VariantTools
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see VariantTools.
Tools for Exploratory Analysis of Variant Calls
Bioconductor version: 3.10
Explore, diagnose, and compare variant calls using filters.
Author: Michael Lawrence, Jeremiah Degenhardt, Robert Gentleman
Maintainer: Michael Lawrence <michafla at gene.com>
Citation (from within R, enter
citation("VariantTools")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("VariantTools")
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("VariantTools")| Introduction to VariantTools | R Script | |
| tutorial.pdf | ||
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneticVariability, Genetics, Sequencing, Software |
| Version | 1.28.1 |
| In Bioconductor since | BioC 2.11 (R-2.15) (11.5 years) |
| License | Artistic-2.0 |
| Depends | S4Vectors(>= 0.17.33), IRanges(>= 2.13.12), GenomicRanges(>= 1.31.8), VariantAnnotation(>= 1.11.16), methods |
| Imports | Rsamtools(>= 1.31.2), BiocGenerics, Biostrings, parallel, GenomicFeatures(>= 1.31.3), Matrix, rtracklayer(>= 1.39.7), BiocParallel, GenomeInfoDb, BSgenome, Biobase |
| System Requirements | |
| URL |
See More
| Suggests | RUnit, LungCancerLines(>= 0.0.6), RBGL, graph, gmapR(>= 1.21.3) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | HTSeqGenie, MMAPPR2, MTseeker |
| Suggests Me | VariantToolsData |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | VariantTools_1.28.1.tar.gz |
| Windows Binary | VariantTools_1.28.1.zip |
| Mac OS X 10.11 (El Capitan) | VariantTools_1.28.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/VariantTools |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/VariantTools |
| Bioc Package Browser | https://code.bioconductor.org/browse/VariantTools/ |
| Package Short Url | https://bioconductor.org/packages/VariantTools/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.10 | Source Archive |