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