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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

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

browseVignettes("ORFik")
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 HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Alignment, Coverage, DataImport, FunctionalGenomics, ImmunoOncology, RNASeq, RiboSeq, Sequencing, Software
Version 1.23.6
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 (>= 1.0.7), 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, utils, XML, xml2 (>= 1.2.0), withr
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_1.23.6.tar.gz
Windows Binary ORFik_1.23.6.zip (64-bit only)
macOS Binary (x86_64) ORFik_1.23.6.tgz
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
Bioc Package Browser https://code.bioconductor.org/browse/ORFik/
Package Short Url https://bioconductor.org/packages/ORFik/
Package Downloads Report Download Stats