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An R package to deal with point sets from single molecule localization microscopy. This package provides four sets of functionalities: - data input: read SMLM data as point sets either from csv files or from TIFF images - registration: point sets registration using different algorithms - topological data analysis: compute similarity between point sets using persistent homology - alpha-shapes: compute alpha-shapes of point sets and derive 3d shape features
A preprint describing the package is available on bioRxiv.
The package is available on CRAN.
(from the RStudio mirror)
install.packages("LOMAR")To install the development version of this package, run (from within R):
library(devtools)
install_git('https://git.embl.de/heriche/lomar')This package depends on these other packages: * data.table * FNN * foreach * parallel * doParallel * proxy * reshape2 * pracma * transport * RANN * ff * dbscan * EBImage (from Bioconductor) * tools * rhdf5 * mclust * alphashape3d
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.