Changelog

Source: NEWS.md

Signac 0.2.5 2020-04-16

  • 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 2020-03-13

  • 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 Unreleased

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

Signac 0.2.2 Unreleased

  • 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 Unreleased

  • 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 Unreleased

  • 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 Unreleased

  • Bug fix for GetCellsInRegion
  • Improve documentation

Signac 0.1.5 Unreleased

  • 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 Unreleased

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

Signac 0.1.3 Unreleased

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

Signac 0.1.2 Unreleased

  • 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 Unreleased

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

Signac 0.1.0 Unreleased

  • This is the first release of Signac!