A B C D E F G H I M O P R S T W X misc
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. |
addMetadata | Add metadata of the GRanges objects used for findOverlapsOfPeaks |
annoGR | Class 'annoGR' |
annoGR-class | Class 'annoGR' |
annoGR-method | Class 'annoGR' |
annoPeaks | Annotate peaks |
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 |
bdp | obtain the peaks near bi-directional promoters |
bindist | Class '"bindist"' |
bindist-class | Class '"bindist"' |
bindist-method | Class '"bindist"' |
binOverFeature | Aggregate peaks over bins from the TSS |
binOverGene | coverage of gene body |
binOverRegions | coverage of chromosome regions |
ChIPpeakAnno | Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. |
ChIPpeakAnno-deprecated | Deprecated Functions in Package ChIPpeakAnno |
cntOverlaps | count overlaps |
coerce | Class 'annoGR' |
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 |
cumulativePercentage | Plot the cumulative percentage tag allocation in sample |
downstreams | Get downstream coordinates |
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 |
enrichmentPlot | plot enrichment results |
EnsDb2GR | EnsDb object to GRanges |
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 sapiens (GRCh37) obtained from biomaRt |
featureAlignedDistribution | plot distribution in given ranges |
featureAlignedExtendSignal | 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 |
findMotifsInPromoterSeqs | Find occurence of input motifs in the promoter regions of the input gene list |
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. |
genomicElementDistribution | Genomic Element distribution |
genomicElementUpSetR | Genomic Element data for upset plot |
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 |
getGO | Obtain gene ontology (GO) terms for given genes |
getVennCounts | Obtain Venn Counts for Venn Diagram, internal function for makeVennDigram |
HOT.spots | High Occupancy of Transcription Related Factors regions |
IDRfilter | Filter peaks by IDR (irreproducible discovery rate) |
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 |
metagenePlot | peak distance to features |
myPeakList | An example GRanges object representing a ChIP-seq peak dataset |
oligoFrequency | get the oligonucleotide frequency |
oligoSummary | Output a summary of consensus in the peaks |
overlappingPeaks | Find the overlapped peaks among two or more set of peaks. |
overlappingPeaks-class | Find the overlapped peaks among two or more set of peaks. |
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 |
plotBinOverRegions | plot the coverage of regions |
preparePool | prepare data for permutation test |
reCenterPeaks | re-center the peaks |
summarizeOverlapsByBins | Perform overlap queries between reads and genomic features by bins |
summarizePatternInPeaks | Output a summary of the occurrence of each pattern in the sequences. |
tileCount | Perform overlap queries between reads and genome by windows |
tileGRanges | Slide windows on a given GRanges object |
toGRanges | Convert dataset to GRanges |
toGRanges-method | 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 |
TxDb2GR | TxDb object to GRanges |
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 |
$-method | Class '"bindist"' |
$-method | Class '"permPool"' |
$<--method | Class '"bindist"' |
$<--method | Class '"permPool"' |
_PACKAGE | Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. |