recipe behst

BEHST reads an input dataset of chromosome regions, and intersects them with the chromatin interactions available in the Hi-C dataset. Of these chromosome regions, BEHST selects those that are presentthe regulatory regions of genes of APPRIS, a dataset of principal isoform annotations. We defined these cis-regulatory regions upon the position of their nearest transcription start site of the APPRIS genes’ principal transcripts (obtained through GENCODE), plus an upstream and downstream extension. Afterwards, BEHST takes the genes of the resulting partner loci found in gene regulatory regions, and performs a gene set enrichment analysis on them through g:Profiler. BEHST, finally, outputs the list of the most significant Gene Ontology terms detected by g:Profiler. Citation: Davide Chicco, Haixin Sarah Bi, Juri Reimand, and Michael M. Hoffman, ‘BEHST: Genomic set enrichment analysis enhanced through integration of chromatin long-range interactions’, 2018. In preparation. Website:






package behst

(downloads) docker_behst


3.7-1, 3.7-0, 3.6-0, 3.5-0, 3.0-0, 2.9-0, 2.8-0, 2.7-0, 2.6-0, 2.5-0, 1.9-0, 1.8-0, 1.7-0, 1.6-0, 1.4-0, 0.9-0, 0.8-0

Depends bedtools

Depends pandas

Depends pybedtools

Depends python

Depends r-base

Depends r-gprofiler

Depends r-rcurl

Depends wget



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

conda install behst

and update with:

conda update behst

or use the docker container:

docker pull<tag>

(see behst/tags for valid values for <tag>)