Version  bump
 

 Replaced link that leads to suspicious website 

 version bump
 

 Remove msigdbdf reference

The extra package is no longer necessary
 

 Update the link to the smaller rds xenium object
 

 news
 

 Add an example of geseca analysis for 10x xenium data
 

 Merge branch 'update-color-for-geseca-plots' into 'master'

Update color for geseca plots

See merge request alserglab/pr/fgsea/fgsea!2 

 Update breaks for color gradient
 

 Merge branch 'update-plots-for-seurat-5' into 'master'

Update addGesecaScores for Seurat-5

See merge request alserglab/pr/fgsea/fgsea!1 

 bugfix

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

 update volcano, genes_plot, assay_plot and vignette from puhti
 

 Merge pull request #205 from sufyansuleman/add-dbsnp-tarball-support

Added support for arbitrary Bioc SNPlocs tarballs (dbS > 156) 

 Added support for arbitrary Bioc SNPlocs tarballs (dbS > 156)
 

 Merge branch 'master' into devel
 

 Update changes on the new version
 

 Update filter report
 

 Change path to manual
 

 Add dbsnpCutoff and nonCutoff to shiny
 

 Handle special case: PON file only has a header
 

 Fix a small bug in text
 

 Merge branch 'WX'
 

 fixed vignette
 

 fix drv
 

 update Description
 

 update dependencies and changed txdbmaker in vignette
 

 fix hyper
 

 update vignette to be compatible with new intergenic
 

 Update Bluesky badge 

 rolled back R requirement from >=4.5 to >=4.2
 

 updating test data to newest object versions
 

 Bump version
 

 Remove R_front script.
 

 bugfix

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

 Bump version to 0.3.0 for Bioconductor devel
 

 add examples of different w_x/w_y for clusters/genes on vignette
 

 bump version number.
 

 Only return unique peaks in `segregate_seqs`
 

 Sanitise peak input names before running FIMO

Too many underscores seem to cause issues
 

 chore: bump version and update NEWS.md
 

 refactor: update logic
 

 Bump V
 

 Update R-CMD-check.yaml 

 removed version C++
 

 updated C++
 

 Bugfixes for saving VLS strings in data frames.

- Avoid overwriting the VLS flag between columns.
- Fetch the missing value placeholder from the correct handle.
- Use the correct flag in the tests.
 

 easyRNASeq 2.45.1: Replace GenomeInfoDb with Seqinfo in Imports
 

 Organism.dplyr 1.37.1: Replace GenomeInfoDb with Seqinfo in Imports
 

 v1.37.2: minor modification: SpikePos dataset now included in biosigner
 

 Merge pull request #1 from federicomarini/hotfix_obsoleteGO

Hotfix obsolete go term 

 Replacing obsolete term - GO:0006629 is the new one and should solve the build error
 

 version bump
 

 Merge branch 'RELEASE_3_21' into devel
 

 Merge pull request #786 from salzcamino/master

runScDblFinder seed 

 bumped version number
 

 removed PhyloProfileData
 

 Devel version number
 

 Use release version number
 

 readd example results
 

 Merge branch 'devel' of github.com:xyang2uchicago/BioTIP into devel
 

 Update DESCRIPTION 

 Update myplotIc.R

corrected typo in line 13 if() sentence 

 Update myplotIc.R

add the parameter p.IC to the function myplotIc.R 

 fix typo in BioTIP wrap
 

 fix typo in BioTIP wrap
 

 added temporarily removed files
 

 Merge branch 'master' into devel
 

 Merge branch 'master' of github.com:jokergoo/ComplexHeatmap
 

 Merge pull request #1154 from skelly001/develop

Fix slow distance matrix calculation 

 names<-,HeatmapAnnotation updates all necessary slots
 

 Fix slow distance matrix calculation when using correlation-based distance and NAs are present
 

 set row_reorder and column_reorder to FALSE

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107788 bc3139a8-67e5-0310-9ffc-ced21a209358
 

 fix an issue in compartment call when fill_NA.
 

