This is the released version of RiboDiPA; for the devel version, see RiboDiPA.

Differential pattern analysis for Ribo-seq data


Bioconductor version: Release (3.22)

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 "4.5") 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")

Details

biocViews Alignment, Coverage, DataImport, DifferentialExpression, GeneExpression, GeneRegulation, ImmunoOncology, Normalization, QualityControl, RNASeq, RiboSeq, Sequencing, Software
Version 1.18.0
In Bioconductor since BioC 3.13 (R-4.1) (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
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Follow Installation instructions to use this package in your R session.