RiboDiPA
Differential pattern analysis for Ribo-seq data
Bioconductor version: Release (3.20)
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("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 | ||
| NEWS | Text |
Details
| biocViews | Alignment, Coverage, DataImport, DifferentialExpression, GeneExpression, GeneRegulation, ImmunoOncology, Normalization, QualityControl, RNASeq, RiboSeq, Sequencing, Software |
| Version | 1.14.0 |
| 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 |
See More
| Suggests | knitr, rmarkdown |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RiboDiPA_1.14.0.tar.gz |
| Windows Binary (x86_64) | RiboDiPA_1.14.0.zip (64-bit only) |
| macOS Binary (x86_64) | RiboDiPA_1.14.0.tgz |
| macOS Binary (arm64) | RiboDiPA_1.14.0.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/ |
| Package Downloads Report | Download Stats |