 Solved issue with max iterations argument in function cellsUniformClustering() (#118)

* Fixed minor bug with `maxIterations` in `cellsUniformClustering()`

Also improved UT check messages by reporting distance from UT

* Added appropriate options()

* Updated NEWS.md

---------

Co-authored-by: Silvia Giulia Galfre <49807846+seriph78@users.noreply.github.com> 

 update actions
 

 txdbmaker 1.5.6: Small fix in makeTxDbFromBiomart()
 

 bump version
 

 fix the layer issue for pdf exporter.
 

 adjust vignette
 

 fix vignette
 

 update tests
 

 address conflict
 

 small tweaks
 

 epivizrData 1.37.1: Add Seqinfo to Imports
 

 minfi 1.55.1: Replace GenomeInfoDb with Seqinfo in Imports
 

 Update NEWS
 

 Fix testthat 3rd edition change
 

 Merge remote-tracking branch 'upstream' into devel
 

 Remove citation updater
 

 Update CITATION.cff
 

 ChIPexoQual 1.33.1: Imports Seqinfo instead of GenomeInfoDb
 

 CAGEr 2.15.1: Imports Seqinfo instead of GenomeInfoDb
 

 Update
 

 Seqinfo 0.99.1: Update updateObject() method for Seqinfo objects
 

 bsseq 1.45.2: Imports Seqinfo instead of GenomeInfoDb
 

 BindingSiteFinder 2.7.1

Update serialized BSFDataSet instance because of Seqinfo move from
GenomeInfoDb package to new Seqinfo package.
 

 bump version
 

 Merge branch 'master' into devel
 

 Improved go analysis
 

 Added GOrilla go analysis on DEG output
 

 Added gorilla go analysis support
 

 Fixed small bug in seqlevels
 

 Small fix for fasta file search
 

 Made fst bigformat safer
 

 amplican 1.31.1: Imports Seqinfo instead of GenomeInfoDb

Also use pwalign:: instead of Biostrings:: as appropriate.
 

 DEXSeq 1.55.1: Add GenomeInfoDb to Suggests
 

 update updateObject() method for GRanges objects
 

 fix: make progress package installation optional
 

 Fixed issue with function `getSelectedGenes()` (#116)

 

 Added new clusterization methods (#115)

* Used `Seurat::RunUMAP()` as algorithm to calculate the UMAP

Used appropriate accessors on Seurat objects instead of direct access

* Fixed minor issues with call to function `Seurat::RunUMAP`

* Moved genes' section to separate function

Now genes' selection has been move to a separate function
`genesSelector()`

split clustering's UMAP plots are now outside
the Seurat clusterization function

The function `cellsUMAPPlot()` now uses the same number of features
as the clusterization

* Separated genes selection from Seurat clustering

Now in the split stage the three results of the `seuratClustering()`
function are separated:
- `genesSelection()` this function has been unified with the
  already existing genes selector that was part of the function
  `cellsUMAPPlot()`
- `suratClustering()` now simply returns the new clusterization and
  the `PCA` used to obtain it
- The creation of the PDF output is now done directly in the
  function `cellsUniformClustering()` via calls to the
  function `UMAPPlot()`

Reduced the maximum point size of the `UMAPPlot()` dots

Solved a few bugs and aligned the tests to the new slightly
different output in the cluster names

* Minor improvement of the `seuratClustering()` function

* Expanded choices for `dataMethod` of the `cellsUMAPPlot() function

Added new choices: BinarizedDiscrepancy, DerivativeLogLikelihood and
SignedLogLikelihood

Added shorcuts strings for all choices

Extended calculate function `calculateLikelihoodOfObserved()` to
get a formula parameter and return all likelihood related data matrices

* Now `cellsUMAPPlot()` scales the data matrix along the genes' direction

* Fixed bug in `calculateLikelihoodOfObserved()`

In case of DerivativeLofLikelihood the formula was wrong

* Fixed bug in `calculateLikelihoodOfObserved()`

In case of DerivativeLofLikelihood the formula was wrong

Updated NEWS.md

* Preparing function `calculateReducedDataMatrix()`

* Started using new `calculateReducedDatamatrix()`

Still buggy and incomplete

* Fixed monot issue with update of pics in GitHub

* Solved issue with `calcDist()`

Fall-back using `stats::dist` was not supporting "cosine" distance
Now it uses `proxy::dist` instead.

Also restored stable PCA/clustering disrupted in previous commits

* Simplified spell-checker word list

* Added support to coex-drived dimensionality reductions

* Used new function for UMAP retriveal of data matrix

* Unified all cells' Reduction Data Matrices calculations

Now all calculations requiring to calculate PCA of cells data,
or reduction via COEX eigen-vectors, is run via the specific
function `calculateReducedDataMatrix()`

* Fixed `seuratClustering()` as was not using the passed `dataMethod`

* Fixed issue with NaN log-likelihood data matrices

* Renamed function `genesSelctor()` to `getSelectedGenes()`

Also fixed minor bug in the "HGDI" case when not enough genes
satisfy the requirement gdi >= 1.4

