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RiboDiPA

This is the development version of RiboDiPA; for the stable release version, see RiboDiPA.

Differential pattern analysis for Ribo-seq data

Bioconductor version: Development (3.18)

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 "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
RiboDiPA HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Alignment, Coverage, DataImport, DifferentialExpression, GeneExpression, GeneRegulation, ImmunoOncology, Normalization, QualityControl, RNASeq, RiboSeq, Sequencing, Software
Version 1.9.0
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
Linking To Rcpp
Suggests knitr, rmarkdown
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Package Archives

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

Source Package RiboDiPA_1.9.0.tar.gz
Windows Binary RiboDiPA_1.9.0.zip (64-bit only)
macOS Binary (x86_64) RiboDiPA_1.9.0.tgz
macOS Binary (arm64)
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