factR v.2

Functional Annotation of Custom Transcriptomes in R

General workflow

factR2 represents a substantial improvement over factR, providing users with more powerful and user-friendly tools to work with custom-assembled transcriptomes.

Below are factR2's latest features:

1. Extracts alternative splicing events and annotate its novelity and contribution to NMD outcome
2. Tests regulatory potential of AS-NMD events
3. Quantifies evolutionary conservation scores of alternative exons
4. Interactive plot of transcript architectures

As well as the following features from factR:

1. Matches gene information on custom transcriptomes to reference annotation
2. Constructs transcript coding (CDS) information using reference-guided approach
3. Predicts sensitivity of coding transcripts to nonsense-mediated decay (NMD)
4. Predicts protein domains on productively spliced transcripts

How to install

The development version can be installed using devtools:

# install.packages("devtools")
devtools::install_github("f-hamidlab/factR2")

Getting started

See our full vignette on how to use factR2.