Bioconductor version: Release (3.11)
R package for analysis of transcript and translation features through manipulation of sequence-, RiboSeq-, RNASeq-, TCPseq- and CAGE-data. Focusing on 5' UTRs (leaders), it is generalized in the sense that any transcript region can be analysed. 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], 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")
):
To install this package, start R (version "4.0") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("ORFik")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ORFik")
HTML | R Script | ORFik Overview |
HTML | R Script | ORFik_Annotation_Alignment.html |
HTML | R Script | ORFikExperiment.html |
Reference Manual | ||
Text | NEWS | |
Text | LICENSE |
biocViews | Alignment, Coverage, DataImport, FunctionalGenomics, ImmunoOncology, RNASeq, RiboSeq, Sequencing, Software |
Version | 1.8.6 |
In Bioconductor since | BioC 3.7 (R-3.5) (2.5 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), biomartr, 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), cowplot (>= 1.0.0), GGally (>= 1.4.0), methods (>= 3.6.0), R.utils, utils, stats, fst (>= 0.9.2), tools |
LinkingTo | Rcpp |
Suggests | testthat, rmarkdown, knitr, BiocStyle, BSgenome, BSgenome.Hsapiens.UCSC.hg19 |
SystemRequirements | |
Enhances | |
URL | https://github.com/Roleren/ORFik |
BugReports | https://github.com/Roleren/ORFik/issues |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | ORFik_1.8.6.tar.gz |
Windows Binary | ORFik_1.8.6.zip (32- & 64-bit) |
macOS 10.13 (High Sierra) | ORFik_1.8.6.tgz |
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/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.11 | Source Archive |
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