analysis code used in Ballgown paper
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GEUVADIS_preprocessing
InSilicoDB
RIN
eQTL eqtl csvs for nbt Dec 3, 2014
negative_control
positive_control
simulations
timing
.gitignore
README.md

README.md

Code for analysis in Ballgown manuscript

Data and code to reproduce the analyses in the Ballgown manuscript is available in this repository. Larger data files are hosted externally, but this repository contains links.

scripts/code

Scripts for each analysis section are available in the relevant subfolder.

simulations

All simulation results from the paper were produced with scripts in this folder. Simulation results include:

  • Supplementary Figure 6
  • Supplementary Figure 7a-b

This code also gives numerical results presented in Supplementary Note 5.

InSilicoDB

The manuscript examines statistical significance results from two datasets downloaded from InSilico DB. This analysis includes Supplementary Figure 5 and some numerical results in the main manuscript.

GEUVADIS_preprocessing

The manuscript includes a re-analysis of the GEUVADIS RNA-sequencing dataset. This folder includes scripts for downloading and aligning reads, assembling the transcriptome, estimating transcript abundances, and organizing the expression measurements into the GEUVADIS ballgown object (see "GEUVADIS ballgown object" in the data section). The ballgown object was used for the eQTL and RIN analyses.

RIN

Analysis investigating the relationship between RNA quality (RIN) and transcript expression was done with the script in this folder. This analysis includes:

  • Figure 1c-d
  • Supplementary Figure 7c
  • Supplementary Figure 8

This code also gives some numerical results in the main manuscript.

eQTL

Analysis of Expression Quantitative Trait Loci in the GEUVADIS dataset. Specifically this analysis includes:

  • Figure 1e-f
  • Supplementary Figure 9
  • Numerical results in the main manuscript and Supplementary Note 8

timing

Computational times for many of the analyses presented in the manuscript. Specifically this folder includes code for:

  • Supplementary Figure 10
  • Supplementary Note 9

data

The following data is currently available on Dropbox. Other relevant data is stored in the subfolders. All Dropbox links are also referenced in subfolder README files.