ORFik
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see ORFik.
Open Reading Frames in Genomics
Bioconductor version: 3.10
Tools for manipulation of sequence-, 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 whole genomes and much more.
Author: Haakon Tjeldnes [aut, cre, dtc], Kornel Labun [aut, cph], Katarzyna Chyzynska [ctb, dtc], Evind Valen [ths, fnd]
Maintainer: Haakon Tjeldnes <hauken_heyken at hotmail.com>
citation("ORFik")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, Coverage, DataImport, FunctionalGenomics, ImmunoOncology, RNASeq, RiboSeq, Sequencing, Software |
| Version | 1.6.9 |
| 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 | S4Vectors(>= 0.21.3), GenomeInfoDb(>= 1.15.5), GenomicFeatures(>= 1.31.10), AnnotationDbi(>= 1.45.0), rtracklayer(>= 1.43.0), Rcpp (>= 1.0.0), data.table (>= 1.11.8), Biostrings(>= 2.51.1), stats, tools, Rsamtools(>= 1.35.0), BiocGenerics(>= 0.29.1), BiocParallel(>= 1.19.0), SummarizedExperiment(>= 1.14.0), DESeq2(>= 1.24.0), ggplot2 (>= 2.2.1), gridExtra (>= 2.3), GGally (>= 1.4.0), methods (>= 3.6.0) |
| System Requirements | |
| URL | https://github.com/Roleren/ORFik |
| Bug Reports | https://github.com/Roleren/ORFik/issues |
See More
| Suggests | testthat, rmarkdown, knitr, BiocStyle, BSgenome, BSgenome.Hsapiens.UCSC.hg19 |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| 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_1.6.9.tar.gz |
| Windows Binary | ORFik_1.6.9.zip |
| Mac OS X 10.11 (El Capitan) | ORFik_1.6.9.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 3.10 | Source Archive |