1.7.0

New functionality:

• Added method parameter to LinkPeaks() (@saketkc; #1030)
• Added ability to plot transcript isoforms (set annotation="transcript" in CoveragePlot())
• Added multiple testing correction to FindMotifs(), and new p.adjust column in output dataframe
• Added p.adjust.method parameter to FindMotifs() to control multiple testing correction method used

Bug fixes:

• Fixed bug in CallPeaks() when project name contained whitespace (#981)
• Fixed bug in CoveragePlot() when tile=TRUE
• Fixed bug in InsertionBias() that set the coordinates beyond the end of some chromosomes (#986)
• Fixed bug in BigwigTrack() when supplying a single bigwig file (#1053)
• Fixed bug in GeneActivity() when specifying biotypes (#1058)
• Fixed bug in GeneActivity() when gene name is an empty string (#1055)
• Fixed bug in FeatureMatrix() when using list of Fragment objects (#1056)
• Fixed bug in RegionMatrix() when running on objects containing renamed cells (#1076)
• Fixed bug in Footprint() when using a FASTA file (#1092)
• Fixed bug in Footprint() when using list of genomic regions (#1098)
• Add check for invalid features in FindMotifs() (#1109)

Other changes:

• Improved error message when no fragment file is supplied in CallPeaks() (#1062)
• Moved Seurat, ggforce, ggrepel, ggseqlogo, lsa, qlcMatrix to suggested packages
• Added progress bar to GetGRangesFromEnsDb()