CHANGES IN VERSION 3.26.4 ------------------------- o Fix the error undefined columns selected in enrichment Plot CHANGES IN VERSION 3.26.3 ------------------------- o bump up the version. CHANGES IN VERSION 3.26.2 ------------------------- o Fix the error that "cannot switch some of GRCm38's seqlevels from NCBI to UCSC style" CHANGES IN VERSION 3.26.1 ------------------------- o Fix the error that "cannot switch some of GRCm38's seqlevels from NCBI to UCSC style" CHANGES IN VERSION 3.25.6 ------------------------- o Fix a bug in estLibSize introduced by last push. CHANGES IN VERSION 3.25.5 ------------------------- o Add LazyDataCompression in description CHANGES IN VERSION 3.25.4 ------------------------- o Add choice endMinusStart to annotatePeakInBatch. CHANGES IN VERSION 3.25.3 ------------------------- o fix the missing link of documentation for rtracklyaer:import. CHANGES IN VERSION 3.25.2 ------------------------- o update documentation. o update findEnhancers to for known interaction data CHANGES IN VERSION 3.25.1 ------------------------- o fix the bug for genomicElementDistribution when the peak length is zero. CHANGES IN VERSION 3.23.12 ------------------------- o fix the bug for genomicElementDistribution when the order of SortedByQueryHits is incorrect. CHANGES IN VERSION 3.23.11 ------------------------- o use seqlevelsStyle to reformat the seqlevels for annotation. CHANGES IN VERSION 3.23.10 ------------------------- o update documentation for genomicElementDistribution CHANGES IN VERSION 3.23.9 ------------------------- o add new function enrichmentPlot, genomicElementDistribution, genomicElementUpSetR, and methagenePlot to improve visualization. CHANGES IN VERSION 3.23.8 ------------------------- o update documentation for findOverlapsOfPeaks. CHANGES IN VERSION 3.23.7 ------------------------- o update documentation for findOverlapsOfPeaks. CHANGES IN VERSION 3.23.6 ------------------------- o change parameter from otherCount to otherCounts to makeVennDiagram function. CHANGES IN VERSION 3.23.5 ------------------------- o add plot parameter to makeVennDiagram function. CHANGES IN VERSION 3.23.4 ------------------------- o update README file. CHANGES IN VERSION 3.23.3 ------------------------- o use roxygen2 to generate the help file. o move multiple package from Imports to Suggests. CHANGES IN VERSION 3.23.2 ------------------------- o fix the issue for new paste output. CHANGES IN VERSION 3.23.1 ------------------------- o remove dependence of Rfast CHANGES IN VERSION 3.21.7 ------------------------- o Fix a potentical bug reported by millerh1. CHANGES IN VERSION 3.21.6 ------------------------- o add new function findMotifsInPromoterSeqs. HANGES IN VERSION 3.21.5 ------------------------- o replace all `class` by `is`. CHANGES IN VERSION 3.21.4 ------------------------- o Fix a bug in getAllPeakSequence when there is peak out side of genome. CHANGES IN VERSION 3.21.3 ------------------------- o Update function summarizePatternInPeaks. CHANGES IN VERSION 3.21.2 ------------------------- o Add function getGO. CHANGES IN VERSION 3.21.1 ------------------------- o remove RangedData from ChIPpeakAnno. CHANGES IN VERSION 3.19.5 ------------------------- o fix the issue that findOverlapsOfPeaks will connect the peaks in same peak list. CHANGES IN VERSION 3.19.4 ------------------------- o add last choice for xget. CHANGES IN VERSION 3.19.3 ------------------------- o fix the colnames of addMetadata. CHANGES IN VERSION 3.19.2 ------------------------- o fix the issue that seqlevelsStyle(peak) == seqlevelsStyle(annotation) are not all TRUE CHANGES IN VERSION 3.19.1 ------------------------- o remove RangedData CHANGES IN VERSION 3.17.2 ------------------------- o fix a bug in toGRanges to accept GTF files. CHANGES IN VERSION 3.17.1 ------------------------- o fix the bug in annotatePeakInBatch which can not accept bindingType parameter. CHANGES IN VERSION 3.15.2 ------------------------- o fix the bug in binOverRegions and binOverGene CHANGES IN VERSION 3.15.1 ------------------------- o Fix the bug in assignChromosomeRegion for the Jaccard index calculation. CHANGES IN VERSION 3.13.19 ------------------------- o Fix the bug in assignChromosomeRegion for the percentage calculation when nucleotideLevel equal to true. CHANGES IN VERSION 3.13.18 ------------------------- o Fix the bug in assignChromosomeRegion for resetting seqlevels. CHANGES IN VERSION 3.13.17 ------------------------- o Fix the bug in annoScore by setting the ignore.strand for punion. CHANGES IN VERSION 3.13.16 ------------------------- o Fix the bug in assignChromosomeRegion for the integer overflow. CHANGES IN VERSION 3.13.14 ------------------------- o Fix the warnings under windows. CHANGES IN VERSION 3.13.12 ------------------------- o Change "class" function to "is" function. CHANGES IN VERSION 3.13.11 ------------------------- o Fix the help file for assignChromosomeRegion. CHANGES IN VERSION 3.13.10 ------------------------- o Improve binOverRegions. CHANGES IN VERSION 3.13.9 ------------------------- o Improve addMetadata. CHANGES IN VERSION 3.13.8 ------------------------- o Fix the warnings under windows. CHANGES IN VERSION 3.13.6 ------------------------- o Improve the functions featureAlignedSignal and featureAlignedExtendSignal CHANGES IN VERSION 3.13.5 ------------------------- o add minFragmentSize parameter to estFragmentLength CHANGES IN VERSION 3.13.4 ------------------------- o suppress the message from featureAlignedExtendSignal o modified help files to make the samples run on local test. CHANGES IN VERSION 3.13.3 ------------------------- o fix the bug in binOverRegions and binOverGene CHANGES IN VERSION 3.13.2 ------------------------- o featureAlignedSignal generate outputs with rownames CHANGES IN VERSION 3.13.1 ------------------------- o change the test value from GNAI3;MIR197 to GNAI3 to avoid the error because of update of annotation database. CHANGES IN VERSION 3.11.8 ------------------------- o make featureAlignedExtendSignal accept GAlignments list object CHANGES IN VERSION 3.11.6 ------------------------- o fix the bugs Codoc mismatches from documentation object 'peakPermTest' CHANGES IN VERSION 3.11.4 ------------------------- o fix the bugs when annoMcols is numeric values. CHANGES IN VERSION 3.11.3 ------------------------- o update the function featureAlignedSignal CHANGES IN VERSION 3.11.2 ------------------------- o add new function binOverGene, binOverRegions, plotBinOverRegions. CHANGES IN VERSION 3.11.1 ------------------------- o make FAQs availble o Fix the bug in annoPeaks for warning of out-of-bound ranges CHANGES IN VERSION 3.9.19 ------------------------- o add FAQs CHANGES IN VERSION 3.9.18 ------------------------- o import rowRanges() generic from DelayedArray instead of SummarizedExperiment CHANGES IN VERSION 3.9.17 ------------------------- o Improve the function featureAlignedExtendSignal CHANGES IN VERSION 3.9.16 ------------------------- o Fix the bug that unable to find an inherited method for function 'reverseComplement' for signature '"BString"' in oligoSummary function. CHANGES IN VERSION 3.9.14 ------------------------- o re-order the signals for cumulativePercentage. CHANGES IN VERSION 3.9.13 ------------------------- o add new function cumulativePercentage. CHANGES IN VERSION 3.9.12 ------------------------- o remove unused code in oligoSummary. CHANGES IN VERSION 3.9.11 ------------------------- o update the documents of featureAlignedSignal. CHANGES IN VERSION 3.9.10 ------------------------- o fix the bug of featureAlignedSignal when there are seqnames in featues but not in cvglists. CHANGES IN VERSION 3.9.9 ------------------------- o add 2 more parameters to getEnrichedGO CHANGES IN VERSION 3.9.8 ------------------------- o update the colnames of toGRanges CHANGES IN VERSION 3.9.7 ------------------------- o fix the bug of findOverlapsOfPeaks when the peaks are exactly same CHANGES IN VERSION 3.9.6 ------------------------- o fix the bug of findOverlapsOfPeaks when there is no peak names for peaklist CHANGES IN VERSION 