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.
|Author||Lihua Julie Zhu, Jianhong Ou, Jun Yu, Herve Pages, Claude Gazin, Nathan Lawson, Ryan Thompson, Simon Lin, David Lapointe and Michael Green|
|Date of publication||None|
|Maintainer||Lihua Julie Zhu <firstname.lastname@example.org>, Jianhong Ou <Jianhong.email@example.com>|
|License||GPL (>= 2)|
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...
addMetadata: Add metadata of the GRanges objects used for...
annoGR: Class 'annoGR'
annoPeaks: Annotate peaks
annotatedPeak: Annotated Peaks
annotatePeakInBatch: Obtain the distance to the nearest TSS, miRNA, and/or exon...
assignChromosomeRegion: Summarize peak distribution over exon, intron, enhancer,...
bdp: obtain the peaks near bi-directional promoters
BED2RangedData: Convert BED format to RangedData
bindist: Class '"bindist"'
binOverFeature: Aggregate peaks over bins from the TSS
ChIPpeakAnno-deprecated: Deprecated Functions in Package ChIPpeakAnno
ChIPpeakAnno-package: Batch annotation of the peaks identified from either ChIP-seq...
condenseMatrixByColnames: Condense matrix by colnames
convert2EntrezID: Convert other common IDs to entrez gene ID.
countPatternInSeqs: Output total number of patterns found in the input sequences
egOrgMap: Convert between the name of the organism annotation package...
enrichedGO: Enriched Gene Ontology terms used as example
estFragmentLength: estimate the fragment length
estLibSize: estimate the library size
ExonPlusUtr.human.GRCh37: Gene model with exon, 5' UTR and 3' UTR information for human...
featureAlignedDistribution: plot distribution in given ranges
featureAlignedExtentSignal: extract signals in given ranges from bam files
featureAlignedHeatmap: Heatmap representing signals in given ranges
featureAlignedSignal: extract signals in given ranges
findEnhancers: Find possible enhancers depend on DNA interaction data
findOverlappingPeaks: Find the overlapping peaks for two peak ranges.
findOverlapsOfPeaks: Find the overlapped peaks among two or more set of peaks.
findVennCounts: Obtain Venn Counts for Venn Diagram, internal function for...
getAllPeakSequence: Obtain genomic sequences around the peaks
getAnnotation: Obtain the TSS, exon or miRNA annotation for the specified...
getEnrichedGO: Obtain enriched gene ontology (GO) terms that near the peaks
getEnrichedPATH: Obtain enriched PATH that near the peaks
getGeneSeq: Get gene sequence using the biomaRt package
getUniqueGOidCount: get the count for each unique GO ID
getVennCounts: Obtain Venn Counts for Venn Diagram, internal function for...
GFF2RangedData: Convert GFF format to RangedData
HOT.spots: High Occupancy of Transcription Related Factors regions
hyperGtest: hypergeometric test
IDRfilter: Filter peaks by IDR (irreproducible discovery rate)
makeVennDiagram: Make Venn Diagram from a list of peaks
mergePlusMinusPeaks: Merge peaks from plus strand and minus strand
myPeakList: An example GRanges object representing a ChIP-seq peak...
oligoFrequency: get the oligonucleotide frequency
oligoSummary: Output a summary of consensus in the peaks
peakPermTest: Permutation Test for two given peak lists
peaksNearBDP: obtain the peaks near bi-directional promoters
Peaks.Ste12.Replicate1: Ste12-binding sites from biological replicate 1 in yeast (see...
Peaks.Ste12.Replicate2: Ste12-binding sites from biological replicate 2 in yeast (see...
Peaks.Ste12.Replicate3: Ste12-binding sites from biological replicate 3 in yeast (see...
permPool: Class '"permPool"'
pie1: Pie Charts
preparePool: prepare data for permutation test
reCenterPeaks: re-center the peaks
summarizeOverlapsByBins: Perform overlap queries between reads and genomic features by...
summarizePatternInPeaks: Output a summary of the occurrence of each pattern in the...
tileCount: Perform overlap queries between reads and genome by windows
tileGRanges: Slide windows on a given GRanges object
toGRanges: Convert dataset to GRanges
translatePattern: translate pattern from IUPAC Extended Genetic Alphabet to...
TSS.human.GRCh37: TSS annotation for human sapiens (GRCh37) obtained from...
TSS.human.GRCh38: TSS annotation for human sapiens (GRCh38) obtained from...
TSS.human.NCBI36: TSS annotation for human sapiens (NCBI36) obtained from...
TSS.mouse.GRCm38: TSS annotation data for Mus musculus (GRCm38.p1) obtained...
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
TSS.rat.Rnor_5.0: TSS annotation data for Rattus norvegicus (Rnor_5.0) obtained...
TSS.zebrafish.Zv8: TSS annotation data for zebrafish (Zv8) obtained from biomaRt
TSS.zebrafish.Zv9: TSS annotation for Danio rerio (Zv9) obtained from biomaRt
wgEncodeTfbsV3: transcription factor binding site clusters (V3) from ENCODE
write2FASTA: Write sequences to a file in fasta format
xget: Return the value from a Bimap objects