| annotatePeakInBatch |
Obtain the distance to the nearest TSS, miRNA, and/or exon for a list
of peaks |
| convert2EntrezID |
Convert other common IDs to entrez gene ID.
|
| countPatternInSeqs |
Output total number of patterns found in the input sequences
|
| getUniqueGOidCount |
get the count for each unique GO ID |
| peakPermTest |
Permutation Test for two given peak lists
|
| getVennCounts |
Obtain Venn Counts for Venn Diagram, internal function for makeVennDigram
|
| Peaks.Ste12.Replicate1 |
Ste12-binding sites from biological replicate 1 in yeast (see reference)
|
| assignChromosomeRegion |
Summarize peak distribution over exon, intron, enhancer, proximal promoter,
5 prime UTR and 3 prime UTR
|
| TSS.rat.Rnor_5.0 |
TSS annotation data for Rattus norvegicus (Rnor_5.0) obtained from biomaRt
|
| TSS.rat.RGSC3.4 |
TSS annotation data for rat (RGSC3.4) obtained from biomaRt
|
| BED2RangedData |
Convert BED format to RangedData |
| bindist-class |
Class "bindist" |
| featureAlignedHeatmap |
Heatmap representing signals in given ranges
|
| featureAlignedSignal |
extract signals in given ranges
|
| ChIPpeakAnno-package |
Batch annotation of the peaks identified from either ChIP-seq or
ChIP-chip experiments.
|
| findOverlapsOfPeaks |
Find the overlapped peaks among two or more set of peaks.
|
| findOverlappingPeaks |
Find the overlapping peaks for two peak ranges.
|
| translatePattern |
translate pattern from IUPAC Extended Genetic Alphabet to regular expression
|
| condenseMatrixByColnames |
Condense matrix by colnames
|
| getEnrichedGO |
Obtain enriched gene ontology (GO) terms that near the peaks |
| hyperGtest |
hypergeometric test |
| getAnnotation |
Obtain the TSS, exon or miRNA annotation for the specified species |
| makeVennDiagram |
Make Venn Diagram from a list of peaks
|
| TSS.human.GRCh37 |
TSS annotation for human sapiens (GRCh37) obtained from biomaRt
|
| ChIPpeakAnno-deprecated |
Deprecated Functions in Package ChIPpeakAnno
|
| egOrgMap |
Convert between the name of the organism annotation package ("OrgDb")
and the name of the organism.
|
| binOverFeature |
Aggregate peaks over bins from the TSS
|
| enrichedGO |
Enriched Gene Ontology terms used as example
|
| getEnrichedPATH |
Obtain enriched PATH that near the peaks |
| getGeneSeq |
Get gene sequence using the biomaRt package |
| GFF2RangedData |
Convert GFF format to RangedData |
| HOT.spots |
High Occupancy of Transcription Related Factors regions
|
| summarizePatternInPeaks |
Output a summary of the occurrence of each pattern in the sequences.
|
| toGRanges |
Convert dataset to GRanges
|
| preparePool |
prepare data for permutation test
|
| pie1 |
Pie Charts
|
| wgEncodeTfbsV3 |
transcription factor binding site clusters (V3) from ENCODE
|
| write2FASTA |
Write sequences to a file in fasta format |
| 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.
|
| ExonPlusUtr.human.GRCh37 |
Gene model with exon, 5' UTR and 3' UTR information for human sapiens (GRCh37)
obtained from biomaRt
|
| mergePlusMinusPeaks |
Merge peaks from plus strand and minus strand |
| featureAlignedDistribution |
plot distribution in given ranges
|
| myPeakList |
An example GRanges object representing a ChIP-seq peak dataset |
| permPool-class |
Class "permPool" |
| peaksNearBDP |
obtain the peaks near bi-directional promoters |
| TSS.zebrafish.Zv8 |
TSS annotation data for zebrafish (Zv8) obtained from biomaRt
|
| TSS.zebrafish.Zv9 |
TSS annotation for Danio rerio (Zv9) obtained from biomaRt
|
| annoGR-class |
Class annoGR
|
| findVennCounts |
Obtain Venn Counts for Venn Diagram, internal function for makeVennDigram
|
| annotatedPeak |
Annotated Peaks |
| 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)
|
| TSS.human.GRCh38 |
TSS annotation for human sapiens (GRCh38) obtained from biomaRt
|
| TSS.human.NCBI36 |
TSS annotation for human sapiens (NCBI36) obtained from biomaRt
|
| getAllPeakSequence |
Obtain genomic sequences around the peaks
|
| TSS.mouse.NCBIM37 |
TSS annotation data for mouse (NCBIM37) obtained from biomaRt
|
| TSS.mouse.GRCm38 |
TSS annotation data for Mus musculus (GRCm38.p1) obtained from biomaRt
|
| No Results! |