Changelog

DEbPeak 1.4.0

New features

  • Added MotifDiscovery to perform de novo motif discovery with STREME.
  • Added MotifCompare to map motifs against a motif database.

Minor changes

  • Added show.html to MotifDiscovery and MotifCompare to control the pop-up window.
  • Fixed bug in InferRegulator.
  • Fixed bug in DEbCA (output ChIP-seq and ATAC-seq peak information).

DEbPeak 1.3.0

New features

  • Added RunChEA3 to identify TFs from gene expression reults with ChEA3.
  • Added RunBART2 to identify TFs from gene expression reults with BART2.
  • Added RunTFEA to identify TFs from gene expression reults with TFEA.ChIP.
  • Added InferRegulator to identify TFs from gene expression reults with ChEA3, BART2 and TFEA.ChIP.
  • Added VizRegulator to visualize the identify TFs.
  • Added ReadProfile to generate reads profile with deepTools.

Minor changes

  • Fixed bug in PeakProfile.
  • Fixed bug in VizRegulator.
  • Optimized bug in FindMotif and DEbPeak.

DEbPeak 1.2.0

New features

  • Added ProcessEnhancer to get near genes of differential peaks.
  • Updated DEbPeak to support enhancer-related data (use species instead of org.db. add enhancer, seq.style, gtf.file, dis.threshold and n.cores).
  • Added NetViz to visualize enhancer-gene network.

Minor changes

  • Fixed bug in ConductFE when no KEGG enrichment results.
  • Fixed bug in ConductDESeq2 when total PCs number is smaller than 5.
  • Fixed bug in AnnoPeak when using gtf file.
  • Fixed bus in PeakMatrix.
  • Added count.matrix parameter in PeakMatrix to support custom count matrix.
  • Simplified the output of enhancer when integrating with RNA-seq.
  • Fixed bug when tibble version > 3.1.8 (do not allow multiple columns with same name).

DEbPeak 1.1.0

New features

  • Added ParseGEO to parse data from GEO.

DEbPeak 1.0.1

New features

  • Added DiffPeakPie to stat genomic regions of differential peaks with pie plot.
  • Added EnrichPlot to create bar or dot plot for functional enrichment analysis, this is useful for visualizing selected terms.

Minor changes

  • Fixed bug in FindMotif

DEbPeak 1.0.0

New features

  • Added DEbDE and DEbDEFE to support integrating two differential expression results.
  • Added PeakbPeak and PeakbPeakFE to support integrating peak annotation/differential expression results.
  • Rewrote InteDiffQuad to support integration results of peak-related data and peak-related data (PeakbPeak), RNA-seq and RNA-seq (DEbDE), RNA-seq and peak-related data (DEbPeak).
  • Added InteFE to replace DEbDEFE, PeakbPeakFE and DEbPeakFE.
  • Added InteVenn to support integration results of peak-related data and peak-related data (PeakbPeak), RNA-seq and RNA-seq (DEbDE), RNA-seq and peak-related data (DEbPeak).

Minor changes

  • Fixed the way PrepareDEPlot filtering.
  • Removed parameter gene.type in DEbPeakFE.
  • Added parameter gene.col in PlotDEbPeak to show genes instead of peaks.
  • Fixed bug in PrepareVenn.
  • Fixed spelling mistakes (consenus -> consensus).

DEbPeak 0.9.0

New features

  • Added MotifEnrich to support motif enrichment for differentially accessible/binding peaks.
  • Updated documents.

Minor changes

  • Fixed bugs in ExtractDA.
  • Fixed bugs in DEbPeak.

DEbPeak 0.8.0

New features

  • Changed DEbPeak, PlotDEbPeak, DEbPeakFE, FindMotif to integrate differential expression analysis results of RNA-seq and ChIP-seq/ATAC-seq.
  • Added InteDiffQuad to create quadrant diagram for differential expression analysis of RNA-seq and Peak-related data.

Minor changes

  • Added peak.anno.key to filter differential expression analysis results of ChIP-seq/ATAC-seq in ConductDESeq2.

DEbPeak 0.7.0

New features

  • Added PeakMatrix to prepare peak matrix for differential expression analysis.
  • Changed ExportPCGenes, LoadingBar, LoadingHeat, LoadingPlot, LoadingGO, ConductDESeq2, ConductFE to support ChIP-seq/ATAC-seq differential expression analysis results.

Minor changes

  • Fixed bugs in ConductDESeq2.

DEbPeak 0.6.0

New features

  • Changed CountQC realted plots to ggplot2.
  • Changed AnnoPeak pie plots to ggplot2.
  • Exported GetGeneLength to get gene length.
  • Added gene.length.file to NormalizedCount to support gene length file as input.

Minor changes

  • Fixed some spelling mistakes (threashold -> threshold).

DEbPeak 0.5.0

New features

  • Added VisGSEA to visualize GSEA results.

DEbPeak 0.4.0

New features

  • Added DEbCA to support integrating RNA-seq, ChIP-seq and ATAC-seq.
  • Modified PlotDEbPeak to support integrating RNA-seq, ChIP-seq and ATAC-seq.
  • Updated all vignettes.

Minor changes

  • Fixed bugs in plot.

DEbPeak 0.3.0

New features

  • Changed package name to DEbPeak to broaden its usage for ChIP-seq, ATAC-seq.

DEbPeak 0.2.0

New features

  • Added FindMotif to find motif in interested peaks (suitable for RNA-seq and ATAC-seq integration).

DEbPeak 0.1.0

  • Added a NEWS.md file to track changes to the package.