adaptiveGPCA

adaptiveGPCA is an R package for structured dimensionality reduction.

The package is available on CRAN, and can be installed using

install.packages("adaptiveGPCA")

[paper] [github] [quick start] [long vignette]

treeDA

treeDA is an R package for sparse, tree-based discriminant analysis for microbiome data.

The package is available on CRAN, and can be installed using

install.packages("treeDA")

[paper] [github] [vignette]

phyloseqGraphTest

phyloseqGraphTest is an R package implementing a permutational version of the Friedman-Rafsky test. It is designed to work with a phyloseq object describing a microbiome experiment, and allows for testing based on minimum spanning trees, k-nearest neighbor graphs, or distance threshold graphs with any of the many distances implemented in phyloseq. It also allows for permutation in stratified designs.

The package can be installed from GitHub using

devtools::install_github("jfukuyama/phyloseqGraphTest")

[poster] [github]