vcfR: Manipulate and Visualize VCF Data

Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file (*.vcf.gz). It also may be converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and familiar R software.

Version: 1.3.0
Depends: R (≥ 3.0.1)
Imports: ape, dplyr, graphics, grDevices, magrittr, memuse, methods, pinfsc50, Rcpp, stats, stringr, tidyr, utils, vegan, viridisLite
LinkingTo: Rcpp
Suggests: adegenet, ggplot2, knitr, poppr, reshape2, rmarkdown, scales, testthat
Published: 2016-12-08
Author: Brian J. Knaus [cre, aut], Niklaus J. Grunwald [aut], Eric C. Anderson [ctb], David J. Winter [ctb], Zhian N. Kamvar [ctb]
Maintainer: Brian J. Knaus <briank.lists at gmail.com>
License: GPL-2 | GPL-3 [expanded from: GPL]
NeedsCompilation: yes
Citation: vcfR citation info
Materials: README
CRAN checks: vcfR results

Downloads:

Reference manual: vcfR.pdf
Vignettes: Converting data
Filtering data
Introduction to vcfR
Ranking data
Sequence coverage
vcf data
Visualization 1
Visualization 2
Package source: vcfR_1.3.0.tar.gz
Windows binaries: r-devel: vcfR_1.3.0.zip, r-release: vcfR_1.3.0.zip, r-oldrel: vcfR_1.2.0.zip
OS X Mavericks binaries: r-release: vcfR_1.3.0.tgz, r-oldrel: vcfR_1.2.0.tgz
Old sources: vcfR archive

Reverse dependencies:

Reverse depends: pcadapt

Linking:

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