RiboDiPA

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see RiboDiPA.

Differential pattern analysis for Ribo-seq data

Bioconductor version: 3.19

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 "4.4") 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")

RiboDiPA HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, Coverage, DataImport, DifferentialExpression, GeneExpression, GeneRegulation, ImmunoOncology, Normalization, QualityControl, RNASeq, RiboSeq, Sequencing, Software

Version 1.12.0

In Bioconductor since BioC 3.13 (R-4.1) (3.5 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, BiocGenerics, txdbmaker

System Requirements

URL

Suggests knitr, rmarkdown

Linking To Rcpp

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

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Package Archives

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

Source Package RiboDiPA_1.12.0.tar.gz

Windows Binary (x86_64) RiboDiPA_1.12.0.zip

macOS Binary (x86_64) RiboDiPA_1.12.0.tgz

macOS Binary (arm64) RiboDiPA_1.12.0.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/

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