gateR: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation (original) (raw)
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: | 0.1.16 |
|---|---|
| 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: | 2025-08-29 |
| DOI: | 10.32614/CRAN.package.gateR |
| Author: | Ian D. Buller  [aut, cre, cph], Elena Hsieh [ctb], Debashis Ghosh [ctb], Lance A. Waller [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:
Downloads:
Linking:
Please use the canonical formhttps://CRAN.R-project.org/package=gateRto link to this page.