SeqVarTools

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see SeqVarTools.

Tools for variant data

Bioconductor version: 3.17

An interface to the fast-access storage format for VCF data provided in SeqArray, with tools for common operations and analysis.

Author: Stephanie M. Gogarten, Xiuwen Zheng, Adrienne Stilp

Maintainer: Stephanie M. Gogarten <sdmorris at uw.edu>

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

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SeqVarTools")

For older versions of R, please refer to the appropriate Bioconductor release.

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SeqVarTools")

Introduction to SeqVarTools	PDF	R Script
Iterators in SeqVarTools	PDF	R Script
Reference Manual	PDF
NEWS	Text

biocViews	GeneticVariability, Genetics, SNP, Sequencing, Software
Version	1.38.0
In Bioconductor since	BioC 2.13 (R-3.0) (10.5 years)
License	GPL-3
Depends	SeqArray
Imports	grDevices, graphics, stats, methods, Biobase, BiocGenerics, gdsfmt, GenomicRanges, IRanges, S4Vectors, GWASExactHW, logistf, Matrix, data.table
System Requirements
URL	https://github.com/smgogarten/SeqVarTools

Follow Installation instructions to use this package in your R session.

Source Package	SeqVarTools_1.38.0.tar.gz
Windows Binary	SeqVarTools_1.38.0.zip
macOS Binary (x86_64)	SeqVarTools_1.38.0.tgz
macOS Binary (arm64)	SeqVarTools_1.38.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SeqVarTools
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SeqVarTools
Bioc Package Browser	https://code.bioconductor.org/browse/SeqVarTools/
Package Short Url	https://bioconductor.org/packages/SeqVarTools/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive