RosR ChIP-chip processing

ChIP-chip processing pipeline for Tonner et al. "A regulatory hierarchy controls the dynamic transcriptional response to extreme oxidative stress in archaea."

• This part of the repository contains the code necessary to recereate table S2 from the manuscript
• Raw data file can be downloaded from GEO: GSE58696

Dependencies

• R (version 2.15.2):
• knitr
• limma - http://www.bioconductor.org/packages/release/bioc/html/limma.html
• maDB - http://www.bioconductor.org/packages//2.7/bioc/html/maDB.html
• MeDiChI - http://cran.r-project.org/src/contrib/Archive/MeDiChI/
• RColorBrewer
• KernSmooth
• yaml
• outliers
• LSD

Steps to recreate table:

• download raw data from GEO, create a folder called 'data/chip/' and unpack into that directory
• run the command 'R CMD Sweave preprocessing.Rnw'
• Download table S5 from Sharma et al. BMC Genomics 2012, and save the tab 'all_data_H2O2' as data/rosr_h2o2_exp.csv
• from R, run 'knit2html(rosr-timcourse-analysis.Rmd)' with the knitr package

RosR ChIP-seq processing and comparison across multiple species of halophilic archaea.

ChIP-seq processing pipeline for Darnell and Hackley et al. "Functional divergence of the RosR transcription factor across species of halophilic archaea."

• This part of the repository contains the code necessary to recereate table X from the manuscript
• Raw data file can be downloaded from GEO: GSEXXXX

Dependences

Steps to recreate table X and figure Y: