1.31.1版本的变化- - - - - - - - - - - - - - - - - - - - - - - - o以下函数更新+ GRbaseCoverage / GRcoverage / GRenrichment: ApplyPileupsParam的maxDepth设置是提高到1000000版本1.15.1变化- - - - - - - - - - - - - - - - - - - - - - - - o + heatmapPlot更新以下函数。R: hclust函数更新删除无用的调用,从而减少了一半所需的时间为集群。+ topGOres。R:函数是sligtly修改为更有效率的去对多个基因集富集分析。本体的索引现在只执行一次,大大提高的速度函数。1.7.4版本的变化- - - - - - - - - - - - - - - - - - - - - - - - o以下函数+ GRcoverageInbins:更新一个小虫子在GRcoverageInbins方法是固定的:问题导致不正确的报道(NA)报道的最后一本(s)很短的时间内,这些箱子的数量的类似于他们的宽度。1.7.3版本的变化- - - - - - - - - - - - - - - - - - - - - - - - o以下函数+ topGOres更新:更新了错误在topGOres返回假定值为字符而不是非常低的数值。1.3.4版本的变化- - - - - - - - - - - - - - - - - - - - - - - - o以下函数更新+ GR2fasta:更新函数处理的限制农庄将不会削减。v1.3.3变化- - - - - - - - - - - - - - - - - - - - - - - - o以下函数更新+ GRannotate GRangesInPromoters getPromoterClass:函数创建更新从txdb如何检索记录的一致性。1.3.2版本的变化- - - - - - - - - - - - - - - - - - - - - - - - o以下函数更新+ GRcoverageSummit: BAM文件基点网现在可以选择修正基于控制文件的BAM(减去控制基点网,正火后的库大小),之前寻找的最大覆盖位置(峰会)。版本1.0.5变化- - - - - - - - - - - - - - - - - - - - - - - - o以下函数更新+ topGOres:果蝇现在支持,大大丰富了基因ids哑音,策划的条款。 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