ORFik

DOI: 10.18129/B9.bioc.ORFik    

Open Reading Frames in Genomics

Bioconductor version: Release (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 CageSeq 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")):

Installation

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

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

BiocManager::install("ORFik")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ORFik")

 

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

Details

biocViews Alignment, Coverage, DataImport, FunctionalGenomics, ImmunoOncology, RNASeq, RiboSeq, Sequencing, Software
Version 1.8.1
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), stats, tools, 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), GGally (>= 1.4.0), methods (>= 3.6.0)
LinkingTo Rcpp
Suggests testthat, rmarkdown, knitr, BiocStyle, BSgenome, BSgenome.Hsapiens.UCSC.hg19
SystemRequirements
Enhances
URL https://github.com/Roleren/ORFik
BugReports https://github.com/Roleren/ORFik/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ORFik_1.8.1.tar.gz
Windows Binary ORFik_1.8.1.zip (32- & 64-bit)
macOS 10.13 (High Sierra) ORFik_1.8.1.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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.11 Source Archive

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