NEWS

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compEpiTools 1.31.1

• The following function is updated + GRbaseCoverage/GRcoverage/GRenrichment: The maxDepth setting of ApplyPileupsParam was raised to 1000000

compEpiTools 1.15.1

• The following function is updated + heatmapPlot.R: the function was updated removing a useless call to hclust, thus reducing by half the time required for clustering. + topGOres.R: the function was sligtly modified to be more efficient in case of GO enrichment analysis of multiple gene sets. The indexing of the ontology is now performed only once, greatly improving the speed of the function.

compEpiTools 1.7.4

• The following function is updated + GRcoverageInbins: A small bug in the GRcoverageInbins method was fixed: the problem resulted in incorrect coverage (reported as NA) in the last bin(s) of short intervals, those for which the number of bins is similar to their width.

compEpiTools 1.7.3

• The following function is updated + topGOres: Updated the bug in topGOres that was returning very low p-values as characters instead of numeric values.

compEpiTools 1.3.4

• The following function is updated + GR2fasta: The function is updated to handle out of limit GRanges which will not be trimmed.

compEpiTools 1.3.3

• The following function is updated + GRannotate, GRangesInPromoters, getPromoterClass: The functions are updated to create consistency in how the transcripts are retreived from txdb.

compEpiTools 1.3.2

• 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).

compEpiTools 1.0.5

• The following function is updated + topGOres: Drosophila is supported now, significantly enriched gene ids are retuned, plotting of GO terms.

compEpiTools 1.0.4

• 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).

compEpiTools 1.0.3

• 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.

compEpiTools 1.0.2

• The following functions are updated + findLncRNA + GRannotateSimple

compEpiTools 1.0.0

• 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