ChIPpeakAnno-package |
Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. |
$-method |
Class '"bindist"' |
$-method |
Class '"permPool"' |
$<--method |
Class '"bindist"' |
$<--method |
Class '"permPool"' |
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. |
annoGR |
Class 'annoGR' |
annoGR-class |
Class 'annoGR' |
annoGR-method |
Class 'annoGR' |
annotatedPeak |
Annotated Peaks |
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 |
BED2RangedData |
Convert BED format to RangedData |
BED2RangedData-deprecated |
Convert BED format to RangedData |
bindist |
Class '"bindist"' |
bindist-class |
Class '"bindist"' |
bindist-method |
Class '"bindist"' |
binOverFeature |
Aggregate peaks over bins from the TSS |
ChIPpeakAnno |
Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. |
ChIPpeakAnno-deprecated |
Deprecated Functions in Package ChIPpeakAnno |
coerce-method |
Class 'annoGR' |
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 ("OrgDb") and the name of the organism. |
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 |
featureAlignedDistribution |
plot distribution in given ranges |
featureAlignedHeatmap |
Heatmap representing signals in given ranges |
featureAlignedSignal |
extract signals in given ranges |
findOverlappingPeaks |
Find the overlapping peaks for two peak ranges. |
findOverlappingPeaks-deprecated |
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 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 |
GFF2RangedData-deprecated |
Convert GFF format to RangedData |
HOT.spots |
High Occupancy of Transcription Related Factors regions |
info |
Class 'annoGR' |
info-method |
Class 'annoGR' |
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 dataset |
peakPermTest |
Permutation Test for two given peak lists |
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 |
permPool |
Class '"permPool"' |
permPool-class |
Class '"permPool"' |
permPool-method |
Class '"permPool"' |
pie1 |
Pie Charts |
preparePool |
prepare data for permutation test |
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 |
wgEncodeTfbsV3 |
transcription factor binding site clusters (V3) from ENCODE |
write2FASTA |
Write sequences to a file in fasta format |