Package: gateR 0.1.15

Ian D. Buller

gateR: 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 estimated using the 'sparr' package. Details about the 'sparr' package methods can be found in the tutorial: Davies et al. (2018) <doi:10.1002/sim.7577>. Details about kernel density estimation can be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>. More information about relative risk functions using kernel density estimation can be found in J. F. Bithell (1991) <doi:10.1002/sim.4780101112>.

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

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Bug tracker:https://github.com/lance-waller-lab/gater/issues

On CRAN:

cytometryflow-cytometrygatingkernel-density-estimationmass-cytometrynon-euclidean-spacesspatial-analysis

6 exports 2 stars 1.03 score 46 dependencies 6 scripts 305 downloads

Last updated 8 months agofrom:35f2530c0b. Checks:OK: 7. Indexed: yes.

Exports:gatinglotrrslrr_plotpval_correctpval_plotrrs

Dependencies:abindclicodetoolsdeldirdoParalleldotCall64fansifastmatrixfieldsforeachgluegoftestiteratorslatticelifecyclemagrittrmapsMatrixmgcvmisc3dnlmepillarpkgconfigpolyclipRcpprlangrpartspamsparrSpatialPackspatstatspatstat.dataspatstat.explorespatstat.geomspatstat.linnetspatstat.modelspatstat.randomspatstat.sparsespatstat.univarspatstat.utilstensorterratibbleutf8vctrsviridisLite