CHANGES IN VERSION 1.3.4 ------------------------ o The following function is updated + GR2fasta: The function is updated to handle out of limit GRanges which will not be trimmed. CHANGES IN VERSION 1.3.3 ------------------------ o The following function is updated + GRannotate, GRangesInPromoters, getPromoterClass: The functions are updated to create consistency in how the transcripts are retreived from txdb. CHANGES IN VERSION 1.3.2 ------------------------ o The following function is updated + GRcoverageSummit: the BAM file base-coverage can now be optionally corrected based on a control BAM file (subtracting the control base-coverage, after normalizing both for library size), before looking for the maximum coverage position (summit). CHANGES IN VERSION 1.0.5 ------------------------ o The following function is updated + topGOres: Drosophila is supported now, significantly enriched gene ids are retuned, plotting of GO terms. CHANGES IN VERSION 1.0.4 ------------------------ o The following functions are updated + GRannotate, distanceFromTSS, matchEnhancers: TxDb with ensemble gene ID are now incorporated for annotation (earlier only TxDb with EntrezID were supported). CHANGES IN VERSION 1.0.3 ------------------------ o The following functions are updated + GRannotate, TSS: Txdb with duplicate transcript name was resulting in error in these functions. Now all the transcripts with duplicate transcript name are removed before performing annotation. CHANGES IN VERSION 1.0.2 ------------------------ o The following functions are updated + findLncRNA + GRannotateSimple CHANGES IN VERSION 1.0.0 ------------------------ o initial version with the following functions implemented: + GRbaseCoverage + GRcoverage + GRcoverageInbins + GRcoverageSummit + GRenrichment + countOverlapsInBins + stallingIndex + TSS + distanceFromTSS + GRangesInPromoters + GRmidpoint + GRannotate + GRannotateSimple + makeGtfFromDb + enhancers + matchEnhancers + topGOres + simplifyGOterms + findLncRNA + getPromoterClass + heatmapData + palette2d + heatmapPlot + plotStallingIndex + GR2fasta + overlapOfGRanges + GRsetwidth + unionMaxScore + GRanges2ucsc + ucsc2GRanges