- 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.
- package epicseg¶
- depends bioconductor-bamsignals:
- depends bioconductor-edger:
- depends bioconductor-genomicranges:
- depends bioconductor-iranges:
- depends bioconductor-s4vectors:
- depends kfoots:
- depends libgcc-ng:
- depends r-base:
- depends r-rcolorbrewer:
- depends r-rcpp:
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install epicseg and update with:: mamba update epicseg
To create a new environment, run:
mamba create --name myenvname epicseg
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).
Alternatively, use the docker container:
docker pull quay.io/biocontainers/epicseg:<tag> (see `epicseg/tags`_ for valid values for ``<tag>``)