Package: funkycells 1.1.1.9000

Jeremy VanderDoes

funkycells: Functional Data Analysis for Multiplexed Cell Images

Compare variables of interest between (potentially large numbers of) spatial interactions and meta-variables. Spatial variables are summarized using K, or other, functions, and projected for use in a modified random forest model. The model allows comparison of functional and non-functional variables to each other and to noise, giving statistical significance to the results. Included are preparation, modeling, and interpreting tools along with example datasets, as described in VanderDoes et al., (2023) <doi:10.1101/2023.07.18.549619>.

Authors:Jeremy VanderDoes [aut, cre, cph], Jack Hywood [aut], Gregory Rice [aut]

funkycells_1.1.1.9000.tar.gz
funkycells_1.1.1.9000.zip(r-4.7)funkycells_1.1.1.9000.zip(r-4.6)funkycells_1.1.1.9000.zip(r-4.5)
funkycells_1.1.1.9000.tgz(r-4.6-any)funkycells_1.1.1.9000.tgz(r-4.5-any)
funkycells_1.1.1.9000.tar.gz(r-4.7-any)funkycells_1.1.1.9000.tar.gz(r-4.6-any)
funkycells_1.1.1.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
funkycells/json (API)

# Install 'funkycells' in R:
install.packages('funkycells', repos = c('https://jrvanderdoes.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jrvanderdoes/funkycells/issues

Pkgdown/docs site:https://jrvanderdoes.github.io

Datasets:
  • TNBC - Triple Negative Breast Cancer Data
  • TNBC_meta - Triple Negative Breast Cancer Phenotypes
  • TNBC_pheno - Triple Negative Breast Cancer Phenotypes

On CRAN:

Conda:

4.60 score 1 stars 16 scripts 258 downloads 11 exports 68 dependencies

Last updated from:53a257086f. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK150
source / vignettesOK249
linux-release-x86_64OK161
macos-release-arm64OK161
macos-oldrel-arm64OK207
windows-develOK131
windows-releaseOK106
windows-oldrelOK91
wasm-releaseOK105

Exports:computePseudoROCCurvesfunkyForestfunkyModelgetCountDatagetKFunctiongetKsPCADataplot_K_functionsplotPPpredict_funkyForestsimulateMetasimulatePP

Dependencies:abindashbitopscliclustercolorspacecpp11deldirdeSolvedplyrfarverfdafdsFNNgenericsggplot2gluegoftestgtablehdrcdeisobandkernlabKernSmoothkslabelinglatticelifecyclelocfitmagrittrMASSMatrixmclustmgcvmulticoolmvtnormnlmepcaPPpillarpkgconfigpolyclippracmapurrrR6rainbowRColorBrewerRcppRCurlrlangrpartS7scalesspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrtensortibbletidyrtidyselectutf8vctrsviridisLitewithr

model_power_curves
Rendered frommodel_power_curves.Rmdusingknitr::rmarkdown

Last update: 2023-07-21
Started: 2023-07-09

model_walkthrough
Rendered frommodel_walkthrough.Rmdusingknitr::rmarkdown

Last update: 2023-07-21
Started: 2023-06-04

TNBC
Rendered fromTNBC.Rmdusingknitr::rmarkdown

Last update: 2023-07-21
Started: 2023-01-04

funkycells
Overview | Data | Model | Other Investigations | Conclusion
Rendered fromfunkycells.Rmdusingknitr::rmarkdown

Last update: 2023-07-18
Started: 2023-05-24

lungcancer
Rendered fromlungcancer.Rmdusingknitr::rmarkdown

Last update: 2023-07-18
Started: 2023-07-09