An R package to deal with point sets from single moleculelocalization microscopy. This package provides four sets offunctionalities: - data input: read SMLM data as point sets either fromcsv files or from TIFF images - registration: point sets registrationusing different algorithms - topological data analysis: computesimilarity between point sets using persistent homology - alpha-shapes:compute alpha-shapes of point sets and derive 3d shape features
Apreprint describing the package is available on bioRxiv.
The package isavailable onCRAN.
(from the RStudio mirror)
install.packages("LOMAR")To install the development version of this package, run (from withinR):
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