RIPAT

DOI: 10.18129/B9.bioc.RIPAT  

This is the development version of RIPAT; for the stable release version, see RIPAT.

Retroviral Integration Pattern Analysis Tool (RIPAT)

Bioconductor version: Development (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>

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("RIPAT")

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

Documentation

PDF		Reference Manual

Details

biocViews	Annotation, Software
Version	1.11.0
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 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
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Build Report

Package Archives

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

Source Package
Windows Binary	RIPAT_1.11.0.zip
macOS Binary (x86_64)	RIPAT_1.11.0.tgz
macOS Binary (arm64)
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/
Package Downloads Report	Download Stats