CHANGES IN VERSION 3.4.6 ------------------------- o add more parameter test for getEnrichedGO and getEnrichedPATH. CHANGES IN VERSION 3.4.5 ------------------------- o fix the bug with timeout error of getBM in getAnnotation function. CHANGES IN VERSION 3.4.4 ------------------------- o fix the bugs when there is NA values in the input of featureAlignedHeatmap. CHANGES IN VERSION 3.4.3 ------------------------- o update the documentation to avoid time-out error. CHANGES IN VERSION 3.4.2 ------------------------- o update the peakPermTest algorithm to make more reasonable result. CHANGES IN VERSION 3.4.1 ------------------------- o update the documentation NEW FEATURE o toGRanges can accept connection object CHANGES IN VERSION 3.3.8 ------------------------- o update the documentation CHANGES IN VERSION 3.3.7 ------------------------- FIX BUGS o fix the problem in creating vignettes in linux platform. CHANGES IN VERSION 3.3.6 ------------------------- NEW FEATURE o add new function featureAlignedSignal, featureAlignedDistribution, featureAlignedHeatmap, pie1 o add new dataset HOT.spots, wgEncodeTfbsV3 o update annoGR class o update vignettes CHANGES IN VERSION 3.3.5 ------------------------- NEW FEATURE o remove all the RangedData o add annoGR class o update vignettes CHANGES IN VERSION 3.3.4 ------------------------- NEW FEATURE o toGRanges from MACS2, narrowPeak. o calculate the p value of overlapping peaks by reagioneR o update documentation CHANGES IN VERSION 3.3.3 ------------------------- NEW FEATURE o mergePlusMinusPeaks CHANGES IN VERSION 3.3.2 ------------------------- NEW FEATURE o update citation CHANGES IN VERSION 3.3.1 ------------------------- NEW FEATURE o add new citation CHANGES IN VERSION 3.0.1 ------------------------- BUG FIXES o give errors when inputs of addGeneIDs is incorrect. CHANGES IN VERSION 3.0.0 ------------------------- NEW FEATURE o From RangedData to Granges o High efficiency o Find Overlaps for more than 2 groups o Add Utility test o Add new function binOverFeature, egOrgMap. CHANGES IN VERSION 2.17.2 ------------------------ NEW FEATURE o add byBase for makeVennDiagram. CHANGES IN VERSION 2.11.4 ------------------------ NEW FEATURE o Add selection of 'shortestDistance' to output parameter of annotatePeakInBatch. CHANGES IN VERSION 2.12.3 ------------------------ BUG FIXES o relative postion for negative strand are not correct when call findOverlappingPeaks. CHANGES IN VERSION 2.11.4 ------------------------ NEW FEATURE o Add selection of 'shortestDistance' to output parameter of annotatePeakInBatch. CHANGES IN VERSION 2.11.3 ------------------------ NEW FEATURE o Improved efficiency of annotatePeakInBatch. CHANGES IN VERSION 2.9.6 ------------------------ BUG FIXES o Changed Enhancer.Silencer to intergenic.Region in assignChromosomeRegion. CHANGES IN VERSION 2.9.5 ------------------------ BUG FIXES o negative widths are not allowed when call findOverlappingPeaks. NEW FEATURES IN VERSION 2.2.0 ------------------------ o Find the peaks with bi-directional promoters with summary statistics (peaksNearBDP). o Summarize the occurrence of motifs in peaks (summarizePatternInPeaks). o Add other IDs to annotated peaks or enrichedGO (addGeneIDs)The function makeVennDiagram supports 4-way venn diagram. o Enriched Gene Ontology (GO) terms are annotated with a list of genes which can be traced back to peaks. o FAQ: http://pgfe.umassmed.edu/ChIPpeakAnno/FAQ.html. o Summarize peak distribution over exon, intron, enhancer, proximal promoter, 5 prime UTR and 3 prime UTR (assignChromosomeRegion)