Other packages > Find by keyword >

vcfR  

Manipulate and Visualize VCF Data
View on CRAN: Click here


Download and install vcfR package within the R console
Install from CRAN:
install.packages("vcfR")

Install from Github:
library("remotes")
install_github("cran/vcfR")

Install by package version:
library("remotes")
install_version("vcfR", "1.16.0")



Attach the package and use:
library("vcfR")
Maintained by
Brian J. Knaus
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2016-02-22
Latest Update: 2023-12-08
Description:
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.
How to cite:
Brian J. Knaus (2016). vcfR: Manipulate and Visualize VCF Data. R package version 1.16.0, https://cran.r-project.org/web/packages/vcfR. Accessed 08 Oct. 2026.
Previous versions and publish date:
(2026-07-09 06:58), 1.0.0 (2016-02-22 22:51), 1.1.0 (2016-05-26 17:54), 1.2.0 (2016-12-05 18:28), 1.3.0 (2016-12-08 15:30), 1.4.0 (2017-01-07 17:45), 1.5.0 (2017-05-18 06:17), 1.6.0 (2017-12-08 01:09), 1.7.0 (2018-02-08 00:34), 1.8.0 (2018-04-17 19:11), 1.9.0 (2020-01-10 11:50), 1.10.0 (2020-02-06 10:50), 1.11.0 (2020-06-05 14:50), 1.12.0 (2020-09-01 10:40), 1.13.0 (2022-07-16 16:30), 1.14.0 (2023-02-10 16:00), 1.15.0 (2023-12-08 01:30)
Other packages that cited vcfR R package
View vcfR citation profile
Other R packages that vcfR depends, imports, suggests or enhances
Complete documentation for vcfR
Functions, R codes and Examples using the vcfR R package
Some associated functions: AD_frequency . INFO2df . addID . check_keys . chromR-class . chromR-method . chromR_example . chromR_functions . chrom_to_vcfR . chromo_plot . create_chromR . drplot . extract_gt . fasta_output . freq_peak . freq_peak_plot . genetic_diff . genotype_matrix . getFIX . heatmap_bp . io_vcfR . is_het . maf . masplit . ordisample . pairwise_genetic_diff . peak_to_ploid . pipe . pop_gen_sum . proc_chromR . queryMETA . query_gt . ranking . rePOS . summary_tables . vcfR-class . vcfR-method . vcfR-package . vcfR2DNAbin . vcfR2hapmap . vcfR2migrate . vcfR_conversion . vcfR_example . vcfR_test . vcfR_to_tidy_conversion . vep . windowing . 
Some associated R codes: AllClass.R . INFO2df.R . RcppExports.R . addID.R . check_keys.R . chromR-method.R . chromR_example.R . chromR_functions.R . chromR_to_vcfR.R . chromo_plot.R . create_chromR.R . drplot.R . extract_gt.R . fasta_output.R . freq_peak_plot.R . genetic_diff.R . genotype_matrix_functions.R . get_methods.R . gt_to_popsum.R . heatmap_bp.R . io_vcfR.R . is_het.R . maf.R . onUnload.R . ordisample.R . pairwise_genetic_diff.R . peak_to_ploid.R . pipe.R . proc_chromR.R . queryMETA.R . query_gt.R . ranking.R . rePOS.R . sandbox.R . summary_tables.R . vcfR-method.R . vcfR-package.R . vcfR.R . vcfR2DNAbin.R . vcfR2hapmap.R . vcfR2migrate.R . vcfR_conversion.R . vcfR_example.R . vcfR_test.R . vcfR_to_tidy_functions.R . vep.R . windowing.R . zzz.R .  Full vcfR package functions and examples
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

dineR  
Differential Network Estimation in R
An efficient and convenient set of functions to perform differential network estimation through the ...
Download / Learn more Package Citations See dependency  
nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
climwin  
Climate Window Analysis
Contains functions to detect and visualise periods of climate sensitivity (climate windows) for a g ...
Download / Learn more Package Citations See dependency  
metafor  
Meta-Analysis Package for R
A comprehensive collection of functions for conducting meta-analyses in R. The package includes func ...
Download / Learn more Package Citations See dependency  
colorfindr  
Extract Colors from Windows BMP, JPEG, PNG, TIFF, and SVG Format Images
Extracts colors from various image types, returns customized reports and plots treemaps and 3D scat ...
Download / Learn more Package Citations See dependency  
abc.data  
Data Only: Tools for Approximate Bayesian Computation (ABC)
Contains data which are used by functions of the 'abc' package. ...
Download / Learn more Package Citations See dependency  

28,905

R Packages

247,686

Dependencies

76,495

Author Associations

28,906

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA