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 for each analysis section are available in the relevant subfolder.
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.
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.
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.
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.
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
Computational times for many of the analyses presented in the manuscript. Specifically this folder includes code for:
- Supplementary Figure 10
- Supplementary Note 9
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.
- Results of MatrixEQTL for GEUVADIS (.rda)
- Results from MatrixEQTL analysis annotated with Ensembl (.rda)
- Filtered GEUVADIS genotypes (.rda)
- Top 3 principal components from GEUVADIS genotype data (.mds; created with PLINK)
- GEUVADIS quality-control statistics (.txt)
- GEUVADIS population information (.txt) - matched to IDs in quality-control statistics file
- GEUVADIS ballgown object (.rda)
- Ensembl Genes from human chr1-22,X,Y -- iGenomes (.gtf)
- Ensembl Genes with chromosome names prefixed with "chr" (.gtf)
- Simulated RNA-seq reads: differential expression at FPKM level (.zip)
- Simulated RNA-seq reads: differential expression at read-count level (.zip)
- Developmental cell types dataset, downloaded from InSilico DB (.tgz)
- Adenocarcinoma dataset, downloaded from InSilico DB (.tgz)