* Added tests about data matrices extraction

Tested `calculateLikelihoodOfObserved()`, `getDataMatrix()`
`getSelectedGenes()` and `calculateReducedDataMatrix()`

* Fixed some minor bugs left in clusterization

Fixed tests

* Updated NEWS.md

* Fixed issue with `cellsUniformClustering()`

when useCoexEigen is TRUE

* Solved spelling issues

* Fixed issue in checks about use of `requires()` 

 Merge pull request #54 from fmicompbio/fix-typos

Fix typos and add GenomeInfoDbData to Suggests 

 Fix some typos
 

 20250621_2
 

 tximeta 1.27.2: Imports Seqinfo instead of GenomeInfoDb
 

 karyoploteR 1.35.3: Add Seqinfo to Imports
 

 csaw 1.43.1: Imports Seqinfo instead of GenomeInfoDb
 

 20250621
 

 gwascat 2.41.1: Add Seqinfo to Imports
 

 txdbmaker 1.5.5: Add Seqinfo to Depends and move GenomeInfoDb to Imports
 

 ensembldb 2.33.1: Add Seqinfo to Imports
 

 BSgenomeForge 1.9.1: Add Seqinfo to Depends
 

 GenomicFeatures 1.61.4: Depends on Seqinfo instead of GenomeInfoDb
 

 rtracklayer 1.69.1: Depends on Seqinfo instead of GenomeInfoDb
 

 GenomicAlignments 1.45.1: Depends on Seqinfo instead of GenomeInfoDb
 

 SummarizedExperiment 1.39.1: Depends on Seqinfo instead of GenomeInfoDb
 

 Biostrings 2.77.2: Depends on Seqinfo instead of GenomeInfoDb
 

 Bump version to 1.13.2
 

 fix a bug in reading mcool file.
 

 Convert CITATION to ASCII

To fix warning from BiocCheckGitClone('SanityR')
 

 Replace std::cerr with Rcpp::Rcerr
 

 Remove Rproj files from Git repo
 

 Deprecate

  - requested on bioc-devel
 

 (1.71.2) incorporates threading improvements
 

 fix crash with stacksize
 

 modifications to ensure that __pthread_get_minstack can be used via dlsym
 

 adding configure.ac
 

 test commit
 

 Removing supraHex
 

 Removing supraHex
 

 Deprecate
 -unresponsive
 

 added example from asdpto in vignette
 

 20250620_fix bugs2
 

 Merge remote-tracking branch 'origin/main'
 

 Resolve merge conflict and bump version to 1.1.1
 

 Update DESCRIPTION
 

 Merge branch 'WX' into devel
 

 Bump up package version and dependency version
 

 Update FilterReport.html
 

 Add info about how to launch shiny app

Also update citation
 

 Handle special case when processing ref and alt

Also add message to users when other special cases happen and CaMutQC does not know how to handle them
 

 State the function of mutType more specifically
 

 Change the default setting of bedFilter to FALSE
 

 Modify Bioc installation guide

Do not suggest users install the devel version of CaMutQC
 

 Add example cases/files for shiny application
 

 Add 0.05 VAF cutoff for Foundation panel
 

 Version bump.
 

 igblastr 0.99.11

Add example of how to combine germline databases from two different
organisms in man page for augment_germline_db_*() utilities.
 

 Bump version to 0.99.13 after bioc-devel subscription
 

 Always use nzvals to extracting sparse data during writes. (#29)

nzvals/nzwhich now work on any SparseArray derivative (i.e. COO_SparseArray and
SVT_SparseArray objects) and sparse representations from the Matrix package.
 

 Add function to call TADs and compartments for spatial distance.
 

 (1.71.1) Disable threading when openblasp found.
 

 Reduce Python dependency to 3.13.3 in v0.11.4 env
 

 Resync with DelayedArray 0.35.2

nzindex() got removed from DelayedArray 0.35.2 (BioC 3.22) after
being deprecated in BioC 3.20 and defunct in BioC 3.21. The
replacement is to use SparseArray::nzwhich(x, arr.ind=TRUE)

Also use nzvals() instead of nzdata(). The latter is just a slot accessor
that only works on COO_SparseArray objects while the former works on **any**
SparseArray derivative (i.e. COO_SparseArray and SVT_SparseArray objects).
It even works on dgCMatrix objects from the Matrix package.
Furthermore, nzdata() is not guaranteed to return the non-zero values in
an order that is consistent with the index returned by nzwhich(), but
nzvals() is. See '?nzwhich' in the SparseArray package.
 

 v2.19.2
 

 Update
 

 Update
 

 Update
 

 add config config<-
 

 fix: nested controller calls; resume_FLAMES ignoring controllers
 

 version bump up in devel
 

 bug fix
 

 Deprecated

 - dependency of same maintainer deprecated last release
 

 fix: issue #803

- Fix issue with `chromPeakChromatograms()` for `XcmsExperiment` objects:
  column (sample) names are omitted in the resulting `XChromatograms`
  object. Sample relationship is expected to be established through the sample
  index. This fixes issue #803 for the devel branch.
 

