recipe bioconductor-chipseeker

This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.







biotools: chipseeker

package bioconductor-chipseeker

(downloads) docker_bioconductor-chipseeker


1.18.0-0, 1.16.1-0, 1.14.2-0, 1.14.0-0, 1.12.1-0, 1.10.0-0, 1.6.6-0

Depends bioconductor-annotationdbi


Depends bioconductor-biocgenerics


Depends bioconductor-enrichplot


Depends bioconductor-genomeinfodb


Depends bioconductor-genomicfeatures


Depends bioconductor-genomicranges


Depends bioconductor-iranges


Depends bioconductor-rtracklayer


Depends bioconductor-s4vectors


Depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene


Depends r-base


Depends r-boot

Depends r-dplyr

Depends r-ggplot2


Depends r-gplots

Depends r-gridbase

Depends r-gtools

Depends r-magrittr

Depends r-plotrix

Depends r-rcolorbrewer

Depends r-upsetr



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

conda install bioconductor-chipseeker

and update with:

conda update bioconductor-chipseeker

or use the docker container:

docker pull<tag>

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