SeqVarTools

DOI: 10.18129/B9.bioc.SeqVarTools    

Tools for variant data

Bioconductor version: Release (3.8)

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 "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("SeqVarTools", version = "3.8")

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   Reference Manual
Text   NEWS

Details

biocViews GeneticVariability, Genetics, SNP, Sequencing, Software
Version 1.20.0
In Bioconductor since BioC 2.13 (R-3.0) (5 years)
License GPL-3
Depends SeqArray
Imports grDevices, graphics, stats, methods, Biobase, gdsfmt, GenomicRanges, IRanges, S4Vectors, GWASExactHW, logistf, Matrix, dplyr, tidyr
LinkingTo
Suggests BiocGenerics, BiocStyle, RUnit, stringr
SystemRequirements
Enhances
URL https://github.com/smgogarten/SeqVarTools
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_1.20.0.tar.gz
Windows Binary SeqVarTools_1.20.0.zip
Mac OS X 10.11 (El Capitan) SeqVarTools_1.20.0.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 http://bioconductor.org/packages/SeqVarTools/
Package Downloads Report Download Stats

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