COHCAP: R package for DNA Methylation Analysis (and Gene Expression Integration) for Illumina Infinium Array and BS-Seq Data

+ The COHCAP package was first developed within the Bioinformatics Core, under the direction of Yate-Ching Yuan.
+ Charles Warden also provided assistance with updates and maintance that include a Bioconductor version of the package
+ while working in the Integrative Genomics Core (with Xiwei Wu as the director) as well as when he was/is not working at City of Hope.
+
+ Accordingly, Charles Warden, Yate-Ching Yuan, and Xiwei Wu were listed as authors (when a Bioconductor version was available). 

You can directly install from this location using devtools:

If you haven't already installed devtools, you can install the package from CRAN using install.packages("devtools"). Once installed, you can run the following commands:

library("devtools")
devtools::install_github("cwarden45/COHCAP")

Publications

Warden et al. 2013 - original publication; not to be confused with citation for corrigendum in 2019.

Warden 2014 - Bioconductor version (most closely related to this code).

Additional Tutorials (including Post-2016 Updates)

COHCAP Demo for Illumina EPIC Array

Additional Acknowledgements

For Post-2016 function additions / updates, we would like to acknowledge:
- Yuan Yuan MD/PhD for having a project used for initial EPIC testing in the standalone version (which also caused me to debug the custom annotation function in COHCAP).
- Susan Neuhausen / Ding Yuan Chun for projects that led to the addition of continuous variable linear regression analysis.
- Yapeng Su (Caltech, at time of support) for having a project to test application of COHCAP to RRBS data
- D. Joe Jerry (UMass-Amherst) for a project that was helpful for general debugging.
- Feng Miao for having a project where I wrote partially similar code to the COHCAP de novo region boundaries for a 3C-Seq dataset (from the Natarajan Lab)
- Shiuan Chen (application to EPIC dataset, collaboration with Susan Neuhausen)