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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 (3.19)

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 "4.4") 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 1.41.0
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
See More
Suggests BiocStyle, RUnit, stringr
Linking To
Enhances
Depends On Me
Imports Me GENESIS
Suggests Me GMMAT, MAGEE
Links To Me
Build Report Build Report

Package Archives

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

Source Package SeqVarTools_1.41.0.tar.gz
Windows Binary SeqVarTools_1.41.0.zip
macOS Binary (x86_64) SeqVarTools_1.41.0.tgz
macOS Binary (arm64) SeqVarTools_1.41.0.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