add HDF5Array to Suggests for Chromium dataset
 

 update github actions
 

 update EHub ID in example
 

 Release 2.11.2
 

 Fix typo
 

 Remove the returnInterquantileWidth option.

Closes #114
 

 Clustering functions return GRangesLists of TagClusters.
 

 Merge branch 'barOikPrivateBranch' into devel
 

 Merge branch 'clustering_refactoring2' into devel
 

 Disable ENCODE and Zebrafish support.

The requireNamespace() calls cause a WARNING if the packages are not
in the Suggests line of DESCRIPTION.  The warnign causes GitHub CI
to stop in error.  Adding the packages in Suggests causes the CI
to crash at package install time because they are only available
from http://promshift.genereg.net/CAGEr/PackageSource.  I attempted
to solve this using the following in DESCRIPTION

Remotes:
    - url::http://promshift.genereg.net/CAGEr/PackageSource/ENCODEprojectCAGE_1.0.1.tar.gz,
    - url::http://promshift.genereg.net/CAGEr/PackageSource/ZebrafishDevelopmentalCAGE_0.99.0.tar.gz

However, this causes crashes because ENCODEprojectCAGE needs
pdflatex to build.  I do not know how to support that in Win
and Mac, therefore I am giving up for the momment.

The best solution would be to get these packages in Bioconductor too.
 

 Add Biostrings to Imports following CI errors 

 Remove packages not in CRAN or Bioc 

 Suggest packages for FANTOM5 import.
 

 Merge branch 'TSSlogo' into devel
 

 Merge pull request #82 from charles-plessy/importPublicData

Restore import public data function. 

 Merge branch 'reverseCumulativesGGplot' into barOikPrivateBranch
 

 Resolve forgotten conflict.
 

 Change default group to 'sampleLabels' in plotAnnot()

No user-visible change expected.  The benefit is that there is always a sampleLabels column in the colData.
 

 Merge branch 'plotAnnotForClusters' into barOikPrivateBranch
 

 Fix example data
 

 Merge branch 'reverseCumulativesGGplot' into barOikPrivateBranch
 

 Merge branch 'devel' into reverseCumulativesGGplot
 

 Support plotting reverse cumulatives for Tag Clusters.

For this, TagCluster objects receive a copy of the parent object's colData.

Also fix check NOTEs related to ggplot2.
 

 Deconstruct the Rle object otherwise it is sloooooowwww!
 

 Roxygen and drop unused multicore options.
 

 Unify track export for TCs and CCs

Closes #70
 

 Merge branch 'clustering_refactoring2' of github.com:charles-plessy/CAGEr into clustering_refactoring2
 

 Add back some accidentally deleted code.
 

 Pre-compute sample-agnostic quantile pos for consensus clusters.
 

 Remove calls to DelayedArray, remove CTSStagCountDA.

See also #87
 

 Merge branch 'devel' into clustering_refactoring2

This brings in the code factorisation made with .ctss_summary_for_clusters
 

 Refactor distclu code

The old implementation is entirely replaced by Bioconductor's reduce function.

The remaining code (which was traniently named .distclu2) is glue, documentation and boilerplate.
 

 Refactor the Paraclu code.

Works on pairs of position and score, or on CTSS objects, or
on RangedSummarizedExperiment objects.

Computes score and dominant CTSS for each cluster.  Closes #73
 

 Port plotReverseCumulatives to ggplot2
 

 Use the .ctss_summary_for_clusters to factorise more code.
 

 Proof of concept for distclu method in Bioconductor.

See #85
 

 Restore documentation (removing some redundancy in the text).
 

 Limited ENCODE import (no merging).
 

 Clean up :: and ::: calls.
 

 Draft import function for FANTOM 3/4

See also #78
 

 Validate sample names.
 

 Load FANTOM5 data using getCTSS().

Also rename function parameter, because "source" is already a function name.

See also #78
 

 Support loading data from URLs.