3.9.5 ------------------------- o update the documents of findOverlapsOfPeaks CHANGES IN VERSION 3.9.4 ------------------------- o update the documents of getEnrichedGO o add more output for findOverlapsOfPeaks. CHANGES IN VERSION 3.9.3 ------------------------- o trim seqnames when using toGRanges CHANGES IN VERSION 3.9.2 ------------------------- o add adjustFragmentLength for featureAlignedExtendSignal. CHANGES IN VERSION 3.9.1 ------------------------- o fix the bug for pair end reads for featureAlignedExtendSignal. CHANGES IN VERSION 3.7.9 ------------------------- o fix the problem in the test when there are names for target but not for current. CHANGES IN VERSION 3.7.8 ------------------------- o remove the dependence of MMDiffBamSubset in documentation becuase it is not availble now. CHANGES IN VERSION 3.7.7 ------------------------- o fix bugs for toGRanges to import MACS2 broad calls. CHANGES IN VERSION 3.7.6 ------------------------- o add new functions tileGRanges, tileCount CHANGES IN VERSION 3.7.5 ------------------------- o add parameter select to annoPeaks CHANGES IN VERSION 3.7.3 ------------------------- o add new function featureAlignedExtendSignal, estLibSize, estFragmentLength CHANGES IN VERSION 3.7.2 ------------------------- o Correct typo in documentation for Z-score. o Improve the efficiency of findOverlapsOfPeaks. CHANGES IN VERSION 3.5.18 ------------------------- o Fix the bugs for featureAlignedSignal when features contain strand info. CHANGES IN VERSION 3.5.17 ------------------------- o Fix the bugs for getEnrichedGO/PATH when recodes in database such as reactome database is not unique. CHANGES IN VERSION 3.5.16 ------------------------- o fix the warning in windows for replacing previous import CHANGES IN VERSION 3.5.15 ------------------------- o not do log2 transform for featureAlignedSingal CHANGES IN VERSION 3.5.14 ------------------------- o remove NA for featureAlignedDistribution o handle NA and infinite value for featureAlignedSingal CHANGES IN VERSION 3.5.13 ------------------------- o throw message when seqlevels are not identical for featureAlignedSignal CHANGES IN VERSION 3.5.12 ------------------------- o add new function summarizeOverlapsByBins. CHANGES IN VERSION 3.5.11 ------------------------- o clean output of findEnhancers CHANGES IN VERSION 3.5.10 ------------------------- o add new function findEnhancers o normalize the output of gene region for binOverFeature o change the documentation to avoid time-out error CHANGES IN VERSION 3.5.9 ------------------------- o merge peaksNearBDP and bdp function. o improve oligoSummary. o update the documentations. CHANGES IN VERSION 3.5.8 ------------------------- o change toGRanges from function to method o update the documentations. CHANGES IN VERSION 3.5.7 ------------------------- o change test from RUnit to testthat o add new function addMetadata o change the output and parameters of annoPeaks o simple the parameter output of annotatePeakInBatch o allow bdp function to accept GRanges annotation o add error bar function for binOverFeature function o remove the log file after plot for makeVennDiagram function o add private function trimPeakList o update the documentation of annoPeaks and annotatePeakInBatch CHANGES IN VERSION 3.5.5 ------------------------- o update the documentation to fix the typo in quickStart. o change the default value of annoPeaks. o update annoGR class to fix the error: identical(colnames(classinfo), colnames(out)) is not TRUE CHANGES IN VERSION 3.5.2 ------------------------- o update the documentation to fix the error on windows (import bigwig error) o avoid the output of addGeneIDs as factors CHANGES IN VERSION 3.5.1 ------------------------- o update the documentation NEW FEATURE o toGRanges can accept connection object o add annoPeaks function o add xget function o update the peakPermTest algorithm to make more reasonable result. o add oligoSummary function o add IDRfilter function o add reCenterPeaks function 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)