An R package for feature selection in topological spaces.
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RayleighSelection.Rproj

README.md

RayleighSelection

RayleighSelection is an R package for feature selection in topological spaces. Features are defined as differential forms on a simplicial complex and their significance is assesed through Rayleigh quotients

Installation

library(devtools)
install_github("CamaraLab/RayleighSelection")

Tutorials

Nerve complex on toy data

Given an open cover and a feature on points, compute the Combinatorial Laplacian scores of that feature on the nerve complex of the cover.

Vietoris-Rips on cyclic scRNA-seq data

Given the PCA results of mouse embryonic cells in two differentiation protocols and an ordering on the cells, create a Vietoris-Rips complex. Compute the Combinatorial Laplacian score of gene expression on either just the 0-forms (fast) or both 0-forms and 1-forms (slow).

Nerve complex on Mapper representation of MNIST

Run Mapper on the MNIST dataset to compute an open cover on the handwriting samples, then compute the Combinatorial Laplacian score of the pixel intensity.