Closes #50
See also #52 and #78
 

 Use match.arg to ensure valid source.
 

 version bump
 

 keep uncompressed openapi.json for easier comparison
 

 More details on constructing SFE object from scratch
 

 Use tempfile instead of re-creating the same directory in tempdir
 

 more work on SVT_SparseArray linear subsetting
 

 Make estGeno() fix the half of parental genotypes for the reverse-direction step
 

 Rf_error calls modified to include format string from @vjcitn
 

 update vignette
 

 docs: expand documentation on combineSpectra

- Expand the documentation for `combineSpectra()` and `combinePeaks()` (issue
  #320).
 

 bug fixed
 

 fix: warning and version bump .2

R CMD check by
importMethodsFrom ProtGenerics scanIndex
 

 fix: add missing import for scalePeaks()
 

 Merge branch 'main' into jomain
 

 version bump 1.29.3
 

 fix: add mz and scanIndex methods
 

 bugfix

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

 update vignette
 

 update vignette
 

 make setCallFilter() faster but RAM burden
 

 update setCallFilter()
 

 update manuals
 

 bug fix in plotDosage()
 

 updata doc
 

 add function to include replicates
 

 FIX: setting eval = FALSE on the ?pkg::fun code blocks
 

 FIX: unnecessary text in pkg man/.Rd file
 

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

 chore: Update WORDLIST.
 

 chore: Update DESCRIPTION.
 

 merge bioc
 

 fix git cmd
 

 change req install order
 

 Don't force users to install the entire tidyverse
 

 That RBioFormats error
 

 Address weird Biobase warning and updated vignette
 

 R CMD check issues
 

 Try R CMD check action. I need to see which unit tests failed.
 

 See if pkg can resolve the dependencies this time
 

 Added tests
 

 Updated docs
 

 Updated heatmap palette
 

 update bioc version
 

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

 Merge pull request #227 from Clearmind777/devel

update CITATION and separate plot-testing code 

 CITATION changed
 

 version bump 1.17.2
 

 add submissionId to return value config and message
 

 bump version in devel
 

 SparseArray 1.5.4

Support for "lacunar leaves" completed.
Set LACUNAR_MODE_IS_ON to 1.
 

 bump
 

 Evaluate minEvents gating argument for CytoExploreR. (#253)

 

 ADD: new function short_sets_detail
 

 UPDATE: NMF imports
 

 ADD: Added new function short_sets_detail
 

 FIX: fixed aggregations with test statistics
 

 gencode 46 M35 ensembl 112
 

 keep rowData after aggregate_cells
 

 Merge branch 'master' of github.com:stemangiola/tidySingleCellExperiment
 

 version UP

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

# Conflicts:
#	DESCRIPTION
 

 more work on "lacunar mode"
 

 Only run the examples when parquet driver is available
 

 more work on "lacunar mode"
 

 bump up version number
 

 FIX: Merge branch 'devel.bk' into devel
 

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

 ADD: suggested packages to DESCRIPTION (vignette)
 

 UPDATE: package version in DESCRIPTION file
 

 ADD: documentation (man)
 

 UPDATE: vignette, DESCRIPTION v.5
 

 UPDATE: vignette from branch master to devel
 

 UPDATE: update functions.R in branch with get_kegg_sets()
 

 FIX: un-ignore man/ documentation
 

 UPDATE: DESCRIPTION version
 

 FIX: update funOmics-package man page
 

 FIX: package man page
 

 FIX: update R version
 

 FIX: permissions - Copy repo from old to new laptop
 

 UPDATE: add processing comment to vignette
 

 UPDATE: DESCRIPTION & README from branch master to devel
 

 UPDATE: update functions.R in branch with get_kegg_sets()
 

