NEWS

---

ChIPpeakAnno 3.39.2

• Fix the documentation for summarizePatterInPeaks.

ChIPpeakAnno 3.39.1

• Unique promoters for genomicElementDistribution.

ChIPpeakAnno 3.37.5

• Update by importing pwalign.

ChIPpeakAnno 3.37.4

• Handle the biofilecache error.

ChIPpeakAnno 3.37.3

• use an updated and unified single vignette to replace the four old ones
• remove oligoNucleotideEnrichment.R and incorporate it into summarizePatternsInPeaks.R
• update findMotifsInPromoterSeqs.R to match changes in summarizePatternsInPeaks.R

ChIPpeakAnno 3.37.2

• export function oligoNucleotideEnrichment

ChIPpeakAnno 3.37.1

• export disable.logging parameter for venn.diagram called by makeVennDiagram

ChIPpeakAnno 3.35.3

• update documentation for the annotatePeakInBatch function

ChIPpeakAnno 3.35.1

• fix the seqlevelsStyle check for custom species.

ChIPpeakAnno 3.33.2

• update the documentation for enrichment analysis

ChIPpeakAnno 3.33.1

• update the disjointExons to exonicParts for ensembldb

ChIPpeakAnno 3.31.4

• update the oligoFrequency function to remove the limitation of sequence length

ChIPpeakAnno 3.31.3

• support 'CSV' format for 'toGRanges'

ChIPpeakAnno 3.31.2

• use 'entrez_id' instead of 'EntrezID' for getEnrichedPATH() output

ChIPpeakAnno 3.31.1

• add parameter check of proximal.promoter.cutoff and immediate.downstream.cutoff for assignChromosomeRegion.
• fix the bug in 'plotBinOverRegions'

ChIPpeakAnno 3.29.6

• update jianhong's email

ChIPpeakAnno 3.29.5

• update the pipeline documentation to avoid the error when converting the GRanges object to data.frame.

ChIPpeakAnno 3.29.3

• handle the error "non standard bed file."

ChIPpeakAnno 3.29.2

• fix the error: trying to generate an object from a virtual class "DataFrame".

ChIPpeakAnno 3.29.1

• add subGroupComparison parameter to getEnrichedGO and getEnrichedPATH.

ChIPpeakAnno 3.27.7

• Fix the error "!anyNA(m32) is not TRUE" in seqlevelsStyle is not handled.

ChIPpeakAnno 3.27.6

• Fix the error "pvalue" undefined columns selected in enrichmentPlot

ChIPpeakAnno 3.27.5

• update documentation of pipeline.rmd

ChIPpeakAnno 3.27.4

• use formatSeqnames function to handle the error from seqlevelsStyle: "cannot switch some of GRCm38's seqlevels from NCBI to UCSC style"

ChIPpeakAnno 3.27.3

• use formatSeqnames function to handle the error from seqlevelsStyle: "!anyNA(m31) is not TRUE "

ChIPpeakAnno 3.27.2

• add keepExonsInGenesOnly for genomicElementDistribution
• add upstream and downstream for assignChromosomeRegion function when define promoter and downstream regions.

ChIPpeakAnno 3.27.1

• Add the possibility of find overlaps by percentage covered of interval for function findOverlapsOfPeaks

ChIPpeakAnno 3.25.6

• Fix a bug in estLibSize introduced by last push.

ChIPpeakAnno 3.25.5

• Add LazyDataCompression in description

ChIPpeakAnno 3.25.4

• Add choice endMinusStart to annotatePeakInBatch.

ChIPpeakAnno 3.25.3

• fix the missing link of documentation for rtracklyaer:import.

ChIPpeakAnno 3.25.2

• update documentation.
• update findEnhancers to for known interaction data

ChIPpeakAnno 3.25.1

• fix the bug for genomicElementDistribution when the peak length is zero.

ChIPpeakAnno 3.23.12

• fix the bug for genomicElementDistribution when the order of SortedByQueryHits is incorrect.

ChIPpeakAnno 3.23.11

• use seqlevelsStyle to reformat the seqlevels for annotation.

