VariantTools
This is the development version of VariantTools; for the stable release version, see VariantTools.
Tools for Exploratory Analysis of Variant Calls
Bioconductor version: Development (3.20)
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 "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("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 | 1.47.0 |
In Bioconductor since | BioC 2.11 (R-2.15) (12 years) |
License | Artistic-2.0 |
Depends | R (>= 3.5.0), 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), TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | HTSeqGenie |
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_1.47.0.tar.gz |
Windows Binary | VariantTools_1.47.0.zip (64-bit only) |
macOS Binary (x86_64) | VariantTools_1.47.0.tgz |
macOS Binary (arm64) | VariantTools_1.47.0.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 |