 Merge pull request #798 from sneumann/jomain

Fix issue in chromPeakSpectra for XcmsExperiment when duplicated chrom peaks are requested 

 fix: add fix to XcmsExperimentHdf5 result object
 

 fix: add fix to XcmsExperimentHdf5 result object
 

 fix: issue #796

- Fix issue #796 in `chromPeakSpectra()` for `XcmsExperiment`: too many spectra
  were returned if parameter `peaks` contained duplicated IDs.
 

 use code Rd tag resolve NOTE
 

 Merge pull request #12 from Bioconductor/update_defunct

Remove defunct functions 

 set deprecated to defunct
 

 remove empty spaces
 

 remove genelocator
 

 remove getLL
 

 add sticker (by Charlotte) to README.md
 

 version bump 1.49.1
 

 Deprecated
 

 auto adjust hight for tax labels; change default input for core gene ident
 

 Changed class() to is(x, 'class')
 

 Update DESCRIPTION 

 Merge pull request #45 from OestLab/si_20250425

Major update 20250425 

 documents
 

 Merge branch 'si_20250425' of https://github.com/OestLab/seqpac into si_20250425
 

 fixed spelling
 

 Updated help page
 

 Change minor errors in examples
 

 Fix help pages
 

 Changed wrappers PAC_analyze and PAC_create
 

 Fixed help guide
 

 Merge branch 'si_20250425' of https://github.com/OestLab/seqpac into si_20250425
 

 Merge branch 'si_20250425' of https://github.com/OestLab/seqpac into si_20250425
 

 Merge branch 'si_20250425' of https://github.com/Danis102/seqpac into si_20250425
 

 Fixing help page
 

 Merge branch 'si_20250425' of https://github.com/OestLab/seqpac into si_20250425
 

 Merge branch 'si_20250425' of https://github.com/OestLab/seqpac into si_20250425
 

 Fixing help page
 

 Update PAC_jitter.R

fix deprecated ggplot2 language 

 Clarified text
 

 Updated description
 

 Update README.md

updating vignette link 

 fixing documentation
 

 Merge pull request #40 from Danis102/ss_codefixes

Fixed bugs, spelling errors and created one wrapper 

 More spelling error fixes
 

 Correction of spelling errors in text (no code changes here)
 

 Update DESCRIPTION 

 Update PAC_pca.R 

 Made other than counts possible and added additional plotting options
 

 Update README.md 

 Update README.md 

 Update README.md 

 add if block in test for rawrr download
 

 Update
 

 Update
 

 added interpro IDs
 

 bump
 

 Update simpleSegHelper.R tweak range for tissueMask otsu 

 Update DESCRIPTION - bump 

 Add sizeSelection to tissueMask 

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

 DelayedArray 0.35.2

Get rid of SparseArraySeed objects, OLD_extract_sparse_array(), and
read_sparse_block(). These were deprecated in BioC 3.20 and defunct
in BioC 3.21.
 

 use 'default' in controllers(ppl)
instead of replicating the same controllers for all possible steps when
setting controllers
 

 add crew controller
 

 bump
 

 Closes #66
drop unused levels in condition
 

 Pray
 

 bump version to 1.18.1
 

 fixed compiler flags for Bioc submission i hope
 

 minor tweaks
 

 updates for bioc re-review
 

 Update chooseCandidateGenes.R
 

 Merge pull request #274 from jr-leary7/devel

Devel 

 version bump in devel
 

 version bump
 

 update README.md
 

 Bug fixes (#146)

* fix: updated toy example object

* fix: download url issues

* fox: version bump

* doc: change of maintainer
 

 bcr_browser() now shows the C regions if the C-region info is available
 

 Add DSDC distance method for cellDistance
 

 see ChangeLog v1.69.2

Merge branch 'devel' of https://github.com/janlisec/Rdisop into devel

# Conflicts:
#	DESCRIPTION
 

 GO updated to 2021
 

 version bump 1.17.8
 

 Change package version.