RT Journal Article
SR Electronic
T1 Flexible isoform-level differential expression analysis with Ballgown
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 003665
DO 10.1101/003665
A1 Frazee, Alyssa C.
A1 Pertea, Geo
A1 Jaffe, Andrew E.
A1 Langmead, Ben
A1 Salzberg, Steven L.
A1 Leek, Jeffrey T.
YR 2014
UL http://biorxiv.org/content/early/2014/03/30/003665.abstract
AB We have built a statistical package called Ballgown for estimating differential expression of genes, transcripts, or exons from RNA sequencing experiments. Ballgown is designed to work with the popular Cufflinks transcript assembly software and uses well-motivated statistical methods to provide estimates of changes in expression. It permits statistical analysis at the transcript level for a wide variety of experimental designs, allows adjustment for confounders, and handles studies with continuous covariates. Ballgown provides improved statistical significance estimates as compared to the Cuffdiff2 differential expression tool included with Cufflinks. We demonstrate the flexibility of the Ballgown package by re-analyzing 667 samples from the GEUVADIS study to identify transcript-level eQTLs and identify non-linear artifacts in transcript data. Our package is freely available from: https://github.com/alyssafrazee/ballgown