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 18 Feb. 2025.
Previous versions and publish date:
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)
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
Get rewarded with contribution points by helping add
Reviews / comments / questions /suggestions ↴↴↴

Today's Hot Picks in Authors and Packages

fclust  
Fuzzy Clustering
Algorithms for fuzzy clustering, cluster validity indices and plots for cluster validity and visuali ...
Download / Learn more Package Citations See dependency  
MOSS  
Multi-Omic Integration via Sparse Singular Value Decomposition
High dimensionality, noise and heterogeneity among samples and features challenge the omic integrat ...
Download / Learn more Package Citations See dependency  
ppmf  
Read Census Privacy Protected Microdata Files
Implements data processing described in to align modern differentially ...
Download / Learn more Package Citations See dependency  
r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  
OptGS  
Near-Optimal Group-Sequential Designs for Continuous Outcomes
Optimal group-sequential designs minimise some function of the expected and maximum sample size whil ...
Download / Learn more Package Citations See dependency  
clustMixType  
k-Prototypes Clustering for Mixed Variable-Type Data
Functions to perform k-prototypes partitioning clustering for mixed variable-type data according to ...
Download / Learn more Package Citations See dependency  

23,712

R Packages

205,795

Dependencies

64,332

Author Associations

23,631

Publication Badges

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