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SeqVarTools

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

Tools for variant data

Bioconductor version: Development (3.18)

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 "4.3") 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

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

Details

biocViews GeneticVariability, Genetics, SNP, Sequencing, Software
Version 1.39.0
In Bioconductor since BioC 2.13 (R-3.0) (10 years)
License GPL-3
Depends SeqArray
Imports grDevices, graphics, stats, methods, Biobase, BiocGenerics, gdsfmt, GenomicRanges, IRanges, S4Vectors, GWASExactHW, logistf, Matrix, data.table
Linking To
Suggests BiocStyle, RUnit, stringr
System Requirements
Enhances
URL https://github.com/smgogarten/SeqVarTools
See More
Depends On Me
Imports Me GENESIS
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package SeqVarTools_1.39.0.tar.gz
Windows Binary SeqVarTools_1.39.0.zip
macOS Binary (x86_64) SeqVarTools_1.39.0.tgz
macOS Binary (arm64) SeqVarTools_1.39.0.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