Chromatin segmentation in R. For a full description and for citing us, see the following article on Genome Biology:

A Mammana, HR Chung (2015). Chromatin segmentation based on a probabilistic model for read counts explains a large portion of the epigenome. Genome Biology 2015, 16:151

For using EpiCSeg from the command line, you can find the full manual HERE!

epicseg needs R 3.2 (or newer) and depends on Bioconductor packages, CRAN packages, and another package from github. For the installation, most of the work is done by the function devtools::install_github. Because lately this function cannot resolve Bioconductor dependencies anymore (see this issue: r-lib/devtools#700), we will need to install some Bioconductor packages manually.

The Bioconductor dependencies are IRanges, GenomicRanges, bamsignals and edgeR. At the interactive R terminal, type:

source("http://bioconductor.org/biocLite.R")
biocLite(c("IRanges", "GenomicRanges", "bamsignals", "edgeR"))

Install and load the devtools package to be able to directly install R packages hosted on github :

install.packages("devtools")
library(devtools)

To install epicseg type:

install_github("lamortenera/kfoots")
install_github("lamortenera/epicseg")

To use EpiCSeg from the command line, you need to:

1. create a launcher to be used with Rscript. This is done by typing epicseg:::getLauncher("epicseg.R") at the R interactive terminal, which will create the file epicseg.R in your working directory. You can move and rename this file the way you want.
2. To use it, type Rscript epicseg.R subprogram arguments. In UNIX you can also simply do ./epicseg.R subprogram arguments provided that you have execution permission on the file .epicseg.R.
3. To see what the available subprograms are, simply type: Rscript epicseg.R
4. To see which arguments each subprogram needs, you can type: Rscript epicseg.R subprogram