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RIPAT

Retroviral Integration Pattern Analysis Tool (RIPAT)


Bioconductor version: Release (3.18)

RIPAT is developed as an R package for retroviral integration sites annotation and distribution analysis. RIPAT needs local alignment results from BLAST and BLAT. Specific input format is depicted in RIPAT manual. RIPAT provides RV integration pattern analysis result as forms of R objects, excel file with multiple sheets and plots.

Author: Min-Jeong Baek [aut, cre]

Maintainer: Min-Jeong Baek <mjbaek16 at korea.ac.kr>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RIPAT")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews Annotation, Software
Version 1.12.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License Artistic-2.0
Depends R (>= 4.0)
Imports biomaRt(>= 2.38.0), GenomicRanges(>= 1.34.0), ggplot2 (>= 3.1.0), grDevices (>= 3.5.3), IRanges(>= 2.16.0), karyoploteR(>= 1.6.3), openxlsx (>= 4.1.4), plyr (>= 1.8.4), regioneR(>= 1.12.0), rtracklayer(>= 1.42.2), stats (>= 3.5.3), stringr (>= 1.3.1), utils (>= 3.5.3)
System Requirements
URL https://github.com/bioinfo16/RIPAT/
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Suggests knitr (>= 1.28)
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Package Archives

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

Source Package
Windows Binary RIPAT_1.12.0.zip
macOS Binary (x86_64) RIPAT_1.12.0.tgz
macOS Binary (arm64) RIPAT_1.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/RIPAT
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RIPAT
Bioc Package Browser https://code.bioconductor.org/browse/RIPAT/
Package Short Url https://bioconductor.org/packages/RIPAT/
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