ORFik: R package for discovery of novel genes with Ribo-Seq and RNA-Seq data.

This package is still under development, although this version is stable and can be used already.

About

ORFik is an R package containing various functions for analysis of Ribo-Seq and RNA-Seq data. Currently it supports:

• Finding Open Reading Frames (very fast) in the genome of interest or on the set of transcripts.
• Metaplots for Ribo-Seq allowing to spot the shift.
• Shifting functions for the Ribo-Seq data.
• Various measurements of gene identity e.g. FLOSS, coverage, ORFscore, entropy.
• Utility functions to extend GenomicRanges, e.g. the functions tile1 and groupGRangesBy.

Installation

Package is currently only available on github

library(devtools)
install_github("JokingHero/ORFik")

More information

After installation run:

library(ORFik)

# Tissue specific 5' utrs using cage-data
?reassignTSSbyCage

# Detecting open reading frames
?findORFs

# get a feature-set from predicted orfs
?computeFeatures

# read vignette
browseVignettes("ORFik")

Feedback

Please feel free to provide feedback or desired functionality. My contact address is Kornel.Labun at uib.no.