1.14.0

New features:

• Added SortIdents() function to automatically order cell metadata according
  to similarity (@JavenTyr)

Other changes:

• Change to SeuratObject v5.0.2 dependency
• Increase R dependency to 4.1
• Deprecate CoverageBrowser()
• Add informative error message for ClosestFeature() when gene annotations are not present in the object (#1681)
• Fix error in CreateChromatinAssay() when supplying a pre-computed Motif object (#1657)
• Fix error in CoveragePlot() when combining cells and group.by parameters (#1724)
• Added warning in FeatureMatrix() when requested features are on seqnames not
  present in the fragment file (#1754)

1.13.0

Bug fixes:

• Fix bug in SetAssayData() for ChromatinAssay objects (#1538)
• Fix bug in TSSEnrichment() causing error on small example dataset (#1563)
• Fix errors when using a CSI index (#1494)
• Fix error in Footprint() when running on a small number of regions (#1614)
• Fix error in CoveragePlot() and PlotFootprint() when setting both ident and split.by parameters (#1660)
• Fix bug in MatchRegionStats() when NA values are present in only some of the feature metadata rows (#1655)

Other changes:

• Add ability to plot links for certain genes only in CoveragePlot() (#1459)
• Add corSparse(), remove qlcMatrix from suggested packages (#1570)
• Update documentation for GetLinkedPeaks() and GetLinkedGenes() (#1654)

1.12.0

Bug fixes:

• Fixed bug in fragment file filtering with FilterCells() (#1509)

Other changes:

• Add support for SeuratObject v5

1.11.0

Bug fixes:

• Fix error when supplying genome string to AddMotifs() function (#1437)
• Fix error in quantification with multiple fragment files (#1474)

Other changes:

• Added region_extension parameter to TSSEnrichment() function to enable changing the size of the region used to compute TSS enrichment scores (#1444; @twmcart)
• Allow fragment files with a CSI index (#1494)

1.10.0

New functionality:

• Added DensityScatter() function
• Added scale.linewidth parameter to LinkPlot() (#1412)

Bug fixes:

• Fixed error in GetReadsInRegion() when no fragments present that overlap the region (@Rockweiler; #1348)
• Make motif names unique to avoid errors in motif-related functions (#1311)
• Ignore missing seqnames when constructing a Motif object (#1381)
• Fixed error in BigwigTrack() (#1389)
• Fixed bug in RegionMatrix() where regions on minus strand were not handled correctly (#1368)

Other changes:

• Improved documentation for AddMotifs() function (#1361)

1.9.0

Bug fixes:

• Fixed Motif object subsetting when using only one feature (#1266)
• Avoid error in chromVAR when matrix contains NA values (#1254)
• Fixed error in CoveragePlot() when setting show.bulk=TRUE (#1294)

Other changes:

• Improved error message when no fragment file information stored (#1236)
• Add tol parameter to RunSVD() to control the irlba::irlba() tol parameter
• Added split.by parameters to CoveragePlot() and PlotFootprint() (#523)

1.8.0

Bug fixes:

• Fixed bug in Motif object subsetting (#1162)
• Fixed bug in FeatureMatrix() where cell names would not be converted correctly when running
  with cells=NULL (#1198)
• Fixed bug causing crash when fragment file line lengths are very large (#723)

Other changes:

• Improved fold change calculation (#1174)
• Added subset() method for Fragment-class objects
• Set random seed within CoverageTrack to enable reproducible coverage plots (#1206)
• Add ability to plot region using gene name in PeakPlot(), LinkPlot(), and
  AnnotationPlot() (#919)
• Change Motif class definition to allow any CsparseMatrix in the data slot

1.7.0

New functionality:

• Added method parameter to LinkPeaks() (@saketkc; #1030)
• Added ability to plot transcript isoforms (set annotation="transcript" in CoveragePlot())
• Added multiple testing correction to FindMotifs(), and new p.adjust column in output dataframe
• Added p.adjust.method parameter to FindMotifs() to control multiple testing correction method used

Bug fixes:

• Fixed bug in CallPeaks() when project name contained whitespace (#981)
• Fixed bug in CoveragePlot() when tile=TRUE
• Fixed bug in InsertionBias() that set the coordinates beyond the end of some chromosomes (#986)
• Fixed bug in BigwigTrack() when supplying a single bigwig file (#1053)
• Fixed bug in GeneActivity() when specifying biotypes (#1058)
• Fixed bug in GeneActivity() when gene name is an empty string (#1055)
• Fixed bug in FeatureMatrix() when using list of Fragment objects (#1056)
• Fixed bug in RegionMatrix() when running on objects containing renamed cells (#1076)
• Fixed bug in Footprint() when using a FASTA file (#1092)
• Fixed bug in Footprint() when using list of genomic regions (#1098)
• Add check for invalid features in FindMotifs() (#1109)

Other changes:

• Improved error message when no fragment file is supplied in CallPeaks() (#1062)
• Moved Seurat, ggforce, ggrepel, ggseqlogo, lsa, qlcMatrix to suggested packages
• Added progress bar to GetGRangesFromEnsDb()

Version 1.6.0

New functionality:

• Added RegionHeatmap() function
• Added RegionPlot() function
• Added RegionMatrix() function
• Added MotifCounts() function
• Added ability to plot multiple assays simultaneously in CoveragePlot() by providing a list of assay names
• Added assay.scale, bigwig.scale, and split.assay parameters to CoveragePlot()
• Added new option to provide quantile ymax value in CoveragePlot()
• Added bigwig.scale and ymax parameters to BigwigTrack()
• Added peak.slot parameter to LinkPeaks() (#932)

Bug fixes:

• Fixed behaviour of min.features parameter in CreateChromatinAssay() to retain cells with >= min.features (#902)
• Fixed behaviour of min.cells parameter in LinkPeaks() (#932)

Other changes:

• Updated documentation for CoveragePlot() (#992)
• Removed method parameter from LinkPeaks() (#932)

Version 1.5.0

Bug fixes:

• Fixed bug in FeatureMatrix() when cells information not present in Fragment object (#803)
• Fixed bug in object merging (#804)
• Add ability to run LinkPeaks() using Ensembl IDs (#858)
• Fix issue in GeneActivity() when gene names are NA (#865)
• Fix bug in FeatureMatrix() when only one region supplied
• Allow negative values in ExpressionPlot() when using scaled data (#893)

Other changes:

• Added idf parameter to RunTFIDF() to use precomputed IDF vector
• Added gene.id parameter to GeneActivity() to allow output genes named using gene ID (#837)
• Added sep parameter to ConnectionsToLinks() (#841)