polyester: Polyester: simulating RNA-seq reads including differential...

In mikelove/polyesterAlpineMs: Simulate RNA-seq reads

Description

Polyester is an R package designed to simulate an RNA sequencing experiment. Given a set of annotated transcripts, polyester will simulate the steps of an RNA-seq experiment (fragmentation, reverse-complementing, and sequencing) and produce files containing simulated RNA-seq reads. Simulated reads can be analyzed using any of several downstream analysis tools.

Details

A single function call produces RNA-seq reads in FASTA format from a case/control experiment including biological replicates. Differential expression between cases and controls can be set by the user, facilitating comparisons of statistical differential expression methods for RNA-seq data. See detailed documentation for simulate_experiment and simulate_experiment_countmat.

See the vignette by typing browseVignettes("polyester") in the R prompt.

Author(s)

Alyssa Frazee, Andrew Jaffe, Jeff Leek

References

Alyssa C Frazee, Geo Pertea, Andrew E Jaffe, Ben Langmead, Steven L Salzberg, Jeffrey T Leek (2014). Flexible isoform-level differential expression analysis with Ballgown. BioRxiv preprint: http://biorxiv.org/content/early/2014/03/30/003665.

mikelove/polyesterAlpineMs documentation built on May 22, 2019, 10:52 p.m.