ChIPpeakAnno v3.6.5

by Lihua Julie Zhu

Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. Starting 2.0.5, new functions have been added for finding the peaks with bi-directional promoters with summary statistics (peaksNearBDP), for summarizing the occurrence of motifs in peaks (summarizePatternInPeaks) and for adding other IDs to annotated peaks or enrichedGO (addGeneIDs). This package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages.

Functions in ChIPpeakAnno

Name Description
bdp obtain the peaks near bi-directional promoters
findOverlapsOfPeaks Find the overlapped peaks among two or more set of peaks.
findOverlappingPeaks Find the overlapping peaks for two peak ranges.
oligoSummary Output a summary of consensus in the peaks
peakPermTest Permutation Test for two given peak lists
HOT.spots High Occupancy of Transcription Related Factors regions
GFF2RangedData Convert GFF format to RangedData
addAncestors Add GO IDs of the ancestors for a given vector of GO ids
addGeneIDs Add common IDs to annotated peaks such as gene symbol, entrez ID, ensemble gene id and refseq id.
BED2RangedData Convert BED format to RangedData
toGRanges Convert dataset to GRanges
ChIPpeakAnno-package Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments.
translatePattern translate pattern from IUPAC Extended Genetic Alphabet to regular expression
ChIPpeakAnno-deprecated Deprecated Functions in Package ChIPpeakAnno
enrichedGO Enriched Gene Ontology terms used as example
getAnnotation Obtain the TSS, exon or miRNA annotation for the specified species
ExonPlusUtr.human.GRCh37 Gene model with exon, 5' UTR and 3' UTR information for human sapiens (GRCh37) obtained from biomaRt
makeVennDiagram Make Venn Diagram from a list of peaks
getEnrichedGO Obtain enriched gene ontology (GO) terms that near the peaks
mergePlusMinusPeaks Merge peaks from plus strand and minus strand
preparePool prepare data for permutation test
reCenterPeaks re-center the peaks
permPool-class Class "permPool"
pie1 Pie Charts
TSS.mouse.NCBIM37 TSS annotation data for mouse (NCBIM37) obtained from biomaRt
TSS.rat.RGSC3.4 TSS annotation data for rat (RGSC3.4) obtained from biomaRt
addMetadata Add metadata of the GRanges objects used for findOverlapsOfPeaks
annoGR-class Class annoGR
getUniqueGOidCount get the count for each unique GO ID
getVennCounts Obtain Venn Counts for Venn Diagram, internal function for makeVennDigram
peaksNearBDP obtain the peaks near bi-directional promoters
TSS.human.NCBI36 TSS annotation for human sapiens (NCBI36) obtained from biomaRt
Peaks.Ste12.Replicate3 Ste12-binding sites from biological replicate 3 in yeast (see reference)
TSS.mouse.GRCm38 TSS annotation data for Mus musculus (GRCm38.p1) obtained from biomaRt
wgEncodeTfbsV3 transcription factor binding site clusters (V3) from ENCODE
TSS.zebrafish.Zv9 TSS annotation for Danio rerio (Zv9) obtained from biomaRt
annotatePeakInBatch Obtain the distance to the nearest TSS, miRNA, and/or exon for a list of peaks
assignChromosomeRegion Summarize peak distribution over exon, intron, enhancer, proximal promoter, 5 prime UTR and 3 prime UTR
condenseMatrixByColnames Condense matrix by colnames
convert2EntrezID Convert other common IDs to entrez gene ID.
findEnhancers Find possible enhancers depend on DNA interaction data
featureAlignedSignal extract signals in given ranges
getEnrichedPATH Obtain enriched PATH that near the peaks
getGeneSeq Get gene sequence using the biomaRt package
TSS.human.GRCh38 TSS annotation for human sapiens (GRCh38) obtained from biomaRt
TSS.human.GRCh37 TSS annotation for human sapiens (GRCh37) obtained from biomaRt
bindist-class Class "bindist"
featureAlignedDistribution plot distribution in given ranges
binOverFeature Aggregate peaks over bins from the TSS
featureAlignedHeatmap Heatmap representing signals in given ranges
Peaks.Ste12.Replicate1 Ste12-binding sites from biological replicate 1 in yeast (see reference)
Peaks.Ste12.Replicate2 Ste12-binding sites from biological replicate 2 in yeast (see reference)
summarizeOverlapsByBins Perform overlap queries between reads and genomic features by bins
summarizePatternInPeaks Output a summary of the occurrence of each pattern in the sequences.
TSS.zebrafish.Zv8 TSS annotation data for zebrafish (Zv8) obtained from biomaRt
TSS.rat.Rnor_5.0 TSS annotation data for Rattus norvegicus (Rnor_5.0) obtained from biomaRt
annoPeaks Annotate peaks
annotatedPeak Annotated Peaks
countPatternInSeqs Output total number of patterns found in the input sequences
egOrgMap Convert between the name of the organism annotation package ("OrgDb") and the name of the organism.
findVennCounts Obtain Venn Counts for Venn Diagram, internal function for makeVennDigram
getAllPeakSequence Obtain genomic sequences around the peaks
IDRfilter Filter peaks by IDR (irreproducible discovery rate)
hyperGtest hypergeometric test
myPeakList An example GRanges object representing a ChIP-seq peak dataset
oligoFrequency get the oligonucleotide frequency
write2FASTA Write sequences to a file in fasta format
xget Return the value from a Bimap objects
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