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: | 1.15.0 |
| Depends: | R (≥ 3.0.1) |
| Imports: | ape, dplyr, graphics, grDevices, magrittr, memuse, methods, pinfsc50, Rcpp, stats, stringr, tibble, utils, vegan, viridisLite |
| LinkingTo: | Rcpp |
| Suggests: | adegenet, ggplot2, knitr, poppr, reshape2, rmarkdown, scales, testthat, tidyr |
| Published: | 2023-12-08 |
| DOI: | 10.32614/CRAN.package.vcfR |
| Author: | Brian J. Knaus 
[cre, aut],
Niklaus J. Grunwald
[aut],
Eric C. Anderson
[ctb],
David J. Winter [ctb],
Zhian N. Kamvar
[ctb],
Javier F. Tabima
[ctb] |
| Maintainer: | Brian J. Knaus <briank.lists at gmail.com> |
| License: | GPL-3 |
| URL: | https://github.com/knausb/vcfR, https://knausb.github.io/vcfR_documentation/ |
| NeedsCompilation: | yes |
| Citation: | vcfR citation info |
| Materials: | README |
| CRAN checks: | vcfR results |
Documentation:
| Reference manual: | vcfR.pdf |
| Vignettes: |
Converting data Introduction to vcfR vcf data vcfR workflow |
Downloads:
| Package source: | vcfR_1.15.0.tar.gz |
| Windows binaries: | r-devel: vcfR_1.15.0.zip, r-release: vcfR_1.15.0.zip, r-oldrel: vcfR_1.15.0.zip |
| macOS binaries: | r-release (arm64): vcfR_1.15.0.tgz, r-oldrel (arm64): vcfR_1.15.0.tgz, r-release (x86_64): vcfR_1.15.0.tgz, r-oldrel (x86_64): vcfR_1.15.0.tgz |
| Old sources: | vcfR archive |
Reverse dependencies:
| Reverse imports: | CaMutQC, cardelino, diemr, epinetr, GARCOM, geneHapR, GenomeAdmixR, MADSEQ, mappoly, MixviR, numbat, onemap, PopGenHelpR, RADstackshelpR, SNPfiltR, vivaldi, whoa, wingen |
| Reverse suggests: | coreCollection, dartR, dartR.base, MoBPS, pcadapt, rehh, sequoia |
Linking:
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