code used for analysis presented in polyester paper
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NA18858 adds geuvadis sample subfolders Nov 27, 2014
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data_sim
de_experiment
error_models
length_sim
ten_genes_experiment
.gitignore
GD667.QCstats.masterfile.txt
README.md
cdna_pos_bias.csv
countmat.rda
dataDrivenEst.Rmd
dataDrivenEst.html
ebseq.Rmd
ebseq.html
length_simulation.Rmd
length_simulation.html
make_countmat.R
make_error_models.py
make_insert_sizes.sh
make_sequences.R
polyester_manuscript.Rmd
polyester_manuscript.html
rnaf_pos_bias.csv
sequences.rda

README.md

code for Polyester paper

Reproduce our updated Polyester paper (available on BiorXiv) with the code/data in this repository!

The document that I reproduced for you is at this link. (That's just a rendered version of polyester_manuscript.html, which lives in this repo).

If you'd like to reproduce the document yourself, clone this repository, read the introduction of polyester_manuscript.Rmd carefully, download/create all the necessary data files, and then use knitr to create the html output: from within R, with the repository main directory as the working directory, run:

library(knitr)
knit2html('polyester_manuscript.Rmd')

The paper also includes three small analyses as supplements. The.Rmd files with code in them and corresponding rendered html are in this repository. You can view the supplements at these links: