Version 1.4.0

Bug fixes:

• Fixed bug in FindMotifs() when using only one region as input (#732)
• Add check for correct number of columns in fragment file (#748)
• Fixed gene lookup when annotations contain NA values (#771)
• Fixed error in ClosestFeature() when query contained regions on contigs not present in gene annotation (#758)
• Fixed bug in TSSEnrichment() when using multiple fragment files (#783)
• Fixed bug in CallPeaks() when multiple fragment files used as input
• Fixed bug in CallPeaks() to account for 0-based starts in called peaks
• Fixed bug in gene name lookup when gene names contain - characters (#759)

Other changes:

• Updated documentation for genome parameter in AddMotifs() and RunChromVAR() (#712)
• Updated the FoldChange() function to use normalized counts rather than raw counts (#795)
• Improved error checking in GeneActivity() (#797)
• Added format parameter to CallPeaks() (#682)

Version 1.3.0

Signac 1.3.0

Bug fixes:

• Fixed LinkPeaks() function when running on a single gene (#629)
• Added fragment.tempdir parameter to CallPeaks() to enable setting directory
  that split fragment files are written to during peak calling (#579)
• Fixed error in FeatureMatrix() when setting sep parameter (#626)
• Fixed peak calling error when group names contain special characters
• Fixed issue with RenameCells() when cell information not present in Fragment object (#704)

Other changes:

• Improved error checking for GeneActivity() (#625)
• Added FoldChange() method for ChromatinAssay() object that sets proper parameters for
  chromatin data. This fixes the calculation of fold changes when running Seurat::FindMarkers() on
  single-cell chromatin data.

Version 1.2.1

New functionality:

• Added head() method for Fragment-class objects.

Bug fixes:

• Fixed bug in ChromatinAssay merging (#596)

Other changes:

• Added support for fragment files containing headers (cellranger-atac v2; #609)

Version 1.2.0

New functionality:

• Added BigwigTrack() function to plot data from bigWig files
• Added bigwig and bigwig.type arguments to CoveragePlot() to
  include bigWig files in CoveragePlot()
• Added region.highlight parameter to CoveragePlot()
• Added biotypes parameter to GeneActivity() and GetTSSPositions() functions
• Added max.width parameter to GeneActivity()
• Added min.distance parameter to LinkPeaks() (#561)

Bug fixes:

• Fixed fragment file reading when only one fragment found in requested region (#474)
• Fixed standard.chromosomes parameter in GetGRangesFromEnsDb() (#513)
• Fixed group.by parameter in PlotFootprint() (#522)
• Fixed bug that would cause some gene coordinates used by GeneActivity() to be
  incorrect (#521)
• Fixed error message in FindMotifs() (#549)
• Fixed bug in CountsInRegion() (#563)

Other changes:

• Improved speed of ChromatinAssay merging
• Improved error message for TSSEnrichment() (#485)
• Improved error messages when trying to run ChromatinAssay-specific functions
  on non-ChromatinAssay assays
• Performance improvements
• Changed default value for n in NucleosomeSignal()
• Enabled parallization in TSSEnrichment() when fast=TRUE
• Added early error checking in LinkPeaks() (#550)
• Change to sparse matrix correlation in LinkPeaks() (#550)
• Moved biovizBase and Biostrings to suggested packages
• Removed ggbio dependency
• Re-implemented AnnotationPlot()

Version 1.1.1

New functionality:

• Added group.by parameter to PeakPlot() to allow coloring plotted genomic
  ranges by metadata variables.
• Added peaks.group.by and ranges.group.by parameters to CoveragePlot() to
  allow coloring plotted genomic ranges in CoveragePlot() to be colored by metadata
  variables.

Bug fixes:

• Update meta feature information (overall peak accessibility) when subsetting
  objects to avoid counts becoming inaccurate (#332)
• Prevent dropping features when creating a merged ChromatinAssay (#340)
• Fix compilation error when using g++ version <5 (#326)
• Retain motif positions during subset (#364)
• Fix assay parameter in CoveragePlot()
• Fix error when merging ChromatinAssay object (#355)
• Add more informative error message when all features or cells removed by parameter choices in CreateChromatinAssay() (#387)
• Fix bug in CreateChromatinAssay() when setting both min.cells and min.features arguments (#390)
• Improved support for remote fragment files
• Fixed bug in PlotFootprint() when only one cell in an identity class (#406)

Other changes:

• Added citation information to the package
• Added SeuratObject dependency

Version 1.1.0

New functionality:

• Added CallPeaks() function to call peaks using MACS2. Peaks can be called
  for different groups of cells separately by setting the group.by parameter
• Added LinkPeaks() function to link peaks to correlated genes.
• Added AddMotifs() function to add motif information to a Seurat object or ChromatinAssay.
• Added AggregateTiles() function to combine adjacent genome tiles
• Added ranges parameter to CoveragePlot() to plot addition sets of genomic ranges
• Added show.bulk parameter to CoveragePlot() to plot accessibility of all cells combined
• Added ability to remove Fragment objects and modify the file path for existing
  fragment objects (#206)

Bug fixes:

• Fixed bugs in AlleleFreq() (#196
  and #260)
• Fixed bug in FeatureMatrix() (#205, #291)
• Fixed bug in CreateChromatinAssay() when setting min.features argument (#194)
• Fixed bug in CreateChromatinAssay() when setting min.cells argument (#292)
• Fixed bug in TSSEnrichment() when cell information not set for fragment files (#203)
• Fixed bug in TSSEnrichment() when no fragments present in TSS region (#244)
• Removed qvalue calculation from FindMotifs() (#223)
• Fixed bug in SetAssayData() when setting the scale.data slot

Other changes:

• Improved feature matching in MatchRegionStats() function when matching distribution of multiple features (eg, GC content and overall accessibility)
• Changed parameter names in MatchRegionStats()

Version 1.0.0

This release includes major updates to the Signac package, including new
functionality, performance improvements, and new data structures.

