1.17.1

• Remove Seqinfo package dependency

1.17.0

New features:

• Added the ATACqc() function to run fragtk qc and store the results
• Added FitMeanVar() and PearsonResidualVar() functions for highly variable feature selection
• Added pca parameter to RunSVD() to compute PCA dimension reduction without storing standardized matrix
• Added the EnrichedTerms() function to run fgsea() on differential testing results from each group of cell identities
• Added layer parameter to RunSVD() to select which layer to use

Bug fixes:

• Added seqinfo to motif positions in AddMotifs() to prevent the extension
  of motif regions beyond the ends of chromosomes
  (#1983; @chenyenchung)

Other changes:

• Deprecated NucleosomeSignal and TSSEnrichment functions in favor of the
  new ATACqc function
• Deprecated TSSPlot
• Deprecated GRangesToString and StringToGRanges
• Deprecated the blacklist region data objects in favor of using the
  excluderanges package
• Changed SVD function in RunSVD() from irlba::irlba() to RSpectra::svds()
• Removed irlba.work parameter from RunSVD()
• Added sparseMatrixStats and RSpectra to package dependencies; removed irlba
• Added fgsea to suggested packages
• Added Seqinfo to dependencies
• Removed RunChromVAR() and AddChromatinModule() due to the chromVAR package
  being unavailable in Bioconductor 3.23
• Removed chromVAR from suggested packages

1.16.0

Signac 1.16.0

Bug fixes:

• Check that macs2 exists at the macs2.path in CallPeaks() (#1678)
• Fix bug in LinkPeaks() that incorrectly excluded additional chromosomes from background peak set

Other changes:

• Remove broken seqinfo links from documentation as functions are moved from GenomeInfoDb to Seqinfo
• Enable faster selection of background peaks if the wrswoR package is installed
• Add wrswoR to suggested packages
• Updated MatchRegionStats() to use likelihood-ratio weighting (query/background probability) to sample regions.
  This produces more accurate matching distributions between query and background features.
  This change will affect how background peaks are selected for the FindMotifs() and LinkPeaks() functions.

1.15.0

New features:

• Added group.order parameter to RegionPlot() and RegionHeatmap() functions to control order of plotted groups (#1745)

Bug fixes:

• Fix object subsetting when RegionMatrix() position enrichment information is present in the object.
• Fix error in RegionPlot() x-axis (@cmf1997; #1899)

Other changes:

• Enable using a 6-column fragment file (#1945)
• Improve error messages for FindMotifs() (#1788)
• Add documentation about the required format for gene annotations, and ensure this format is present when creating the assay (#1797; @lldelisle)
• Add an option to force FeatureMatrix() to return as many rows as input granges (@lldelisle; #1803)

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)