lbroseus / fakir

An R package for detecting and interpreting Intron Retention (IR) events

FakIR: a First-aid kit for investigating Intron Retention events

FakIR is an R package for Intron Retention (IR) detection, quantification and exploration using Second and Third Generation Sequencing data.

A pdf version of the tutorial is available here: Tutorial.

Package installation

Please note that FakIR requires rlang version >= 0.4.5.

Also, FakIR makes use of functionalities from several packages from Bioconductor you might need to install first. This can be done by copy-pasting the following code in a R session:

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install()


BiocManager::install(c("IsoformSwitchAnalyzeR", "DEXSeq", "BSgenome.Hsapiens.UCSC.hg38"))
  

Also, so as to install FakIR directly in a R session from GitHub, you will need to have devtools installed:

install.packages("devtools")
   

Then, install FakIR using:

devtools::install_github("lbroseus/FakIR", build_vignettes = T)
   

Alternatively, source files can be downloaded from the following link, and installed manually:

git clone https://github.com/lbroseus/FakIR.git
   

Detecting Intron Retention events using RNA-seq data

Typical workflows for detecting and analysing intron retention using RNA-seq data are detailed in the vignette and can be accessed in a R session using:

require(FakIR)

vignette("IR-events-detection-and-interpretation")
  

Especially, it illustrates how to perform the following tasks:

1. IR events detection from short read RNA-seq data
2. Differential analysis from short read RNA-seq data (using DEXSeq)
3. IR events detection from long read RNA-seq data
4. IR-transcripts reconstruction from long read RNA-seq data
5. Prediction of IR-NMD-targets

References

1. Broseus and Ritchie Challenges in detecting and quantifying intron retention from NGS data. CSBJ. (2020)
2. Grabski, DF, Broseus, L, Kumari, B, Rekosh, D, Hammarskjold, M‐L, Ritchie, W. Intron retention and its impact on gene expression and protein diversity: A review and a practical guide. WIREs RNA. 2021; 12:e1631. https://doi.org/10.1002/wrna.1631

fakir's Issues

N/A