PT  - JOURNAL ARTICLE
AU  - Alyssa C. Frazee
AU  - Geo Pertea
AU  - Andrew E. Jaffe
AU  - Ben Langmead
AU  - Steven L. Salzberg
AU  - Jeffrey T. Leek
TI  - Flexible isoform-level differential expression analysis with Ballgown
AID  - 10.1101/003665
DP  - 2014 Jan 01
TA  - bioRxiv
PG  - 003665
4099  - http://biorxiv.org/content/early/2014/03/30/003665.short
4100  - http://biorxiv.org/content/early/2014/03/30/003665.full
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