SeqVarTools
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see SeqVarTools.
Tools for variant data
Bioconductor version: 3.11
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 "4.0") 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")| Introduction to SeqVarTools | R Script | |
| Iterators in SeqVarTools | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneticVariability, Genetics, SNP, Sequencing, Software |
| Version | 1.26.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (10.5 years) |
| License | GPL-3 |
| Depends | SeqArray |
| Imports | grDevices, graphics, stats, methods, Biobase, gdsfmt, GenomicRanges, IRanges, S4Vectors, GWASExactHW, logistf, Matrix, dplyr, rlang, tidyr |
| System Requirements | |
| URL | https://github.com/smgogarten/SeqVarTools |
See More
| Suggests | BiocGenerics, BiocStyle, RUnit, stringr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | GENESIS, VariantExperiment |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SeqVarTools_1.26.0.tar.gz |
| Windows Binary | SeqVarTools_1.26.0.zip |
| macOS 10.13 (High Sierra) | SeqVarTools_1.26.0.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 |
| Old Source Packages for BioC 3.11 | Source Archive |