 FIX: un-ignore man/ documentation
 

 FIX: add dplyr:: before mutate
 

 UPDATE: rename test filename
 

 FEATURE: add get_kegg_sets() function
 

 merge upstream/devel
 

 use mkTxDb* functions from `txdbmaker` (will be removed from `GenomicFeatures` in BioC 3.20)
 

 fix format specifiers for long int and unsigned long int (WARNING from R CMD check)
 

 update depreciated r-lib/actions/setup-pandoc from v1 to v2
 

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

 more work on "lacunar mode"
 

 document source and derivation of extdata
 

 bump to 1.23.2, fix to empty masking
 

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

 fix to qualityMask producing the same mask with different option
 

 Change back to devel version
 

 Version bump, since the old SpatRadterImage bug is quite urgent
 

 Merge branch 'main' of https://github.com/pachterlab/SpatialFeatureExperiment
 

 Pubs in edgeR-package.Rd now in reverse chronological order
 

 edgeR 4.3.3
- New arguments for catchRSEM().
 

 edgeR 4.3.2
- Add new function catchRSEM().
 

 Copy .weightedFDR() from csaw to avoid use of ":::"
 

 Fix typo in package title
 

 Remove requirement for a specific version (version 11) of C++
 

 version bump in devel
 

 version bump in devel
 

 version bump 1.1.1
 

 merge
 

 Update changelog and release.
 

 Ensure robustness against different structures encoding the dominant CTSS.

See #70
 

 Merge branch 'fix-issue-70' into charles_2024_05
 

 Use Roxygen to transfer package DESCRIPTION to documentation.

Also take this opportunity to revamp package description.
 

 Fix formatting issues that were causing some NOTES.
 

 Update Roxygen
 

 edgeR 4.3.1
- Add checks for negative or NA counts to cpm, cpmByGroup, normLibSizes.
- Edits DGEGLM and glmFit help pages to clarify that coef are on loge scale.
 

 Added examples
 

 Unit test for old SpatRasterImage conversion in readRDS method #44
 

 Use tempdir for testing and examples. Just learnt that we shouldn't write to the user's directory according to the Writing R Extensions manual.
 

 Refactoring, added formatTxTech and addTxTech so it's easier to format the transcript spots for technologies without having to look up things like gene_col
 

 Added unit tests for readXenium
 

 Moved internal functions out of the Seurat coercion function so other functions can use them
 

 Version number

Merge branch 'devel' of git.bioconductor.org:packages/scDesign3 into devel
 

 This version 0.99.2 is identical to v.0.99.1 except for email adress updated to fix error about no subscription to Bioc-devel mailing list
 

 This is updated package (v.0.99.1) that addresses al reviewer's comments
 

 bumped version to 1.1.0 and removed a ghost statement in ggplotSampleMDS()
 

 don't use 'skip_if_offline()'

- tests for environment variable 'NOT_CRAN'
- instead test for curl (in Suggests:) and use nslookup()
 

 Fixed the build issue due to removal of ensurer package from CRAN
 

 Version bump consistent with Bioconductor guidelines
 

 Update citation info for spatialDLPFC
 

 Update LICENSE

Updated license to remove bug reporting clauses and academic usage clause to MIT license 

 bump version
 

 update github check
 

 Update version number

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

# Conflicts:
#	DESCRIPTION
 

 Remove dendextend, added shinyjs and shinythemes to required packages
 

 bump version
 

 ADD: suggested packages to DESCRIPTION (vignette)
 

 UPDATE: package version in DESCRIPTION file
 

 ADD: documentation (man)
 

 Merge pull request #169 from rcastelo/168-result-of-gsva-is-all-na

change misleading warning messages 

 news updates
 

 Fixed conflicts in version change
 

 updates version to 1.0.1
 

 version
 

 update readme following Bioc release
 

 FIX: permissions - Copy repo from old to new laptop
 

 Merge branch 'devel' into read_compounddiscoverer
 

 Fix various issues unearthed by `R CMD check`;
 

 Merge branch 'devel' into read_compounddiscoverer
 

 Initial implementation of a reader for Thermo CompoundDiscoverer metabolomics output;
 

 Bump version
 

 `fcor` and `fcluster` : develop further
 

 biplot : geom_text -> geom_text_repel
 

 Merge branch 'main' into devel
 

 chore: update puml img
 

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

 more work on "lacunar mode"
 

 Update README.md 

 Update README.md 

 Bumped version and date, added a NEWS file.
 

