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 that is 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>.

Version: 0.1.9
Depends: R (≥ 3.5.0), spatstat.geom, spatstat.core, spatstat.linnet, spatstat (≥ 2.0-0)
Imports: fields, graphics, grDevices, lifecycle, raster, rlang, sparr, SpatialPack, stats, tibble, utils
Suggests: R.rsp, spelling, testthat
Published: 2021-06-25
Author: Ian D. Buller ORCID iD [aut, cre, cph], Elena Hsieh ORCID iD [ctb], Debashis Ghosh ORCID iD [ctb], Lance A. Waller ORCID iD [ctb], NCI [cph]
Maintainer: Ian D. Buller <ian.buller at nih.gov>
BugReports: https://github.com/Waller-SUSAN/gateR/issues
License: Apache License (≥ 2.0)
URL: https://github.com/Waller-SUSAN/gateR
NeedsCompilation: no
Language: en-US
Materials: README NEWS
CRAN checks: gateR results

Documentation:

Reference manual: gateR.pdf
Vignettes: gateR: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation

Downloads:

Package source: gateR_0.1.9.tar.gz
Windows binaries: r-devel: gateR_0.1.9.zip, r-release: gateR_0.1.9.zip, r-oldrel: gateR_0.1.9.zip
macOS binaries: r-release (arm64): gateR_0.1.9.tgz, r-release (x86_64): gateR_0.1.9.tgz, r-oldrel: gateR_0.1.9.tgz
Old sources: gateR archive

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