ChIPpeakAnno 3.23.10

• update documentation for genomicElementDistribution

ChIPpeakAnno 3.23.9

• add new function enrichmentPlot, genomicElementDistribution, genomicElementUpSetR, and methagenePlot to improve visualization.

ChIPpeakAnno 3.23.8

• update documentation for findOverlapsOfPeaks.

ChIPpeakAnno 3.23.7

• update documentation for findOverlapsOfPeaks.

ChIPpeakAnno 3.23.6

• change parameter from otherCount to otherCounts to makeVennDiagram function.

ChIPpeakAnno 3.23.5

• add plot parameter to makeVennDiagram function.

ChIPpeakAnno 3.23.4

• update README file.

ChIPpeakAnno 3.23.3

• use roxygen2 to generate the help file.
• move multiple package from Imports to Suggests.

ChIPpeakAnno 3.23.2

• fix the issue for new paste output.

ChIPpeakAnno 3.23.1

• remove dependence of Rfast

ChIPpeakAnno 3.21.7

• Fix a potentical bug reported by millerh1.

ChIPpeakAnno 3.21.6

• add new function findMotifsInPromoterSeqs. HANGES IN VERSION 3.21.5
• replace all 'class' by 'is'.

ChIPpeakAnno 3.21.4

• Fix a bug in getAllPeakSequence when there is peak out side of genome.

ChIPpeakAnno 3.21.3

• Update function summarizePatternInPeaks.

ChIPpeakAnno 3.21.2

• Add function getGO.

ChIPpeakAnno 3.21.1

• remove RangedData from ChIPpeakAnno.

ChIPpeakAnno 3.19.5

• fix the issue that findOverlapsOfPeaks will connect the peaks in same peak list.

ChIPpeakAnno 3.19.4

• add last choice for xget.

ChIPpeakAnno 3.19.3

• fix the colnames of addMetadata.

ChIPpeakAnno 3.19.2

• fix the issue that seqlevelsStyle(peak) == seqlevelsStyle(annotation) are not all TRUE

ChIPpeakAnno 3.19.1

• remove RangedData

ChIPpeakAnno 3.17.2

• fix a bug in toGRanges to accept GTF files.

ChIPpeakAnno 3.17.1

• fix the bug in annotatePeakInBatch which can not accept bindingType parameter.

ChIPpeakAnno 3.15.2

• fix the bug in binOverRegions and binOverGene

ChIPpeakAnno 3.15.1

• Fix the bug in assignChromosomeRegion for the Jaccard index calculation.

ChIPpeakAnno 3.13.19

• Fix the bug in assignChromosomeRegion for the percentage calculation when nucleotideLevel equal to true.

ChIPpeakAnno 3.13.18

• Fix the bug in assignChromosomeRegion for resetting seqlevels.

ChIPpeakAnno 3.13.17

• Fix the bug in annoScore by setting the ignore.strand for punion.

ChIPpeakAnno 3.13.16

• Fix the bug in assignChromosomeRegion for the integer overflow.

ChIPpeakAnno 3.13.14

• Fix the warnings under windows.

ChIPpeakAnno 3.13.12

• Change "class" function to "is" function.

ChIPpeakAnno 3.13.11

• Fix the help file for assignChromosomeRegion.

ChIPpeakAnno 3.13.10

• Improve binOverRegions.

ChIPpeakAnno 3.13.9

• Improve addMetadata.

ChIPpeakAnno 3.13.8

• Fix the warnings under windows.

ChIPpeakAnno 3.13.6

• Improve the functions featureAlignedSignal and featureAlignedExtendSignal

ChIPpeakAnno 3.13.5

• add minFragmentSize parameter to estFragmentLength

ChIPpeakAnno 3.13.4

• suppress the message from featureAlignedExtendSignal
• modified help files to make the samples run on local test.

ChIPpeakAnno 3.13.3

• fix the bug in binOverRegions and binOverGene

ChIPpeakAnno 3.13.2

• featureAlignedSignal generate outputs with rownames

ChIPpeakAnno 3.13.1

• change the test value from GNAI3;MIR197 to GNAI3 to avoid the error because of update of annotation database.

