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Bioconductor - ORFik

ORFik

This is the released version of ORFik; for the devel version, see ORFik.

Open Reading Frames in Genomics

Bioconductor version: Release (3.21)

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 "4.5") 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")

Details biocViews Alignment, Coverage, DataImport, FunctionalGenomics, ImmunoOncology, RNASeq, RiboSeq, Sequencing, Software Version 1.28.2 In Bioconductor since BioC 3.7 (R-3.5) (7 years) License MIT + file LICENSE Depends R (>= 4.1.0), 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), BiocFileCache, 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, txdbmaker, 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 Package Archives

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

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