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Old 10-12-2010, 11:58 AM   #2
Senior Member
Location: WashU

Join Date: Aug 2010
Posts: 117

R is a language/analysis platform known for having a somewhat steep learning curve. The documentation available for each function can be thorough and is consistently available. However, this documentation tends to be written by statisticians, for statisticians. Furthermore, the user forums are not nearly as welcoming as this one is. They are full of people who have read the documentation, not understood it, asked for help, and essentially been told to read the documentation. Having said all that I would still encourage you to try R as it can be powerful and rewarding and many tools are being actively developed.

The r-project has a list of suggested books. There are some good ones to get you going there. Many genome centers will have some local R experts, and these people sometimes offer tutorials.

There are also many posts in this forum relating to various R tools. Hopefully someone with specific experience analyzing ChIP-seq data in R will respond. At a glance the following links seem relevant:
R_ChIP-Seq wiki, Advanced RNA-Seq and ChiP-Seq data analysis, HT Sequence Analysis with R and Bioconductor, Advanced RNA-Seq and ChiP-Seq data analysis, ...
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