbb17063e7d849f60664019a7be726
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2022-04-26 16:54:48 +0000
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_15 branchPackage: davidTiling
Commit: 1bfaac5dae2432fb709ef18b07d1532783a649d2
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2021-10-26 11:39:05 -0400
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_14 branchPackage: davidTiling
Commit: 14ec2538c547c5d416f98b77923e407365feea8b
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2021-10-26 11:39:05 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_14 branchPackage: davidTiling
Commit: c05e0bfadfe57b21a800ada01715de9c2d4b5e22
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2021-05-19 11:23:36 -0400
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_13 branchPackage: davidTiling
Commit: f6f8b9cdfe862c032dafbcca69fbfc9f47ca71f3
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2021-05-19 11:23:36 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_13 branchPackage: davidTiling
Commit: 0eef93b35cfcd9d18c61d5b1bdf009383d1edc1b
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2020-10-27 09:45:05 -0400
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_12 branchPackage: davidTiling
Commit: aa8f8d70214e9c534c2050c777f82d7b82d8fb46
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2020-10-27 09:45:05 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_12 branchPackage: davidTiling
Commit: 8733ae22db5cb1e87ed2d4c1bd3c9340b6d15ab8
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-04-27 14:52:44 -0400
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_11 branchPackage: davidTiling
Commit: 188c7c4febe052f48f01a0d216ee81c28a361054
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-04-27 14:52:44 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_11 branchPackage: davidTiling
Commit: 2faf2cb9c19836133d8e1306c9edf357832cc480
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-10-29 13:36:59 -0400
Commit message:
bump x.y.z version to odd y after creation of RELEASE_3_10 branchPackage: davidTiling
Commit: d26f22540b48a498a7d353b1ecd2c4d0e61228de
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-10-29 13:29:33 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_10 branchPackage: davidTiling
Commit: abba5d83f976776edea0c6d15399d4f00ef4d482
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-05-02 12:06:10 -0400
Commit message:
bump x.y.z versions to odd y after creation of RELEASE_3_9 branchPackage: davidTiling
Commit: a128836744c08cee9cbadd13b979f0243c92b9b9
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-05-02 11:56:14 -0400
Commit message:
bump x.y.z versions to even y prior to creation of RELEASE_3_9 branchPackage: davidTiling
Commit: b8bcefc82499e9499603010375dd0ed198f3c9e9
Author: nturaga <nitesh.turaga@gmail.com>
Date: 2018-10-30 11:38:33 -0400
Commit message:
bump x.y.z versions to odd y after creation of RELEASE_3_8 branchPackage: davidTiling
Commit: 1c529b42bbb090d27ca66c94e2f40b68a7d158b3
Author: nturaga <nitesh.turaga@gmail.com>
Date: 2018-10-30 11:36:20 -0400
Commit message:
bump x.y.z versions to even y prior to creation of RELEASE_3_8 branchPackage: davidTiling
Commit: 2907c4f5c8a92c3d95bfe74427275a5de0c24580
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2018-04-30 10:34:47 -0400
Commit message:
bump x.y.z versions to odd y after creation of RELEASE_3_7 branchPackage: davidTiling
Commit: f93554c9b87eeb95a8479b10b06511db7654fc7a
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2018-04-30 10:31:24 -0400
Commit message:
bump x.y.z versions to even y prior to creation of RELEASE_3_7 branchPackage: davidTiling
Commit: 10f95573c75263531ec69dd63dacfe29d2112a32
Author: vobencha <valerie.obenchain@roswellpark.org>
Date: 2017-10-30 12:09:07 -0400
Commit message:
bump x.y.z versions to odd y after creation of RELEASE_3_6 branchPackage: davidTiling
Commit: 0fae20151fb6d14885538593d99678e229003fd2
Author: vobencha <valerie.obenchain@roswellpark.org>
Date: 2017-10-30 11:58:21 -0400
Commit message:
bump x.y.z versions to even y prior to creation of RELEASE_3_6 branchPackage: davidTiling
Commit: cf565e2f6c462113fb78776279e16cacf2f48dd6
