Package: mxfda 0.2.2-1

Alex Soupir

mxfda: A Functional Data Analysis Package for Spatial Single Cell Data

Methods and tools for deriving spatial summary functions from single-cell imaging data and performing functional data analyses. Functions can be applied to other single-cell technologies such as spatial transcriptomics. Functional regression and functional principal component analysis methods are in the 'refund' package <https://cran.r-project.org/package=refund> while calculation of the spatial summary functions are from the 'spatstat' package <https://spatstat.org/>.

Authors:Julia Wrobel [aut], Alex Soupir [aut, cre]

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mxfda.pdf |mxfda.html✨
mxfda/json (API)

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

Bug tracker:https://github.com/julia-wrobel/mxfda/issues

Pkgdown site:https://juliawrobel.com

Datasets:
  • lung_FDA - Multiplex imaging data from a non-small cell lung cancer study
  • lung_df - Multiplex imaging data from a non-small cell lung cancer study.
  • ovarian_FDA - Multiplex imaging data from an ovarian cancer tumor microarray

On CRAN:

Conda:

5.08 score 1 stars 8 scripts 282 downloads 35 exports 121 dependencies

Last updated 1 months agofrom:bc5cfaf8e7. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 21 2025
R-4.5-winOKMar 21 2025
R-4.5-macOKMar 21 2025
R-4.5-linuxOKMar 21 2025
R-4.4-winOKMar 21 2025
R-4.4-macOKMar 21 2025
R-4.4-linuxOKMar 21 2025
R-4.3-winOKMar 21 2025
R-4.3-macOKMar 21 2025

Exports:%>%add_summary_functionbivariatecan_permuteentropyextract_cextract_entropyextract_fpca_objectextract_fpca_scoresextract_modelextract_spatial_summaryextract_summary_functionsextract_surfacefilter_datafilter_spatialGcrossGestget_datais.emptyKcrossKestLcrossLestmake_mxfdametric.existsone_zeroplot_fpcplot_mfpcrun_fcmrun_fpcarun_mfcmrun_mfpcarun_sofrspatialTIME_summary_functionsunivariate

Dependencies:abindashaudiobeeprbitopsbootbriocallrcliclustercodetoolscolorspacecpp11crayondeldirdescdeSolvediffobjdigestdplyrevaluatefansifarverfdafdsFNNfsfuturefuture.applygamm4genericsggplot2globalsgluegoftestgrpreggtablehdrcdeisobandjsonlitekernlabKernSmoothkslabelinglatticelifecyclelistenvlme4locfitmagicmagrittrMASSMatrixmclustmgcvminqamulticoolmunsellmvtnormnlmenloptrparallellypbapplypbspcaPPpillarpkgbuildpkgconfigpkgloadplyrpolyclippracmapraiseprocessxprogressrpspurrrR.methodsS3R.ooR.utilsR6rainbowrbibutilsRColorBrewerRcppRcppEigenRCurlRdpackreformulasrefundreshape2rlangRLRsimrpartrprojrootscalessessioninfoSimDesignSpatEntropyspatstatspatstat.dataspatstat.explorespatstat.geomspatstat.linnetspatstat.modelspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrtensortestthattibbletidyrtidyselectutf8vctrsviridisLitewaldowithr

Defining an mxFDA object

Rendered frommx_fda.Rmdusingknitr::rmarkdownon Mar 21 2025.

Last update: 2024-10-04
Started: 2023-05-16

Functional principal component analysis for spatial summary functions

Rendered frommx_fpca.Rmdusingknitr::rmarkdownon Mar 21 2025.

Last update: 2024-10-04
Started: 2023-11-16

Functional regression with spatial summary functions as covariates

Rendered frommx_funreg.Rmdusingknitr::rmarkdownon Mar 21 2025.

Last update: 2024-10-04
Started: 2023-05-16