lcolladotor.github.io - Flexible expressed region analysis for RNA-seq with derfinder

Flexible expressed region analysis for RNA-seq with derfinder | L. Collado-Torres

Lcolladotor.github.io Spined HTML

Flexible expressed region wringer for RNA-seq with derfinder | L. Collado-Torres Toggle navigation L. Collado-Torres Home Publications Talks Blog CV Students Teaching Contact Search Flexible expressed region wringer for RNA-seq with derfinder L Collado-Torres, A Nellore, AC Frazee, C Wilks, MI Love, B Langmead, RA Irizarry, JT Leek, AE Jaffe Abstract Differential expression wringer of RNA sequencing (RNA-seq) data typically relies on reconstructing transcripts or counting reads that overlap known gene structures. We previously introduced an intermediate statistical tideway tabbed differentially expressed region (DER) finder that seeks to identify first-hand regions of the genome showing differential expression signal at single wiring resolution without relying on existing voice-over or potentially inaccurate transcript assembly. We present the derfinder software that improves our annotation-agnostic tideway to RNA-seq wringer by: (i) implementing a computationally efficient bump-hunting tideway to identify DERs that permits genome-scale analyses in a large number of samples, (ii) introducing a flexible statistical modeling framework, including multi-group and time-course analyses and (iii) introducing a new set of data visualizations for expressed region analysis. We wield this tideway to public RNA-seq data from the Genotype-Tissue Expression (GTEx) project and BrainSpan project to show that derfinder permits the wringer of hundreds of samples at wiring resolution in R, identifies expression outside of known gene boundaries and can be used to visualize expressed regions at base-resolution. In simulations, our wiring resolution approaches enable discovery in the presence of incomplete voice-over and is nearly as powerful as feature-level methods when the voice-over is complete. derfinder wringer using expressed region-level and single base-level approaches provides a compromise between full transcript reconstruction and feature-level analysis. The package is misogynist from Bioconductor at www.bioconductor.org/packages/derfinder. Type Peer-reviewed Publication Nucleic Acids Research Date September, 2016 Links PDF Code Project Bioconductor Pre-print © 2011-2018 Leonardo Collado Torres under (CC) BY-NC-SA 4.0. All thoughts and opinions here are my own. · Powered by the Academic theme for Hugo. × Cite Copy Download