DOI: 10.18129/B9.bioc.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>

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


To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))


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


biocViews Annotation, Software
Version 1.8.0
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)
Suggests knitr (>= 1.28)
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Source Package RIPAT_1.8.0.tar.gz
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