phylobar - Interactive construction of stacked barplots using hierarchies
The phylobar package supports interactive visualization of microbiome data by allowing a stacked barplot to be constructed using a guiding taxonomic or phylogenetic hierarchy. The package provides a strategy for collapsing and expanding the hierarchy to different levels of resolution and then for interactively "painting" the stacked barplot by placing the mouse over different subtrees. This makes it possible to interactively test different color palettes at different resolution and identify taxonomic groups with interesting variation before settling on a final stacked barplot. One advantage of the approach is that multiple levels of taxonomic resolution can be compared at once within the same view.
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softwaremicrobiomephylogeneticsvisualization
7.26 score 3 stars 28 scripts 72 downloads
multimedia - Multimodal Mediation Analysis
Multimodal mediation analysis is an emerging problem in microbiome data analysis. Multimedia make advanced mediation analysis techniques easy to use, ensuring that all statistical components are transparent and adaptable to specific problem contexts. The package provides a uniform interface to direct and indirect effect estimation, synthetic null hypothesis testing, bootstrap confidence interval construction, and sensitivity analysis. More details are available in Jiang et al. (2024) "multimedia: Multimodal Mediation Analysis of Microbiome Data" <doi:10.1101/2024.03.27.587024>.
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coveragemicrobiomeregressionsequencingsoftwarestatisticalmethodstructuralequationmodelscausal-inferencedata-integrationmediation-analysis
5.16 score 3 stars 24 scripts 274 downloadsstructSSI - Multiple Testing for Hypotheses with Hierarchical or Group Structure
Performs multiple testing corrections that take specific structure of hypotheses into account, as described in Sankaran & Holmes (2014) <doi:10.18637/jss.v059.i13>.
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software
4.88 score 7 stars 27 scripts 257 downloads