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.
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.
install.packages("devtools")
devtools::install_github("matthiasheinig/histoneHMM")
We provide a small test data set to try out the package:
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
We have a new and improved version with a high level interface for more convenience. Please check out the package vignette:
Please check out the project website
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
Matthias Heinig: matthias.heinig@helmholtz-muenchen.de