 Fix itemized lists in signature object documentation
 

 bump version to 1.5.3
 

 Merge pull request #167 from rcastelo/166-res-igsva-seem-not-work-when-use-data-from-workspace

fix issue by updating argument name used in shiny app 

 Added community analysis -graph clustering- function and plot to identify super-groups from the group similarities computed by clusterFoldSimilarity - colors modified
 

 Added community analysis -graph clustering- function and plot to identify super-groups from the group similarities computed by clusterFoldSimilarity
 

 Added forwarding of sample information from NanoMethResult to BSSeq objects
 

 Increment version
 

 Make good use of \VignetteIndexEntry to get vignettes listed in right order
 

 bump version
 

 Update droplet-processing.Rmd and protein-abundance.Rmd

- `scRNAseq::StoeckiusHashingData()` and `scRNAseq::KotliarovPBMCData()` again produce an SCE with altExp stored as SCE rather than SE
  - See https://github.com/LTLA/scRNAseq/issues/49#issuecomment-2065871509 and https://github.com/LTLA/scRNAseq/commit/2b0b5ea1c5960482b62a3b3fff1106172c58e873
- Also revert unintentional change (committed in f20d141) to use of serial instead of parallel processing with `computeCorrelations()` and `findTopCorrelations()` in in protein-abundance.Rmd
 

 Bump minimum version of scRNAseq dependency
 

 update NEWS file
 

 version bump 1.29.1
 

 use "_PACKAGE" for roxygen
 

 version bump 1.17.1
 

 update NEWS file
 

 bump version to 1.5.2
 

 Fix for Clang 16

See https://github.com/Bioconductor/SparseArray/issues/9

Note on previous commit: commit 2fc4998 added back and forth coersions
between ngCMatrix and SVT_SparseMatrix objects.
 

 Merge pull request #120 from sanchit-saini/ucsc-web-testcases

Add test cases to check if the UCSC scraping logic works properly 

 Add testcases for more functions
 

 Fixed issue with torch library (#70)

When the torch library has not been fully installed
the code was throwing an error

Moved all torch loading code into a separate utility function 

 Updated vignette with the new link_data parameter.
 

 Fix the issue for importMatrix when 'w' is missing.
 

 bump to version 1.13.1
 

 Update check-bioc.yml
 

 add batch2 and ... as arguments in batchCorrectionAssay
 

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

 Bioconductor 3.20 devel
 

 Bioconductor 3.19 release
 

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

* upstream/devel:
  bump x.y.z version to odd y following creation of RELEASE_3_19 branch
 

 Merge remote-tracking branch 'upstream/RELEASE_3_19' into devel

* upstream/RELEASE_3_19:
  bump x.y.z version to even y prior to creation of RELEASE_3_19 branch
 

 Fixed reading when Inf is present
 

 fix gsva API update
 

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

 citecontact_1.3.1
 

 citecontact_1.1.1
 

 added TOMFlowPlot
 

 Minor fixes
 

 bump version to 1.5.1
 

 Version bump after bugfix
 

 Bump SVT_VERSION from 0 to 1

The layout of the Sparse Vector Tree (SVT) used in SVT_SparseArray objects
is now versioned, and internal global variable SVT_VERSION keeps track of
that.
In SVT_VERSION 1, the order of the nzvals/nzoffs components in the SVT
leaves is switched w.r.t. SVT_VERSION 0: new order is nzvals/nzoffs;
previous order was nzoffs/nzvals.
Version 0 was used in SparseArray < 1.5.0. This means that SVT_SparseArray
objects created and serialized with SparseArray < 1.5.0 are not compatible
with SparseArray >= 1.5.0 for now. An updateObject() method might be added
later.
 

 fix to contrast output column names in vignette
 

 test for empty output
 

 Increment version
 

 bump version
 

 Merge branch 'devel' into RELEASE_3_19
 

 bump version to test gitactions
 

 update news