recipe epicseg

EpiCSeg (Epigenome Count-based Segmentation) is a software for annotating the genome based on the state of the chromatin. It provides tools for extracting count data from BAM files, typlically corresponding to ChIP-seq experiments for histone marks (but other choices are possible) it learns a statistical model for the read counts based on a HMM, it annotates the genome, and it provides tools for displaying and analyzing the obtained models and segmentations. EpiCSeg can be used as an R package or from the command line via Rscript.

Homepage

http://github.com/lamortenera/epicseg

License

GPL-3

Recipe

/epicseg/meta.yaml

package epicseg

(downloads) docker_epicseg

Versions

1.0-2, 1.0-1, 1.0-0

Depends bioconductor-bamsignals

Depends bioconductor-edger

Depends bioconductor-genomicranges

Depends bioconductor-iranges

Depends bioconductor-s4vectors

Depends kfoots

Depends libgcc-ng

>=7.3.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-rcolorbrewer

Depends r-rcpp

>=0.10.6

Requirements

Installation

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

conda install epicseg

and update with:

conda update epicseg

or use the docker container:

docker pull quay.io/biocontainers/epicseg:<tag>

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