Look at the source code here.
Look at the documentation here.
Goal
chromHMMviewR is an R package to visualize data from ChromHMM.
After running chromHMM, I always had problems to integrate the results in my reports, so I started developping some functions to visualize the heatmaps that chromHMM shows you, but using ggplot2
instead. Finally, in order to practice the creation of R packages, I decided to follow these guides to turn the functions into a package.
Install chromHMMviewR
To install chromHMMveiwR
, you have to run:
# install the devtools package from CRAN (only if you don't have it)
install.packages("devtools")
# install chromHMMviewR from this Github repository devtools::install_github("amitjavilaventura/chromHMMviewR")
Cite
If you use this package, please cite this repository and give it an star.
More
Go to the ChromHMM official website to get more information about how to use ChromHMM.
ChromHMM paper: Ernst J, Kellis M. (2012) ChromHMM: automating chromatin-state discovery and characterization. Nature Methods. doi: https://doi.org/10.1038/nmeth.1906