ChIPpeakAnno 3.11.8

• make featureAlignedExtendSignal accept GAlignments list object

ChIPpeakAnno 3.11.6

• fix the bugs Codoc mismatches from documentation object 'peakPermTest'

ChIPpeakAnno 3.11.4

• fix the bugs when annoMcols is numeric values.

ChIPpeakAnno 3.11.3

• update the function featureAlignedSignal

ChIPpeakAnno 3.11.2

• add new function binOverGene, binOverRegions, plotBinOverRegions.

ChIPpeakAnno 3.11.1

• make FAQs availble
• Fix the bug in annoPeaks for warning of out-of-bound ranges

ChIPpeakAnno 3.9.19

• add FAQs

ChIPpeakAnno 3.9.18

• import rowRanges() generic from DelayedArray instead of SummarizedExperiment

ChIPpeakAnno 3.9.17

• Improve the function featureAlignedExtendSignal

ChIPpeakAnno 3.9.16

• Fix the bug that unable to find an inherited method for function 'reverseComplement' for signature '"BString"' in oligoSummary function.

ChIPpeakAnno 3.9.14

• re-order the signals for cumulativePercentage.

ChIPpeakAnno 3.9.13

• add new function cumulativePercentage.

ChIPpeakAnno 3.9.12

• remove unused code in oligoSummary.

ChIPpeakAnno 3.9.11

• update the documents of featureAlignedSignal.

ChIPpeakAnno 3.9.10

• fix the bug of featureAlignedSignal when there are seqnames in featues but not in cvglists.

ChIPpeakAnno 3.9.9

• add 2 more parameters to getEnrichedGO

ChIPpeakAnno 3.9.8

• update the colnames of toGRanges

ChIPpeakAnno 3.9.7

• fix the bug of findOverlapsOfPeaks when the peaks are exactly same

ChIPpeakAnno 3.9.6

• fix the bug of findOverlapsOfPeaks when there is no peak names for peaklist

ChIPpeakAnno 3.9.5

• update the documents of findOverlapsOfPeaks

ChIPpeakAnno 3.9.4

• update the documents of getEnrichedGO
• add more output for findOverlapsOfPeaks.

ChIPpeakAnno 3.9.3

• trim seqnames when using toGRanges

ChIPpeakAnno 3.9.2

• add adjustFragmentLength for featureAlignedExtendSignal.

ChIPpeakAnno 3.9.1

• fix the bug for pair end reads for featureAlignedExtendSignal.

ChIPpeakAnno 3.7.9

• fix the problem in the test when there are names for target but not for current.

ChIPpeakAnno 3.7.8

• remove the dependence of MMDiffBamSubset in documentation becuase it is not availble now.

ChIPpeakAnno 3.7.7

• fix bugs for toGRanges to import MACS2 broad calls.

ChIPpeakAnno 3.7.6

• add new functions tileGRanges, tileCount

ChIPpeakAnno 3.7.5

• add parameter select to annoPeaks

ChIPpeakAnno 3.7.3

• add new function featureAlignedExtendSignal, estLibSize, estFragmentLength

ChIPpeakAnno 3.7.2

• Correct typo in documentation for Z-score.
• Improve the efficiency of findOverlapsOfPeaks.

ChIPpeakAnno 3.5.18

• Fix the bugs for featureAlignedSignal when features contain strand info.

ChIPpeakAnno 3.5.17

• Fix the bugs for getEnrichedGO/PATH when recodes in database such as reactome database is not unique.

ChIPpeakAnno 3.5.16

• fix the warning in windows for replacing previous import

ChIPpeakAnno 3.5.15

• not do log2 transform for featureAlignedSingal

ChIPpeakAnno 3.5.14

• remove NA for featureAlignedDistribution
• handle NA and infinite value for featureAlignedSingal

ChIPpeakAnno 3.5.13

• throw message when seqlevels are not identical for featureAlignedSignal

ChIPpeakAnno 3.5.12

• add new function summarizeOverlapsByBins.

ChIPpeakAnno 3.5.11

• clean output of findEnhancers

ChIPpeakAnno 3.5.10

• add new function findEnhancers
• normalize the output of gene region for binOverFeature
• change the documentation to avoid time-out error

ChIPpeakAnno 3.5.9

• merge peaksNearBDP and bdp function.
• improve oligoSummary.
• update the documentations.

