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]

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funkycells.pdf |funkycells.html
funkycells/json (API)
NEWS

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

Peer review:

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

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

On CRAN:

4.44 score 1 stars 11 scripts 140 downloads 11 exports 69 dependencies

Last updated 1 years agofrom:53a257086f. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 03 2024
R-4.5-winOKNov 03 2024
R-4.5-linuxOKNov 03 2024
R-4.4-winOKNov 03 2024
R-4.4-macOKNov 03 2024
R-4.3-winOKNov 03 2024
R-4.3-macOKNov 03 2024

Exports:computePseudoROCCurvesfunkyForestfunkyModelgetCountDatagetKFunctiongetKsPCADataplot_K_functionsplotPPpredict_funkyForestsimulateMetasimulatePP

Dependencies:abindashbitopscliclustercolorspacecpp11deldirdeSolvedplyrfansifarverfdafdsFNNgenericsggplot2gluegoftestgtablehdrcdeisobandkernlabKernSmoothkslabelinglatticelifecyclelocfitmagrittrMASSMatrixmclustmgcvmulticoolmunsellmvtnormnlmepcaPPpillarpkgconfigpolyclippracmapurrrR6rainbowRColorBrewerRcppRCurlrlangrpartscalesspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrtensortibbletidyrtidyselectutf8vctrsviridisLitewithr

funkycells

Rendered fromfunkycells.Rmdusingknitr::rmarkdownon Nov 03 2024.

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

lungcancer

Rendered fromlungcancer.Rmdusingknitr::rmarkdownon Nov 03 2024.

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

model_power_curves

Rendered frommodel_power_curves.Rmdusingknitr::rmarkdownon Nov 03 2024.

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

model_walkthrough

Rendered frommodel_walkthrough.Rmdusingknitr::rmarkdownon Nov 03 2024.

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

TNBC

Rendered fromTNBC.Rmdusingknitr::rmarkdownon Nov 03 2024.

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