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.

• runme.R
• autosim.R
• plot_stuff.R
• 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
• PePr
• multiGPS
• MACS
• SICER
• SAMtools

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.

 

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Comments/Questions? Contact Aaron Lun.
Last modified: 5 October 2016