ORFik

DOI: 10.18129/B9.bioc.ORFik    

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

Open Reading Frames in Genomics

Bioconductor version: Development (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 <hauken_heyken at hotmail.com>, Kornel Labun <kornellabun at gmail.com>, Michal Swirski <michal.swirski at uw.edu.pl>, Katarzyna Chyzynska <katchyz at gmail.com>, Yamila Torres Cleuren <yamilatorrescleuren at gmail.com>, Evind Valen <eivind.valen at gmail.com>

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 (!requireNamespace("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

PDF   Reference Manual

Details

biocViews Alignment, Coverage, DataImport, FunctionalGenomics, ImmunoOncology, RNASeq, RiboSeq, Sequencing, Software
Version 1.15.0
In Bioconductor since BioC 3.7 (R-3.5) (3.5 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), 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), GGally (>= 1.4.0), httr (>= 1.3.0), 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)
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
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
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/
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