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bioc
LEA:LEA: an R package for Landscape and Ecological Association Studies
LEA is an R package dedicated to population genomics, landscape genomics and genotype-environment association tests. LEA can run analyses of population structure and genome-wide tests for local adaptation, and also performs imputation of missing genotypes. The package includes statistical methods for estimating ancestry coefficients from large genotypic matrices and for evaluating the number of ancestral populations (snmf). It performs statistical tests using latent factor mixed models for identifying genetic polymorphisms that exhibit association with environmental gradients or phenotypic traits (lfmm2). In addition, LEA computes values of genetic offset statistics based on new or predicted environments (genetic.gap, genetic.offset). LEA is mainly based on optimized programs that can scale with the dimensions of large data sets.
Maintained by Olivier Francois. Last updated 5 days ago.
softwarestatistical methodclusteringregressionopenblas
20.8 match 6.63 score 534 scripts
kfarleigh
PopGenHelpR:Streamline Population Genomic and Genetic Analyses
Estimate commonly used population genomic statistics and generate publication quality figures. 'PopGenHelpR' uses vcf, 'geno' (012), and csv files to generate output.
Maintained by Keaka Farleigh. Last updated 8 months ago.
diversityfstheterozygosityinterpolationneispopulation-geneticspopulation-genomicsprivate-allelessnmfstructurevcf
11.0 match 3 stars 5.17 score 14 scripts
evolecolgroup
tidypopgen:Tidy Population Genetics
We provide a tidy grammar of population genetics, facilitating the manipulation and analysis of data on biallelic single nucleotide polymorphisms (SNPs).
Maintained by Andrea Manica. Last updated 3 days ago.
3.6 match 4 stars 5.83 score 8 scripts