DOI: 10.18129/B9.bioc.ORFik    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see ORFik.

Open Reading Frames in Genomics

Bioconductor version: 3.11

R package for analysis of transcript and translation features through manipulation of sequence-, RiboSeq-, RNASeq-, TCPseq- and CAGE-data. Focusing on 5' UTRs (leaders), it is generalized in the sense that any transcript region can be analysed. 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.

Author: Haakon Tjeldnes [aut, cre, dtc], Kornel Labun [aut, cph], Katarzyna Chyzynska [ctb, dtc], Yamila Torres Cleuren [ctb, ths], Evind Valen [ths, fnd]

Maintainer: Haakon Tjeldnes <hauken_heyken at hotmail.com>

Citation (from within R, enter citation("ORFik")):


To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


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HTML R Script ORFik Overview
HTML R Script ORFik_Annotation_Alignment.html
HTML R Script ORFikExperiment.html
PDF   Reference Manual
Text   NEWS


biocViews Alignment, Coverage, DataImport, FunctionalGenomics, ImmunoOncology, RNASeq, RiboSeq, Sequencing, Software
Version 1.8.6
In Bioconductor since BioC 3.7 (R-3.5) (2.5 years)
License MIT + file LICENSE
Depends R (>= 3.6.0), IRanges(>= 2.17.1), GenomicRanges(>= 1.35.1), GenomicAlignments(>= 1.19.0)
Imports S4Vectors(>= 0.21.3), GenomeInfoDb(>= 1.15.5), GenomicFeatures(>= 1.31.10), AnnotationDbi(>= 1.45.0), rtracklayer(>= 1.43.0), Rcpp (>= 1.0.0), data.table (>= 1.11.8), Biostrings(>= 2.51.1), biomartr, Rsamtools(>= 1.35.0), BiocGenerics(>= 0.29.1), BiocParallel(>= 1.19.0), SummarizedExperiment(>= 1.14.0), DESeq2(>= 1.24.0), ggplot2 (>= 2.2.1), gridExtra (>= 2.3), cowplot (>= 1.0.0), GGally (>= 1.4.0), methods (>= 3.6.0), R.utils, utils, stats, fst (>= 0.9.2), tools
LinkingTo Rcpp
Suggests testthat, rmarkdown, knitr, BiocStyle, BSgenome, BSgenome.Hsapiens.UCSC.hg19
URL https://github.com/Roleren/ORFik
BugReports https://github.com/Roleren/ORFik/issues
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Follow Installation instructions to use this package in your R session.

Source Package ORFik_1.8.6.tar.gz
Windows Binary ORFik_1.8.6.zip (32- & 64-bit)
macOS 10.13 (High Sierra) ORFik_1.8.6.tgz
Source Repository git clone https://git.bioconductor.org/packages/ORFik
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ORFik
Package Short Url https://bioconductor.org/packages/ORFik/
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