Author: nturaga <nitesh.turaga@gmail.com>
Date: 2017-08-16 19:07:15 +0000
Commit message:
Committing experiment data for davidTilingPackage: Hiiragi2013
Commit: 430f9aa78909ce8d39f7d39ae0a8e27a628f69ce
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-19 11:01:03 +0200
Commit message:
Bump versionPackage: Hiiragi2013
Commit: 0765457acc637bc5fae0e6280057a370e90c4ca8
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-08-19 11:00:40 +0200
Commit message:
Add stub with deprecation warning for 'a' datasetPackage: Hiiragi2013
Commit: 48d60f5f562be312ee55c3e595618c56f7fe385c
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-06-11 22:09:10 +0200
Commit message:
Bump versionPackage: Hiiragi2013
Commit: a51238f4c0cb2350c59bf8c44a24c6f7218979f9
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-06-11 22:08:53 +0200
Commit message:
Add missing plotPackage: Hiiragi2013
Commit: 08cd3f8f8dd56da601d3b5c6ba4d602ade1b017b
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-05-26 16:32:06 +0200
Commit message:
Bump versionPackage: Hiiragi2013
Commit: ea836d60dc8ee4c9e142ebe703f85b98febb863b
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-05-26 16:31:50 +0200
Commit message:
Use texttt instead of codePackage: Hiiragi2013
Commit: db7d9b86c6e278fcd1b0d513f17ef6a4e067d6d5
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-05-21 11:44:54 +0200
Commit message:
Bump versionPackage: Hiiragi2013
Commit: d2cf73fde92002f698f4c242bc31aff307b26170
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-05-21 11:44:43 +0200
Commit message:
Load packages required for the vignettePackage: Hiiragi2013
Commit: 40ef00f4b1d0e25aff6c297348751e9684c57a23
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2026-04-28 08:25:35 -0400
Commit message:
bump x.y.z version to odd y following creation of RELEASE_3_23 branchPackage: Hiiragi2013
Commit: b7490527d14ae5b84b55f9c5d2cd2de64f595843
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2026-04-28 08:25:35 -0400
Commit message:
bump x.y.z version to even y prior to creation of RELEASE_3_23 branchPackage: Hiiragi2013
Commit: 597de83c2392faccf95c2cd37b8f976d0e12345c
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 14:48:37 +0100
Commit message:
Bump versionPackage: Hiiragi2013
Commit: 172c619ef004fa2e6b24b7a162221ca17295d485
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 16:28:49 +0100
Commit message:
Use AuthorsRPackage: Hiiragi2013
Commit: 9ed8076f21c54fd4b063581041fe5607c609233b
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 16:27:58 +0100
Commit message:
Mention Depends and NAMESPACE changes in DESCRIPTIONPackage: Hiiragi2013
Commit: 96eccd583030ef5db038b486ce2c88073720a164
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 16:27:31 +0100
Commit message:
Fix examplePackage: Hiiragi2013
Commit: d95a43a5f16b891f0aa9aa85ef54e59f3a75696b
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 16:20:12 +0100
Commit message:
Clean up NAMESPACE and move packages to SuggestsPackage: Hiiragi2013
Commit: a7b822e604b9a8af003d2a36253d60ac931316d8
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 15:58:06 +0100
Commit message:
Fix long lines in RdPackage: Hiiragi2013
Commit: ee883e6f6215a2230a086329fd2864f9c37ea0d1
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 15:50:48 +0100
Commit message:
Move packages from Depends to ImportsPackage: Hiiragi2013
Commit: a0f2fe093c2936d556dfea21b3aa76511ab52b74
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 14:48:31 +0100
Commit message:
Add note about data("a") removal in NEWSPackage: Hiiragi2013
Commit: 4fa683efe67c5fa15fc11250851e2811734c9949
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 14:53:57 +0100
Commit message:
Remove references to a in docsPackage: Hiiragi2013
Commit: a798fbad0b35bef504a9fe3bdf56a03d183e6ab6
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 14:43:08 +0100
Commit message:
Add more details about why "a" is not included and how to get itPackage: Hiiragi2013
Commit: 39ff87bf49985c6611f9f9d74f07902ab3149038
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-03 16:13:58 +0100
Commit message:
Make vignette section using "a" static
</div> </div>