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.

Required software packages

The above code also requires publicly available software:

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