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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>.

Version: 0.1.15
Depends: R (≥ 3.5.0)
Imports: fields, graphics, grDevices, lifecycle, rlang, sparr, SpatialPack, spatstat.geom, stats, terra, tibble
Suggests: dplyr, R.rsp, spelling, testthat, usethis, utils
Published: 2024-01-23
DOI: 10.32614/CRAN.package.gateR
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 alumni.emory.edu>
BugReports: https://github.com/lance-waller-lab/gateR/issues
License: Apache License (≥ 2.0)
URL: https://github.com/lance-waller-lab/gateR
NeedsCompilation: no
Language: en-US
Citation: gateR citation info
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_0.1.15.tar.gz
Windows binaries: r-devel: gateR_0.1.15.zip, r-release: gateR_0.1.15.zip, r-oldrel: gateR_0.1.15.zip
macOS binaries: r-release (arm64): gateR_0.1.15.tgz, r-oldrel (arm64): gateR_0.1.15.tgz, r-release (x86_64): gateR_0.1.15.tgz, r-oldrel (x86_64): gateR_0.1.15.tgz
Old sources: gateR archive

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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.