RiboDiPA
Differential pattern analysis for Ribo-seq data
Bioconductor version: 3.24 · Package version: 1.21.1
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("RiboDiPA")Details
| Maintainer | Ji-Ping Wang <jzwang@northwestern.edu> |
| Author | Keren Li [aut], Matt Hope [aut], Xiaozhong Wang [aut], Ji-Ping Wang [aut, cre] |
| License | LGPL (>= 3) |
| Downloads rank | 454 |
| Source branch | devel |
| biocViews | Alignment, Coverage, DataImport, DifferentialExpression, GeneExpression, GeneRegulation, ImmunoOncology, Normalization, QualityControl, RNASeq, RiboSeq, Sequencing, Software |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | RiboDiPA_1.21.1.tar.gz |
| Windows binary (x86_64) | RiboDiPA_1.21.1.zip |
| macOS binary (arm64) | RiboDiPA_1.21.1.tgz |
| macOS binary (x86_64) | RiboDiPA_1.21.1.tgz |
Dependencies
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
LinkingTo: Rcpp