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")

Author

This package has been developed by Adrià Mitjavila Ventura.

If you want to contribute to this package, make a post in the issues section in this repository or fork this repository adding your code and do a pull request.

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