SeqVarTools

DOI: 10.18129/B9.bioc.SeqVarTools  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see SeqVarTools.

Tools for variant data

Bioconductor version: 3.16

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>

Installation

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.

Documentation

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

browseVignettes("SeqVarTools")

 

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

Details

biocViews	GeneticVariability, Genetics, SNP, Sequencing, Software
Version	1.36.0
In Bioconductor since	BioC 2.13 (R-3.0) (9.5 years)
License	GPL-3
Depends	SeqArray
Imports	grDevices, graphics, stats, methods, Biobase, BiocGenerics, gdsfmt, GenomicRanges, IRanges, S4Vectors, GWASExactHW, logistf, Matrix, data.table
LinkingTo
Suggests	BiocStyle, RUnit, stringr
SystemRequirements
Enhances
URL	https://github.com/smgogarten/SeqVarTools
Depends On Me
Imports Me	GENESIS, VariantExperiment
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	SeqVarTools_1.36.0.tar.gz
Windows Binary	SeqVarTools_1.36.0.zip (64-bit only)
macOS Binary (x86_64)	SeqVarTools_1.36.0.tgz
macOS Binary (arm64)	SeqVarTools_1.36.0.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