ORFik

DOI: 10.18129/B9.bioc.ORFik  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see ORFik.

Open Reading Frames in Genomics

Bioconductor version: 3.17

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.

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

Maintainer: Haakon Tjeldnes <hauken_heyken at hotmail.com>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("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	Annotation & Alignment
HTML	R Script	Data management
HTML	R Script	Importing data
HTML	R Script	ORFik Overview
HTML	R Script	Ribo-seq pipeline
HTML	R Script	Working with transcripts
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Alignment, Coverage, DataImport, FunctionalGenomics, ImmunoOncology, RNASeq, RiboSeq, Sequencing, Software
Version	1.20.2
In Bioconductor since	BioC 3.7 (R-3.5) (5.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.6.0), IRanges(>= 2.17.1), GenomicRanges(>= 1.35.1), GenomicAlignments(>= 1.19.0)
Imports	AnnotationDbi(>= 1.45.0), Biostrings(>= 2.51.1), biomaRt, biomartr, BiocGenerics(>= 0.29.1), BiocParallel(>= 1.19.0), BSgenome, cowplot (>= 1.0.0), curl, RCurl, data.table (>= 1.11.8), DESeq2(>= 1.24.0), dplyr, downloader, fst (>= 0.9.2), GenomeInfoDb(>= 1.15.5), GenomicFeatures(>= 1.31.10), ggplot2 (>= 2.2.1), gridExtra (>= 2.3), httr (>= 1.3.0), jsonlite, methods (>= 3.6.0), R.utils, Rcpp (>= 1.0.0), readr, Rsamtools(>= 1.35.0), rtracklayer(>= 1.43.0), stats, stringr, SummarizedExperiment(>= 1.14.0), S4Vectors(>= 0.21.3), tools, tibble, utils, XML, xml2 (>= 1.2.0), withr
LinkingTo	Rcpp
Suggests	testthat, rmarkdown, knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19
SystemRequirements
Enhances
URL	https://github.com/Roleren/ORFik
BugReports	https://github.com/Roleren/ORFik/issues
Depends On Me	RiboCrypt
Imports Me	TFHAZ
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	ORFik_1.20.2.tar.gz
Windows Binary	ORFik_1.19.7.zip
macOS Binary (x86_64)	ORFik_1.20.2.tgz
macOS Binary (arm64)	ORFik_1.20.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ORFik
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ORFik
Bioc Package Browser	https://code.bioconductor.org/browse/ORFik/
Package Short Url	https://bioconductor.org/packages/ORFik/
Package Downloads Report	Download Stats