rhierbaps - Clustering Genetic Sequence Data Using the HierBAPS Algorithm
Implements the hierarchical Bayesian analysis of populations structure (hierBAPS) algorithm of Cheng et al. (2013) <doi:10.1093/molbev/mst028> for clustering DNA sequences from multiple sequence alignments in FASTA format. The implementation includes improved defaults and plotting capabilities and unlike the original 'MATLAB' version removes singleton SNPs by default.
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population-geneticspopulation-genomicspopulation-structure
5.89 score 36 stars 43 scripts 357 downloadsstrainspy - Strain Level Microbiome Wide Association Studies
Fits statistical models to detect microbial strains associated with a phenotype. For small sample sizes, models can be fitted using empirical Bayes maximum a posteriori (MAP) priors to improve detection power. Supports various experimental design scenarios, including repeated measures.
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softwaremicrobiomemetagenomicsmicrobialstraindifferentialexpressionregressionexperimentaldesignsequencing
5.86 score 13 stars 46 scripts