obtain the peaks near bi-directional promoters
Find the overlapped peaks among two or more set of peaks.
Find the overlapping peaks for two peak ranges.
Output a summary of consensus in the peaks
Permutation Test for two given peak lists
High Occupancy of Transcription Related Factors regions
Convert GFF format to RangedData
Add GO IDs of the ancestors for a given vector of GO ids
Add common IDs to annotated peaks such as gene symbol, entrez ID, ensemble gene
id and refseq id.
Convert BED format to RangedData
Convert dataset to GRanges
Batch annotation of the peaks identified from either ChIP-seq or
ChIP-chip experiments.
translate pattern from IUPAC Extended Genetic Alphabet to regular expression
Deprecated Functions in Package ChIPpeakAnno
Enriched Gene Ontology terms used as example
Obtain the TSS, exon or miRNA annotation for the specified species
Gene model with exon, 5' UTR and 3' UTR information for human sapiens (GRCh37)
obtained from biomaRt
Make Venn Diagram from a list of peaks
Obtain enriched gene ontology (GO) terms that near the peaks
Merge peaks from plus strand and minus strand
prepare data for permutation test
re-center the peaks
Class "permPool"
Pie Charts
TSS annotation data for mouse (NCBIM37) obtained from biomaRt
TSS annotation data for rat (RGSC3.4) obtained from biomaRt
Add metadata of the GRanges objects used for findOverlapsOfPeaks
Class annoGR
get the count for each unique GO ID
Obtain Venn Counts for Venn Diagram, internal function for makeVennDigram
obtain the peaks near bi-directional promoters
TSS annotation for human sapiens (NCBI36) obtained from biomaRt
Ste12-binding sites from biological replicate 3 in yeast (see reference)
TSS annotation data for Mus musculus (GRCm38.p1) obtained from biomaRt
transcription factor binding site clusters (V3) from ENCODE
TSS annotation for Danio rerio (Zv9) obtained from biomaRt
Obtain the distance to the nearest TSS, miRNA, and/or exon for a list
of peaks
Summarize peak distribution over exon, intron, enhancer, proximal promoter,
5 prime UTR and 3 prime UTR
Condense matrix by colnames
Convert other common IDs to entrez gene ID.
Find possible enhancers depend on DNA interaction data
extract signals in given ranges
Obtain enriched PATH that near the peaks
Get gene sequence using the biomaRt package
TSS annotation for human sapiens (GRCh38) obtained from biomaRt
TSS annotation for human sapiens (GRCh37) obtained from biomaRt
Class "bindist"
featureAlignedDistribution
plot distribution in given ranges
Aggregate peaks over bins from the TSS
Heatmap representing signals in given ranges
Ste12-binding sites from biological replicate 1 in yeast (see reference)
Ste12-binding sites from biological replicate 2 in yeast (see reference)
Perform overlap queries between reads and genomic features by bins
Output a summary of the occurrence of each pattern in the sequences.
TSS annotation data for zebrafish (Zv8) obtained from biomaRt
TSS annotation data for Rattus norvegicus (Rnor_5.0) obtained from biomaRt
Annotate peaks
Annotated Peaks
Output total number of patterns found in the input sequences
Convert between the name of the organism annotation package ("OrgDb")
and the name of the organism.
Obtain Venn Counts for Venn Diagram, internal function for makeVennDigram
Obtain genomic sequences around the peaks
Filter peaks by IDR (irreproducible discovery rate)
hypergeometric test
An example GRanges object representing a ChIP-seq peak dataset
get the oligonucleotide frequency
Write sequences to a file in fasta format
Return the value from a Bimap objects