SeqVarTools

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13

Tools for variant data

Bioconductor version: Development (3.24)

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")):

Stephanie M. Gogarten, Xiuwen Zheng, Adrienne Stilp. SeqVarTools: Tools for variant data. doi:10.18129/B9.bioc.SeqVarTools, R package version 1.51.3, https://bioconductor.org/packages/SeqVarTools.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneticVariability, Genetics, SNP, Sequencing, Software
Version	1.51.3
In Bioconductor since	BioC 2.13 (R-3.0) (13 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

Suggests	BiocStyle, RUnit, stringr, knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me	GENESIS
Suggests Me	GMMAT, MAGEE
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	SeqVarTools_1.51.3.tar.gz
Windows Binary (x86_64)	SeqVarTools_1.51.3.zip (64-bit only)
macOS Binary (big-sur-x86_64)	SeqVarTools_1.51.3.tgz
macOS Binary (sonoma-arm64)	SeqVarTools_1.51.3.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