SeqVarTools

DOI: 10.18129/B9.bioc.SeqVarTools    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see SeqVarTools.

Tools for variant data

Bioconductor version: 3.13

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 "4.1") and enter:

if (!requireNamespace("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 1.30.0
In Bioconductor since BioC 2.13 (R-3.0) (8 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_1.30.0.tar.gz
Windows Binary SeqVarTools_1.30.0.zip
macOS 10.13 (High Sierra) SeqVarTools_1.30.0.tgz
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/
Package Downloads Report Download Stats

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