This repository contains the post-processing results necessary to reproduce the figures and analysis that was performed in the paper

• "An Erythroid Intron Retention Program Regulates Gene Expression During Terminal Erythropoiesis" by Harold Pimentel, Marilyn Parra, Sherry Gee, Narla Mohandas, Lior Pachter, John Conboy.

Most people will likely be interested in the knitr result file, which is essentially a report. This file can be found at R/analysis.html

• The main code can be found in R/
  • It depends on several packages, all of which can be found on CRAN, with the exception of kma
• To run the code, you also need the expression estimates to be stored in a data directory
  • The data directory can be download from here
    • The directory should exist under data so that the R code knows how to find it

Here is an example of how you might run this analysis.

First, clone the reposistory:

git clone [email protected]:pimentel/erythroid_ir_analysis.git
cd erythroid_ir_analysis

Now download the data directory and extract it into the same folder

wget http://math.mcb.berkeley.edu/~pimentel/erythroid_ir_analysis/data.tar.gz
tar -xf data.tar.gz

Fire up R and open R/analysis.Rmd with your favorite editor