RIPAT

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see RIPAT.

Retroviral Integration Pattern Analysis Tool (RIPAT)

Bioconductor version: 3.16

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 "4.2") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("RIPAT")

RIPAT : Retroviral Integration Pattern Analysis Tool HTML R Script

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, Software

Version 1.8.0

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/

Suggests knitr (>= 1.28)

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Package Archives

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

Source Package RIPAT_1.8.0.tar.gz

Windows Binary RIPAT_1.8.0.zip (64-bit only)

macOS Binary (x86_64) RIPAT_1.8.0.tgz

macOS Binary (arm64) RIPAT_1.8.0.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/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.16 Source Archive