RiboDiPA

DOI: 10.18129/B9.bioc.RiboDiPA  

Differential pattern analysis for Ribo-seq data

Bioconductor version: Release (3.16)

This package performs differential pattern analysis for Ribo-seq data. It identifies genes with significantly different patterns in the ribosome footprint between two conditions. RiboDiPA contains five major components including bam file processing, P-site mapping, data binning, differential pattern analysis and footprint visualization.

Author: Keren Li [aut], Matt Hope [aut], Xiaozhong Wang [aut], Ji-Ping Wang [aut, cre]

Maintainer: Ji-Ping Wang <jzwang at northwestern.edu>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RiboDiPA")

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("RiboDiPA")

 

HTML	R Script	RiboDiPA
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, Coverage, DataImport, DifferentialExpression, GeneExpression, GeneRegulation, ImmunoOncology, Normalization, QualityControl, RNASeq, RiboSeq, Sequencing, Software
Version	1.6.0
In Bioconductor since	BioC 3.13 (R-4.1) (2 years)
License	LGPL (>= 3)
Depends	R (>= 4.1), Rsamtools, GenomicFeatures, GenomicAlignments
Imports	Rcpp (>= 1.0.2), graphics, stats, data.table, elitism, methods, S4Vectors, IRanges, GenomicRanges, matrixStats, reldist, doParallel, foreach, parallel, qvalue, DESeq2, ggplot2, BiocFileCache, BiocGenerics
LinkingTo	Rcpp
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	RiboDiPA_1.6.0.tar.gz
Windows Binary	RiboDiPA_1.6.0.zip
macOS Binary (x86_64)	RiboDiPA_1.6.0.tgz
macOS Binary (arm64)	RiboDiPA_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RiboDiPA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RiboDiPA
Bioc Package Browser	https://code.bioconductor.org/browse/RiboDiPA/
Package Short Url	https://bioconductor.org/packages/RiboDiPA/
Package Downloads Report	Download Stats