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