SeqVarTools

This is the development version of SeqVarTools; for the stable release version, see SeqVarTools.

Tools for variant data

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DOI: 10.18129/B9.bioc.SeqVarTools

Bioconductor version: Development (3.23)

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")):

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("SeqVarTools")

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

Documentation

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneticVariability, Genetics, SNP, Sequencing, Software

Version 1.49.0

In Bioconductor since BioC 2.13 (R-3.0) (12 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

Suggests BiocStyle, RUnit, stringr

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Package Archives

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

Source Package

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64)

Source Repository git clone https://git.bioconductor.org/packages/SeqVarTools

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SeqVarTools

Package Short Url https://bioconductor.org/packages/SeqVarTools/

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