ORFik

DOI: 10.18129/B9.bioc.ORFik    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see ORFik.

Open Reading Frames in Genomics

Bioconductor version: 3.10

Tools for manipulation of sequence-, RiboSeq-, RNASeq- and CageSeq data. 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], Evind Valen [ths, fnd]

Maintainer: Haakon Tjeldnes <hauken_heyken at hotmail.com>

Installation

To install this package, start R (version "3.6") 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
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Alignment, Coverage, DataImport, FunctionalGenomics, ImmunoOncology, RNASeq, RiboSeq, Sequencing, Software
Version	1.6.9
In Bioconductor since	BioC 3.7 (R-3.5) (2 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_1.6.9.tar.gz
Windows Binary	ORFik_1.6.9.zip
Mac OS X 10.11 (El Capitan)	ORFik_1.6.9.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