The entire package has been updated to use the new ChromatinAssay class for the
storage of single-cell chromatin data. This is an extension of the standard
Seurat Assay that adds additional slots needed for the analysis of chromatin
data, including genomic ranges, genome information, fragment file information,
motifs, gene annotations, and genomic links.

In addition, we have defined a new Fragment class to store information
relating to a fragment file. This makes use of the fragment files within Signac
more robust, as checks are now performed to verify that the expected cells are
present in the fragment file, and that the fragment file or index are not
modified on disk.

Key new functionality:

• Store multiple fragment files: you can now store as many fragment
  files as needed in a single object, and all functions that use the fragment file
  will pull data from each of the files. Cell barcodes in the fragment files do
  not need to match the cell barcodes in the object.
• Use remote fragment files: you can now use all the same functionality with
  fragment files hosted on remote servers accessible through http or ftp.
• Transcription factor footprinting: New Footprint() and PlotFootprint()
  functions for TF footprinting analysis.
• Bioconductor methods: call granges(), findOverlaps(), seqinfo(), and
  other Bioconductor generic functions directly on the ChromatinAssay or
  Seurat object.
• New multi-modal visualization methods: Jointly visualize RNA expression
  and chromatin accessibility using the CoveragePlot() function.
• New interactive visualizations: Interactively browse the genome using the
  CoverageBrowser() function.
• Mitochondrial lineage tracing: New functions to identify informative
  mitochondrial alleles, find clonotypes, and predict cell lineage relationships
  using mitochondrial mutations.

Other changes:

• Updates to NucleosomeSignal(): we have greatly improved the scalability of
  NucleosomeSignal(), and fixed a bug present in previous versions. The score
  computed by NucleosomeSignal() in 1.0.0 will be different to that computed by
  previous versions of Signac.
• New CountFragments() function: a fast, memory-efficient function implemented
  in C++ that counts the total number of fragments for each cell barcode present
  in a fragment file.
• New fast option in the TSSEnrichment() function. Setting this to TRUE
  will compute the TSS enrichment score per cell without storing the entire
  cell by TSS position matrix. This can significantly reduce memory requirements
  for large datasets, but does not allow subsequent plotting of the TSS signal
  for different groups of cells.
• New TilePlot() function and tile parameter for CoveragePlot() to plot
  Tn5 integration events in a genomic region for individual cells.
• Performance improvements for FeatureMatrix(), CoveragePlot(), and
  TSSEnrichment()
• Added the manually curated hg38 genomic blacklist regions curated by Anshul
  Kundaje and Anna Shcherbina. These are available as the blacklist_hg38_unified
  object.
• Updated the FRiP() function to use total fragment counts per cell stored
  in object metadata.

Version 0.2.5

• New DepthCor function to compute the correlation between sequencing depth and
  reduced dimension components.
• Performance improvements for RunTFIDF.
• Removed option to use EnsDb object in ClosestFeatures and CoveragePlot. Use GRanges instead.
• Removed ucsc parameter from CoveragePlot.
• Fixed bug in FeatureMatrix that would cause fragments to be counted multiple
  times if nchunk was greater than the number of features used.
• Fixed bug in CoveragePlot that would prevent plotting multiple regions when
  using GRanges.
• Fixed bug in CoveragePlot that would prevent plotting when a different
  assay was active.
• Removed dependencies: GenomicFeatures
• Moved dependencies to suggests: Biostrings, BSgenome
• Removed from suggests: BSgenome.Hsapiens.UCSC.hg19, EnsDb.Hsapiens.v75, JASPAR2018

Version 0.2.1

Changes:

• Removed SingleCoveragePlot from exported functions
• Added executable examples for all functions
• Store raw SVD output in DimReduc misc slot in RunSVD
• Fixed strand orientation for gene plot in CoveragePlot
• Fix missing x-axis when plotting peaks but not genes in CoveragePlot

Version 0.2.0

Changes:

• Removed dependency on TFBSTools, motifmatchr, AnnotationDbi, ggbio, AnnotationFilter
• Renamed PeriodPlot to FragmentHistogram
• Removed motif dimension reduction functions
• Removed motif clustering functions
• Removed neighbors and reductions slots from motif class
• Added motif.names slot to motif class
• Added ability to plot peak ranges in CoveragePlot
• Added ability to plot gene annotations from GRanges object
• Changed gene plot style in CoveragePlot
• Allow passing additional arguments to FilterFragments
• Add inst/extdata
• Change DESCRIPTION file so that Bioconductor dependencies are automatically installed