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thibautjombart
adegenet:Exploratory Analysis of Genetic and Genomic Data
Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.
Maintained by Zhian N. Kamvar. Last updated 2 months ago.
182 stars 12.60 score 1.9k scripts 29 dependents
jgx65
hierfstat:Estimation and Tests of Hierarchical F-Statistics
Estimates hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in the hierarchy, following the algorithm of Yang (Evolution(1998), 52:950). Tests via randomisations the significance of each F and variance components, using the likelihood-ratio statistics G (Goudet et al. (1996) <https://academic.oup.com/genetics/article/144/4/1933/6017091>). Estimates genetic diversity statistics for haploid and diploid genetic datasets in various formats, including inbreeding and coancestry coefficients, and population specific F-statistics following Weir and Goudet (2017) <https://academic.oup.com/genetics/article/206/4/2085/6072590>.
Maintained by Jerome Goudet. Last updated 4 months ago.
devtoolsfstatisticsgwashierfstatkinshippopulation-geneticspopulation-genomicsquantitative-geneticssimulations
25 stars 11.06 score 560 scripts 5 dependents