ChIPpeakAnno-package |
Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. |
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. |
annotatedPeak |
Annotated Peaks |
annotatePeakInBatch |
obtain the distance to the nearest TSS, miRNA, exon et al for a list of peak intervals |
assignChromosomeRegion |
Summarizing peak distribution over exon, intron, enhancer, proximal promoter, 5 prime UTR and 3 prime UTR |
BED2RangedData |
convert BED format to RangedData |
binOverFeature |
peak aggregation over bins from TSS |
ChIPpeakAnno |
Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. |
ChIPpeakAnno-deprecated |
Deprecated Functions in Package ChIPpeakAnno |
condenseMatrixByColnames |
condense matrix by colnames |
convert2EntrezID |
Convert other common IDs such as ensemble gene id, gene symbol, refseq id to entrez gene ID. |
countPatternInSeqs |
Output total number of patterns found in the input sequences |
egOrgMap |
map organism annotation dataset to specie name or revese. |
enrichedGO |
Enriched Gene Ontology terms used as example |
ExonPlusUtr.human.GRCh37 |
Gene model with exon, 5' UTR and 3' UTR information for human sapiens (GRCh37) obtained from biomaRt |
findOverlappingPeaks |
Find the overlapping peaks for two peak ranges. |
findOverlappingPeaks-deprecated |
Find the overlapping peaks for two peak ranges. |
findOverlapsOfPeaks |
Find the overlapping peaks for two or more peak ranges. |
findVennCounts |
Obtain Venn Counts for Venn Diagram, internal function for makeVennDigram |
getAllPeakSequence |
Obtain genomic sequences around the peaks |
getAnnotation |
Obtain the TSS, exon or miRNA annotation for the specified species |
getEnrichedGO |
Obtain enriched gene ontology (GO) terms that near the peaks |
getEnrichedPATH |
Obtain enriched PATH that near the peaks |
getVennCounts |
Obtain Venn Counts for Venn Diagram, internal function for makeVennDigram |
GFF2RangedData |
convert GFF format to RangedData |
makeVennDiagram |
Make Venn Diagram from two peak ranges |
myPeakList |
ChIP-seq peak dataset |
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) |
Peaks.Ste12.Replicate3 |
Ste12-binding sites from biological replicate 3 in yeast (see reference) |
peaksNearBDP |
obtain the peaks near bi-directional promoters |
summarizePatternInPeaks |
Output a summary of the occurrence of each pattern in the sequences. |
toGRanges |
Convert dataset to GRanges |
translatePattern |
translate pattern from IUPAC Extended Genetic Alphabet to regular expression |
TSS.human.GRCh37 |
TSS annotation for human sapiens (GRCh37) obtained from biomaRt |
TSS.human.GRCh38 |
TSS annotation for human sapiens (GRCh38) obtained from biomaRt |
TSS.human.NCBI36 |
TSS annotation for human sapiens (NCBI36) obtained from biomaRt |
TSS.mouse.GRCm38 |
TSS annotation data for Mus musculus (GRCm38.p1) obtained from biomaRt |
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 from biomaRt |
TSS.zebrafish.Zv8 |
TSS annotation data for zebrafish (Zv8) obtained from biomaRt |
TSS.zebrafish.Zv9 |
TSS annotation for Danio rerio (Zv9) obtained from biomaRt |
write2FASTA |
write sequences to a file in fasta format |