SeqVarTools

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see SeqVarTools.

Tools for variant data

Bioconductor version: 3.15

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 "4.2") 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

Version 1.34.0

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

Suggests BiocStyle, RUnit, stringr

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

Windows Binary SeqVarTools_1.34.0.zip

macOS Binary (x86_64) SeqVarTools_1.34.0.tgz

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

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

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Old Source Packages for BioC 3.15 Source Archive