DOI: 10.18129/B9.bioc.ORFik  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see ORFik.

Open Reading Frames in Genomics

Bioconductor version: 3.16

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], Evind Valen [ths, fnd]

Maintainer: Haakon Tjeldnes <hauken_heyken at hotmail.com>

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


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HTML R Script Data management
HTML R Script ORFik Overview
HTML R Script ORFik_Annotation_Alignment
HTML R Script Ribo-seq pipeline
PDF   Reference Manual
Text   NEWS


biocViews Alignment, Coverage, DataImport, FunctionalGenomics, ImmunoOncology, RNASeq, RiboSeq, Sequencing, Software
Version 1.18.2
In Bioconductor since BioC 3.7 (R-3.5) (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), biomaRt, 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), 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, xml2 (>= 1.2.0)
LinkingTo Rcpp
Suggests testthat, rmarkdown, knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19
URL https://github.com/Roleren/ORFik
BugReports https://github.com/Roleren/ORFik/issues
Depends On Me RiboCrypt
Imports Me TFHAZ
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package ORFik_1.18.2.tar.gz
Windows Binary ORFik_1.18.2.zip (64-bit only)
macOS Binary (x86_64) ORFik_1.18.2.tgz
macOS Binary (arm64) ORFik_1.18.2.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/
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