Signac 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

Signac 0.2.4

• First CRAN release.
• New SubsetMatrix function to subset a matrix based on number of non-zero elements in the rows or columns.
• Removed seed.use parameter from RunSVD.

Signac 0.2.3

• New UnifyPeaks function to create a merged set of peaks from multiple samples.

Signac 0.2.2

• Bug fix for RunSVD: previously, scaling was applied to each cell rather than each component. Now, mean centering and SD scaling are applied to the cell embeddings within a component.
• Added scale.embeddings option to RunSVD to control whether embeddings are scaled and centered.
• Added irlba.work parameter to RunSVD.
• Update to allow comment characters in fragment file cell names

Signac 0.2.1

• 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

Signac 0.2.0

• 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

Signac 0.1.6

• Bug fix for GetCellsInRegion
• Improve documentation

Signac 0.1.5

• New TSSEnrichment and TSSPlot functions for TSS enrichment scoring
• New InsertionBias function
• New options in CoveragePlot for scaling tracks
• Major speed improvements for CoveragePlot
• Improved documentation (added examples)

Signac 0.1.4

• Updates to CoveragePlot: now plots a Tn5 integration score per base, rather than the whole fragment.

Signac 0.1.3

• New GetIntersectingFeatures function to find overlapping peaks between objects
  
• New MergeWithRegions function to perform region-aware Seurat object merging

Signac 0.1.2

• New RunChromVAR function to run chromVAR through Signac
  
• New RegionStats function to add statistics about peak sequences to the feature metadata
  
• Improvements to FindMotifs: now selects a set of background peaks matching the sequence characteristics of the input

Signac 0.1.1

• Added IntersectMatrix
  
• Added unit tests
  
• Bug fixes for ChunkGRanges

Signac 0.1.0

• This is the first release of Signac!