ORFik

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see ORFik.

Open Reading Frames in Genomics


Bioconductor version: 3.15

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], 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 "4.2") 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")
Annotation_Alignment.html HTML R Script
ORFik Overview HTML R Script
ORFikExperiment.html HTML R Script
Ribo-seq_pipeline.html HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Alignment, Coverage, DataImport, FunctionalGenomics, ImmunoOncology, RNASeq, RiboSeq, Sequencing, Software
Version 1.16.6
In Bioconductor since BioC 3.7 (R-3.5) (6 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), data.table (>= 1.11.8), DESeq2(>= 1.24.0), 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, utils, xml2 (>= 1.2.0)
System Requirements
URL https://github.com/Roleren/ORFik
Bug Reports https://github.com/Roleren/ORFik/issues
See More
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 ORFik_1.16.6.tar.gz
Windows Binary ORFik_1.16.6.zip
macOS Binary (x86_64) ORFik_1.16.6.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
Old Source Packages for BioC 3.15 Source Archive