ORFik

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see ORFik.

Open Reading Frames in Genomics

Bioconductor version: 3.8

Tools for manipulation of RiboSeq, RNASeq and CageSeq data. ORFik is extremely fast through use of C, data.table and GenomicRanges. Package allows to reassign starts of the transcripts with the use of CageSeq data, automatic shifting of RiboSeq reads, finding of Open Reading Frames for the whole genomes and many more.

Author: Kornel Labun [aut, cre, cph], Haakon Tjeldnes [aut, dtc], Katarzyna Chyzynska [ctb, dtc], Evind Valen [ths, fnd]

Maintainer: Kornel Labun <kornellabun at gmail.com>

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

Installation

To install this package, start R (version "3.5") 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")

ORFik Overview HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, Coverage, DataImport, FunctionalGenomics, ImmunoOncology, RNASeq, RiboSeq, Sequencing, Software

Version 1.2.1

In Bioconductor since BioC 3.7 (R-3.5) (6 years)

License MIT + file LICENSE

Depends R (>= 3.5.0), IRanges(>= 2.13.28), GenomicRanges(>= 1.31.23), GenomicAlignments(>= 1.15.13)

Imports S4Vectors(>= 0.17.39), GenomeInfoDb(>= 1.15.5), GenomicFeatures(>= 1.31.10), rtracklayer(>= 1.39.9), Rcpp (>= 0.12.16), data.table (>= 1.10.4-3), Biostrings(>= 2.47.12), stats, tools, Rsamtools(>= 1.31.3), BiocGenerics(>= 0.25.3)

System Requirements

URL https://github.com/JokingHero/ORFik

Bug Reports https://github.com/JokingHero/ORFik/issues

Suggests testthat, rmarkdown, knitr, BiocStyle, BSgenome, BSgenome.Hsapiens.UCSC.hg19, ggplot2 (>= 2.2.1)

Linking To Rcpp

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