RIPAT
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This is the development version of RIPAT; for the stable release version, see RIPAT.
Retroviral Integration Pattern Analysis Tool (RIPAT)
Bioconductor version: Development (3.19)
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("RIPAT")):
Installation
To install this package, start R (version "4.4") 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
| Reference Manual |
Details
| biocViews | Annotation, Software |
| Version | 1.13.1 |
| 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/ |
See More
| Suggests | knitr (>= 1.28) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary | |
| macOS Binary (x86_64) | RIPAT_1.13.1.tgz |
| macOS Binary (arm64) | RIPAT_1.13.1.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 |