ORFik
Open Reading Frames in Genomics
Bioconductor version: Release (3.17)
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("ORFik")):
Installation
To install this package, start R (version "4.3") 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")| Data management | HTML | R Script |
| Importing data | HTML | R Script |
| ORFik Overview | HTML | R Script |
| ORFik_Annotation_Alignment | HTML | R Script |
| Ribo-seq pipeline | HTML | R Script |
| Working with transcripts | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, Coverage, DataImport, FunctionalGenomics, ImmunoOncology, RNASeq, RiboSeq, Sequencing, Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (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) |
| Linking To | Rcpp |
| Suggests | testthat, rmarkdown, knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19 |
| System Requirements | |
| Enhances | |
| URL | https://github.com/Roleren/ORFik |
| Bug Reports | https://github.com/Roleren/ORFik/issues |
See More
| 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_1.20.0.tar.gz |
| Windows Binary | ORFik_1.19.7.zip |
| macOS Binary (x86_64) | ORFik_1.20.0.tgz |
| macOS Binary (arm64) | ORFik_1.20.0.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 3.17 | Source Archive |