Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation

Estimates statistically significant marker combination values within which one immunologically distinctive group (i.e., disease case) is more associated than another group (i.e., healthy control), successively, using various combinations (i.e., "gates") of markers to examine features of cells that may be different between groups. For a two-group comparison, the 'gateR' package uses the spatial relative risk function that is estimated using the 'sparr' package. Details about the 'sparr' package methods can be found in the tutorial: Davies et al. (2018) . Details about kernel density estimation can be found in J. F. Bithell (1990) . More information about relative risk functions using kernel density estimation can be found in J. F. Bithell (1991) .


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install.packages("gateR")

0.1.9 by Ian D. Buller, 3 months ago


https://github.com/Waller-SUSAN/gateR


Report a bug at https://github.com/Waller-SUSAN/gateR/issues


Browse source code at https://github.com/cran/gateR


Authors: Ian D. Buller [aut, cre, cph] , Elena Hsieh [ctb] , Debashis Ghosh [ctb] , Lance A. Waller [ctb] , NCI [cph]


Documentation:   PDF Manual  


Apache License (>= 2.0) license


Imports fields, graphics, grDevices, lifecycle, raster, rlang, sparr, SpatialPack, stats, tibble, utils

Depends on spatstat.geom, spatstat.core, spatstat.linnet, spatstat

Suggests R.rsp, spelling, testthat


See at CRAN