Supplementary Information for
csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows
by Aaron Lun and Gordon K. Smyth
Nucleic Acids Research 44, e45 (2015). [Full text]
Simulation R code
The following files provide R function and code for reproducing the simulations presented in the article.
- xscss_1.1.3.tar.gz. Install this package before running the above scripts.
Required software packages
The above code also requires publicly available software:
- csaw, a Bioconductor package
- DiffBind, a Bioconductor package
- DBChIP, a Bioconductor package
All Bioconductor packages can be installed as described here, and should be accessible from the R prompt.
SAMtools, MACS and HOMER commands should be accessible from the shell, i.e., as system commands. Note that the code in autosim.R uses UNIX-like syntax to execute these commands, which will not work on Windows.
All other methods should be placed in a methods subdirectory. If they are downloaded as compressed files, they should be unpackaged within that directory. See the system calls within autosim.R for the expected file path of each executable.
Comments/Questions? Contact Aaron Lun.
Last modified: 5 October 2016