vcfR: Manipulate and Visualize VCF Data

Canonical link: https://rscholar.com/pkg/vcfR

Brian J. Knaus • Niklaus J. Grunwald • Eric C. Anderson • David J. Winter • Zhian N. Kamvar • Javier F. Tabima • View description and downloads View dependencies GitHub project

2016 Published

0 Citations

6 Authors

15 Revisions

1.15.0 Version

GPL-3 License

Referenced by ⇅	Year
LDheatmap: Graphical Display of Pairwise Linkage Disequilibria Between SNPs (Version 1.0-6)	2005
perfectphyloR: Reconstruct Perfect Phylogenies from DNA Sequence Data (Version 0.2.1)	2019
prewas: Data Pre-Processing for Bacterial Genome-Wide Association Studies (Version 1.1.1)	2020
utr.annotation: Annotate Variants in the Untranslated Regions (Version 1.0.4)	2021
dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis (Version 2.9.9.5)	2017
diemr: Genome Polarization via Diagnostic Index Expectation Maximization (Version 1.5.3)	2022
geneHapR: Gene Haplotype Statistics, Phenotype Association and Visualization (Version 1.2.4)	2022
rehh: Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests (Version 3.2.2)	2012
coreCollection: Core Collection (Version 0.9.5)	2022
geneHapR Visualization: (Version )	0
ApplyPolygenicScore: Utilities for the Application of a Polygenic Score to a VCF (Version 4.0.0)	2025
BIGr Species: (Version )	0
GARCOM: Gene and Region Counting of Mutations ("GARCOM") (Version 1.2.2)	2020
GenePopStats: Population Genetics Statistics for Selective Sweep (Version 0.1.0)	2025
GenomeAdmixR: Simulate Admixture of Genomes (Version 2.1.12)	2021
MixviR: Analysis and Exploration of Mixed Microbial Genomic Samples (Version 3.5.0)	2022
MoBPS: Modular Breeding Program Simulator (Version 1.13.1)	2020
PopGenHelpR: Streamline Population Genomic and Genetic Analyses (Version 1.4.2)	2023
RADstackshelpR: Optimize the De Novo Stacks Pipeline via R (Version 0.1.0)	2021
SNPfiltR: Interactively Filter SNP Datasets (Version 1.0.7)	2021
castgen: Estimate Sample Size for Population Genomic Studies (Version 1.0.2)	2025
dartR.base: Analysing 'SNP' and 'Silicodart' Data - Basic Functions (Version 1.0.7)	2023
diemr Maximization: (Version )	0
epinetr: Epistatic Network Modelling with Forward-Time Simulation (Version 0.96)	2020
geneNR: Automated Gene Identification for Post-GWAS and QTL Analysis (Version 2.0.1)	2025
mappoly: Genetic Linkage Maps in Autopolyploids (Version 0.4.2)	2020
numbat: Haplotype-Aware CNV Analysis from scRNA-Seq (Version 1.5.1)	2022
onemap: Construction of Genetic Maps in Experimental Crosses (Version 3.2.4)	2008
pcadapt: Fast Principal Component Analysis for Outlier Detection (Version 4.4.1)	2015
sequoia: Pedigree Inference from SNPs (Version 3.2.0)	2017
statgenGWAS: Genome Wide Association Studies (Version 1.0.12)	2020
tidypopgen: Tidy Population Genetics (Version 0.4.1)	2025
vivaldi: Viral Variant Location and Diversity (Version 1.0.1)	2022
whoa: Evaluation of Genotyping Error in Genotype-by-Sequencing Data (Version 0.0.2)	2019
wingen: Continuous Mapping of Genetic Diversity (Version 2.2.0)	2024

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