histoneHMM

histoneHMM is a software to analyse ChIP-seq data of histone modifications with broad genomic footprints like H3K27me3. It allows for calling modified regions in single samples as well as for calling differentially modified regions in a comparison of two samples.

News

Version 1.7 is an update that works with the new Rcpp package (Verion > 0.12)

Version 1.6 fixes some smaller bugs and removes the dependency on the GNU scientific library

We released version 1.5 introduces a command line interface (see vignette), improved preprocessing and an updated vignette.

We have just released the new and improved version 1.4 with a high level interface for more convenience.

Installation

install.packages("devtools")
devtools::install_github("matthiasheinig/histoneHMM")

Usage

We provide a small test data set to try out the package:

Preprocessed data:

BN.txt

SHR.txt

Raw data:

BN.bam

BN.bam.bai

SHR.bam

SHR.bam.bai

chroms.txt : table of chromosome lengths

ensembl59-genes.gff : gene annotation in gff format (only gene bodies, no exon information)

expression.txt: RNA-seq gene expression

Highlevel interface

We have a new and improved version with a high level interface for more convenience. Please check out the package vignette:

histoneHMM.pdf

histoneHMM.R

Packaged versions

Please check out the project website

Citation

Heinig M, Colome-Tatche M, Rintisch C, Schäfer S, Pravenec M, Hubner N, Vingron M, Johannes F. histoneHMM: Differential analysis of histone modifications with broad genomic footprints. BMC Bioinformatics 2015; 16:60

Contact

Matthias Heinig: matthias.heinig@helmholtz-muenchen.de