RIPAT

DOI: 10.18129/B9.bioc.RIPAT    

Retroviral Integration Pattern Analysis Tool (RIPAT)

Bioconductor version: Release (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>

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

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) (< 6 months)
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 (32- & 64-bit)
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

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