recipe bioconductor-chippeakanno

The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. Starting 2.0.5, new functions have been added for finding the peaks with bi-directional promoters with summary statistics (peaksNearBDP), for summarizing the occurrence of motifs in peaks (summarizePatternInPeaks) and for adding other IDs to annotated peaks or enrichedGO (addGeneIDs). This package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages.



GPL (>= 2)




biotools: chippeakanno

package bioconductor-chippeakanno

(downloads) docker_bioconductor-chippeakanno


3.16.0-0, 3.14.2-0, 3.12.0-0, 3.10.2-0

Depends bioconductor-annotationdbi


Depends bioconductor-biobase


Depends bioconductor-biocgenerics


Depends bioconductor-biomart


Depends bioconductor-biostrings


Depends bioconductor-bsgenome


Depends bioconductor-delayedarray


Depends bioconductor-ensembldb


Depends bioconductor-genomeinfodb


Depends bioconductor-genomicalignments


Depends bioconductor-genomicfeatures


Depends bioconductor-genomicranges


Depends bioconductor-go.db


Depends bioconductor-graph


Depends bioconductor-iranges


Depends bioconductor-limma


Depends bioconductor-multtest


Depends bioconductor-rbgl


Depends bioconductor-regioner


Depends bioconductor-rsamtools


Depends bioconductor-s4vectors


Depends bioconductor-summarizedexperiment


Depends r-base


Depends r-biocmanager

Depends r-dbi

Depends r-idr

Depends r-matrixstats

Depends r-seqinr

Depends r-venndiagram



With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-chippeakanno

and update with:

conda update bioconductor-chippeakanno

or use the docker container:

docker pull<tag>

(see bioconductor-chippeakanno/tags for valid values for <tag>)