RIPAT : Retroviral Integration Pattern Analysis Tool
27 October, 2020
Contents
1 Introduction
RIPAT is an R package for Retroviral vector integration site analysis. This package is developed to
find integration regions on the target sequence and study biological meaning of the integration
pattern such as distance from important genomic factors and genomic features.
It’s distributed from our Github repository (https://github.com/bioinfo16/RIPAT) and Bioconductor.
2 Dependencies
RIPAT will be run on all R versions but, we strongly recommend that user install the R version 3.5.3 or higher. Plus, RIPAT needs these packages below to run. By the install command (writted below), RIPAT install all packages automatically. If user already install some of packages listed up, RIPAT will be reinstall proper version of these packages itself.
| Package | Version |
|---|---|
| GenomicRanges | >= 1.34.4 |
| ggplot2 | >= 3.1.0 |
| grDevices | >= 3.5.3 |
| karyoploteR | >= 1.6.3 |
| openxlsx | >= 4.1.4 |
| plyr | >= 1.8.4 |
| RColorBrewer | >= 1.1-2 |
| regioneR | >= 1.12.0 |
| stats | >= 3.5.3 |
| stringr | >=1.3.1 |
| utils | >= 3.5.3 |
| biomaRt | >= 2.38.0 |
| rtracklayer | >= 1.42.2 |
3 Installation
We strongly recommand the way using devtools package in R.
But, you can download this package as zip-file format from our github repository.
Plus, we will upload this package to Bioconductor repository. It’s in progress.
Bioconductor (Recommended)
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("RIPAT")- By devtools R package
devtools::install_github("bioinfo16/RIPAT")- Or, download it through the menu releases and enter the following command in the console. But, this way doesn’t install package which is needed for running RIPAT.
R CMD INSTALL [PACKAGE_DOWNLOAD_PATH]4 Databases
RIPAT provides four types of site annotation analysis, Gene, CpG site, Repeat and pathogenic variant.
This R package uses Ensembl database, UCSC genome database and NCBI ClinVar in site annotation. Ensembl database is used to gene annotation. UCSC genome database is needed to annotation by gene, CpG site and repeat sequence. Pathogenic variant annotation uses from NCBI Clinvar database. This package can annotate integration sites on the human genome only. Avaliable target version is GRCh37 and GRCh38.
5 Input format
RIPAT can do integration pattern analysis with local alignment tools such as BLAST and BLAT. Each of cases makes the tab-delimited result file. Specific format for RIPAT is depicted to the table below.