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NEWS
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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 2.11.4
------------------------
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)