SIRFindeR: Stable Estimation of Intron Retention levels from RNA-seq data

SIRFindeR is an R package for detecting and quantifying Intron Retention levels using Second and Third Generation RNA-Sequencing data.

Package installation

So as to install SIRFindeR in a R session from GitHub, you will need the R package devtools. You can install it using:

install.packages("devtools")

Then, install SIRFindeR with:

devtools::install_github("lbroseus/SIRFindeR", build_vignette = TRUE)

Using SIRFindeR

Guidelines to run SIRFindeR on short or long RNA-seq data can be found in the accompanying Tutorial; or within a R session:

require(SIRFindeR)

vignette("SIRFindeR")

References

1. Broseus and Ritchie. Challenges in detecting and quantifying intron retention from RNA-seq data. CSBJ. (2020)
2. Broseus and Ritchie. S-IRFindeR: stable and accurate measurement of intron retention. bioRXiv. (2020)