DOI: 10.18129/B9.bioc.RiboDiPA  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see RiboDiPA.

Differential pattern analysis for Ribo-seq data

Bioconductor version: 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>

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


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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
Depends On Me
Imports Me
Suggests Me
Links To Me
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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/
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