ChIPpeakAnno 3.5.8

• change toGRanges from function to method
• update the documentations.

ChIPpeakAnno 3.5.7

• change test from RUnit to testthat
• add new function addMetadata
• change the output and parameters of annoPeaks
• simple the parameter output of annotatePeakInBatch
• allow bdp function to accept GRanges annotation
• add error bar function for binOverFeature function
• remove the log file after plot for makeVennDiagram function
• add private function trimPeakList
• update the documentation of annoPeaks and annotatePeakInBatch

ChIPpeakAnno 3.5.5

• update the documentation to fix the typo in quickStart.
• change the default value of annoPeaks.
• update annoGR class to fix the error: identical(colnames(classinfo), colnames(out)) is not TRUE

ChIPpeakAnno 3.5.2

• update the documentation to fix the error on windows (import bigwig error)
• avoid the output of addGeneIDs as factors

ChIPpeakAnno 3.5.1

• update the documentation NEW FEATURE
• toGRanges can accept connection object
• add annoPeaks function
• add xget function
• update the peakPermTest algorithm to make more reasonable result.
• add oligoSummary function
• add IDRfilter function
• add reCenterPeaks function

ChIPpeakAnno 3.3.8

• update the documentation

ChIPpeakAnno 3.3.7

FIX BUGS

• fix the problem in creating vignettes in linux platform.

ChIPpeakAnno 3.3.6

NEW FEATURE

• add new function featureAlignedSignal, featureAlignedDistribution, featureAlignedHeatmap, pie1
• add new dataset HOT.spots, wgEncodeTfbsV3
• update annoGR class
• update vignettes

ChIPpeakAnno 3.3.5

NEW FEATURE

• remove all the RangedData
• add annoGR class
• update vignettes

ChIPpeakAnno 3.3.4

NEW FEATURE

• toGRanges from MACS2, narrowPeak.
• calculate the p value of overlapping peaks by reagioneR
• update documentation

ChIPpeakAnno 3.3.3

NEW FEATURE

• mergePlusMinusPeaks

ChIPpeakAnno 3.3.2

NEW FEATURE

• update citation

ChIPpeakAnno 3.3.1

NEW FEATURE

• add new citation

ChIPpeakAnno 3.0.1

BUG FIXES

• give errors when inputs of addGeneIDs is incorrect.

ChIPpeakAnno 3.0.0

NEW FEATURE

• From RangedData to Granges
• High efficiency
• Find Overlaps for more than 2 groups
• Add Utility test
• Add new function binOverFeature, egOrgMap.

ChIPpeakAnno 2.17.2

NEW FEATURE

• add byBase for makeVennDiagram.

ChIPpeakAnno 2.12.3

BUG FIXES

• relative postion for negative strand are not correct when call findOverlappingPeaks.

ChIPpeakAnno 2.11.4

NEW FEATURE

• Add selection of 'shortestDistance' to output parameter of annotatePeakInBatch.
• Add selection of 'shortestDistance' to output parameter of annotatePeakInBatch.

ChIPpeakAnno 2.11.3

NEW FEATURE

• Improved efficiency of annotatePeakInBatch.

ChIPpeakAnno 2.9.6

BUG FIXES

• Changed Enhancer.Silencer to intergenic.Region in assignChromosomeRegion.

ChIPpeakAnno 2.9.5

BUG FIXES

• negative widths are not allowed when call findOverlappingPeaks.

NEW FEATURES IN VERSION 2.2.0

• Find the peaks with bi-directional promoters with summary statistics (peaksNearBDP).
• Summarize the occurrence of motifs in peaks (summarizePatternInPeaks).
• Add other IDs to annotated peaks or enrichedGO (addGeneIDs)The function makeVennDiagram supports 4-way venn diagram.
• Enriched Gene Ontology (GO) terms are annotated with a list of genes which can be traced back to peaks.
• FAQ: http://pgfe.umassmed.edu/ChIPpeakAnno/FAQ.html.
• Summarize peak distribution over exon, intron, enhancer, proximal promoter, 5 prime UTR and 3 prime UTR (assignChromosomeRegion)