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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 22 Dec. 2024.
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
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