Changes in version 3.47.1 o Add warning message when the input is not unique for genomicElementDistribution. Changes in version 3.45.3 o Fix the issue for biomaRt in vignettes. Changes in version 3.45.2 o Remove microRNAs from annoGR Changes in version 3.45.1 o Remove microRNAs from assignChromosomeRegion. Changes in version 3.43.2 o Fix an issue for the corrdinates changes of GRCh37 annotation. Changes in version 3.43.1 o Fix an issue in genomicElementDistribution when convert seqlevelsStyle. Changes in version 3.41.1 o Update Jianhong's email address. Changes in version 3.39.3 o Fix the documentation for Vennerable. Changes in version 3.39.2 o Fix the documentation for summarizePatterInPeaks. Changes in version 3.39.1 o Unique promoters for genomicElementDistribution. Changes in version 3.37.5 o Update by importing pwalign. Changes in version 3.37.4 o Handle the biofilecache error. Changes in version 3.37.3 o use an updated and unified single vignette to replace the four old ones o remove oligoNucleotideEnrichment.R and incorporate it into summarizePatternsInPeaks.R o update findMotifsInPromoterSeqs.R to match changes in summarizePatternsInPeaks.R Changes in version 3.37.2 o export function oligoNucleotideEnrichment Changes in version 3.37.1 o export disable.logging parameter for venn.diagram called by makeVennDiagram Changes in version 3.35.3 o update documentation for the annotatePeakInBatch function Changes in version 3.35.1 o fix the seqlevelsStyle check for custom species. Changes in version 3.33.2 o update the documentation for enrichment analysis Changes in version 3.33.1 o update the disjointExons to exonicParts for ensembldb Changes in version 3.31.4 o update the oligoFrequency function to remove the limitation of sequence length Changes in version 3.31.3 o support `CSV` format for `toGRanges` Changes in version 3.31.2 o use 'entrez_id' instead of 'EntrezID' for getEnrichedPATH() output Changes in version 3.31.1 o add parameter check of proximal.promoter.cutoff and immediate.downstream.cutoff for assignChromosomeRegion. o fix the bug in `plotBinOverRegions` Changes in version 3.29.6 o update jianhong's email Changes in version 3.29.5 o update the pipeline documentation to avoid the error when converting the GRanges object to data.frame. Changes in version 3.29.3 o handle the error "non standard bed file." Changes in version 3.29.2 o fix the error: trying to generate an object from a virtual class "DataFrame". Changes in version 3.29.1 o add subGroupComparison parameter to getEnrichedGO and getEnrichedPATH. Changes in version 3.27.7 o Fix the error "!anyNA(m32) is not TRUE" in seqlevelsStyle is not handled. Changes in version 3.27.6 o Fix the error "pvalue" undefined columns selected in enrichmentPlot Changes in version 3.27.5 o update documentation of pipeline.rmd Changes in version 3.27.4 o use formatSeqnames function to handle the error from seqlevelsStyle: "cannot switch some of GRCm38's seqlevels from NCBI to UCSC style" Changes in version 3.27.3 o use formatSeqnames function to handle the error from seqlevelsStyle: "!anyNA(m31) is not TRUE " Changes in version 3.27.2 o add keepExonsInGenesOnly for genomicElementDistribution o add upstream and downstream for assignChromosomeRegion function when define promoter and downstream regions. Changes in version 3.27.1 o Add the possibility of find overlaps by percentage covered of interval for function findOverlapsOfPeaks 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 2.12.3 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. 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)