ORFik

This is the development version of ORFik; for the stable release version, see ORFik.

Open Reading Frames in Genomics

Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("ORFik")

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

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, Coverage, DataImport, FunctionalGenomics, ImmunoOncology, RNASeq, RiboSeq, Sequencing, Software
Version	1.23.10
In Bioconductor since	BioC 3.7 (R-3.5) (6 years)
License	MIT + file LICENSE
Depends	R (>= 4.4.0), IRanges(>= 2.17.1), GenomicRanges(>= 1.35.1), GenomicAlignments(>= 1.19.0)
Imports	AnnotationDbi(>= 1.45.0), Biostrings(>= 2.51.1), biomaRt, biomartr (>= 1.0.7), BiocFileCache, BiocGenerics(>= 0.29.1), BiocParallel(>= 1.19.0), BSgenome, cowplot (>= 1.0.0), curl, RCurl, data.table (>= 1.11.8), DESeq2(>= 1.24.0), 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), Rsamtools(>= 1.35.0), rtracklayer(>= 1.43.0), stats, SummarizedExperiment(>= 1.14.0), S4Vectors(>= 0.21.3), tools, txdbmaker, utils, XML, xml2 (>= 1.2.0), withr
System Requirements
URL	https://github.com/Roleren/ORFik
Bug Reports	https://github.com/Roleren/ORFik/issues

Suggests	testthat, rmarkdown, knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19
Linking To	Rcpp
Enhances
Depends On Me	RiboCrypt
Imports Me	TFHAZ
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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