ORFik: Open Reading Frames in Genomics

R package for analysis of transcript and translation features through manipulation of sequence data and NGS data like Ribo-Seq, RNA-Seq, TCP-Seq and CAGE. It is generalized in the sense that any transcript region can be analysed, as the name hints to it was made with investigation of ribosomal patterns over Open Reading Frames (ORFs) as it's primary use case. ORFik is extremely fast through use of C++, data.table and GenomicRanges. Package allows to reassign starts of the transcripts with the use of CAGE-Seq data, automatic shifting of RiboSeq reads, finding of Open Reading Frames for whole genomes and much more.

Package details

AuthorHaakon Tjeldnes [aut, cre, dtc], Kornel Labun [aut, cph], Katarzyna Chyzynska [ctb, dtc], Yamila Torres Cleuren [ctb, ths], Evind Valen [ths, fnd]
Bioconductor views Alignment Coverage DataImport FunctionalGenomics ImmunoOncology RNASeq RiboSeq Sequencing Software
MaintainerHaakon Tjeldnes <hauken_heyken@hotmail.com>
LicenseMIT + file LICENSE
URL https://github.com/Roleren/ORFik
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
if (!requireNamespace("BiocManager", quietly = TRUE))


Try the ORFik package in your browser

Any scripts or data that you put into this service are public.

ORFik documentation built on March 27, 2021, 6 p.m.