RIPAT

DOI: 10.18129/B9.bioc.RIPAT    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see RIPAT.

Retroviral Integration Pattern Analysis Tool (RIPAT)

Bioconductor version: 3.12

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>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("RIPAT")

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("RIPAT")

 

HTML	R Script	RIPAT : Retroviral Integration Pattern Analysis Tool
PDF		Reference Manual

Details

biocViews	Annotation, Software
Version	1.0.0
In Bioconductor since	BioC 3.12 (R-4.0) (0.5 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)
LinkingTo
Suggests	knitr (>= 1.28)
SystemRequirements
Enhances
URL	https://github.com/bioinfo16/RIPAT/
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	RIPAT_1.0.0.tar.gz
Windows Binary	RIPAT_1.0.0.zip
macOS 10.13 (High Sierra)	RIPAT_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RIPAT
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RIPAT
Package Short Url	https://bioconductor.org/packages/RIPAT/
Package Downloads Report	Download Stats