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", "1.15.0")



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 1.15.0, https://cran.r-project.org/web/packages/vcfR. Accessed 26 Aug. 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

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  
RCytoGPS  
Using Cytogenetics Data in R
Defines classes and methods to process text-based cytogenetics using the CytoGPS web site, then imp ...
Download / Learn more Package Citations See dependency  
ncodeR  
Techniques for Automated Classifiers
A set of techniques that can be used to develop, validate, and implement automated classifiers. A po ...
Download / Learn more Package Citations See dependency  
leafgl  
High-Performance 'WebGl' Rendering for Package 'leaflet'
Provides bindings to the 'Leaflet.glify' JavaScript library which extends the 'leaflet' JavaScript l ...
Download / Learn more Package Citations See dependency  
PCADSC  
Tools for Principal Component Analysis-Based Data Structure Comparisons
A suite of non-parametric, visual tools for assessing differences in data structures for two datase ...
Download / Learn more Package Citations See dependency  
SelvarMix  
Regularization for Variable Selection in Model-Based Clustering and Discriminant Analysis
Performs a regularization approach to variable selection in themodel-based clustering and classifica ...
Download / Learn more Package Citations See dependency  

28,332

R Packages

239,283

Dependencies

75,113

Author Associations

28,333

Publication Badges

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