RiboDiPA

DOI: 10.18129/B9.bioc.RiboDiPA    

Differential pattern analysis for Ribo-seq data

Bioconductor version: Release (3.14)

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>

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

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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 1.2.0
In Bioconductor since BioC 3.13 (R-4.1) (0.5 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
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_1.2.0.tar.gz
Windows Binary RiboDiPA_1.2.0.zip (64-bit only)
macOS 10.13 (High Sierra) RiboDiPA_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/RiboDiPA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RiboDiPA
Package Short Url https://bioconductor.org/packages/RiboDiPA/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive

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