Package: mxnorm 1.0.3

mxnorm: Apply Normalization Methods to Multiplexed Images

Implements methods to normalize multiplexed imaging data, including statistical metrics and visualizations to quantify technical variation in this data type. Reference for methods listed here: Harris, C., Wrobel, J., & Vandekar, S. (2022). mxnorm: An R Package to Normalize Multiplexed Imaging Data. Journal of Open Source Software, 7(71), 4180, <doi:10.21105/joss.04180>.

Authors:Coleman Harris [aut, cre]

mxnorm_1.0.3.tar.gz
mxnorm_1.0.3.zip(r-4.5)mxnorm_1.0.3.zip(r-4.4)mxnorm_1.0.3.zip(r-4.3)
mxnorm_1.0.3.tgz(r-4.5-any)mxnorm_1.0.3.tgz(r-4.4-any)mxnorm_1.0.3.tgz(r-4.3-any)
mxnorm_1.0.3.tar.gz(r-4.5-noble)mxnorm_1.0.3.tar.gz(r-4.4-noble)
mxnorm_1.0.3.tgz(r-4.4-emscripten)mxnorm_1.0.3.tgz(r-4.3-emscripten)
mxnorm.pdf |mxnorm.html
mxnorm/json (API)

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

Bug tracker:https://github.com/colemanrharris/mxnorm/issues

Datasets:
  • mx_sample - Sample multiplexed dataset for 'mxnorm'.

On CRAN:

Conda:

4.54 score 7 stars 7 scripts 283 downloads 9 exports 127 dependencies

Last updated 2 years agofrom:ac6cd78772. Checks:1 OK, 8 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 21 2025
R-4.5-winNOTEMar 21 2025
R-4.5-macNOTEMar 21 2025
R-4.5-linuxNOTEMar 21 2025
R-4.4-winNOTEMar 21 2025
R-4.4-macNOTEMar 21 2025
R-4.4-linuxNOTEMar 21 2025
R-4.3-winNOTEMar 21 2025
R-4.3-macNOTEMar 21 2025

Exports:mx_datasetmx_normalizeplot_mx_densityplot_mx_discordanceplot_mx_proportionsplot_mx_umaprun_otsu_discordancerun_reduce_umaprun_var_proportions

Dependencies:ashBHbitopsbootcaretclasscliclockclustercodetoolscolorspacecpp11data.tabledeSolvediagramdigestdplyrdqrnge1071fansifarverfdafdsFNNforeachforeignfossilfuturefuture.applygenericsggplot2globalsgluegowerGPArotationgtablehardhathdrcdehereipredirlbaisobanditeratorsjsonlitekernlabKernSmoothkskSampleslabelinglatticelavalifecyclelistenvlme4locfitlubridatemagrittrmapsMASSMatrixmclustmgcvminqamnormtModelMetricsmulticoolmunsellmvtnormnlmenloptrnnetnumDerivparallellypcaPPpillarpkgconfigplyrpngpracmapROCprodlimprogressrproxypsychpurrrR6rainbowrappdirsrbibutilsRColorBrewerRcppRcppAnnoyRcppEigenRcppProgressRcppTOMLRCurlRdpackrecipesreformulasreshape2reticulaterlangrpartrprojrootRSpectrascalesshapeshapefilessitmospsparsevctrsSQUAREMstringistringrSuppDistssurvivaltibbletidyrtidyselecttimechangetimeDatetzdbutf8uwotvctrsviridisLitewithr

The mxnorm package for removing slide-to-slide variation in multiplexed imaging data

Rendered frommxnorm-vignette.Rmdusingknitr::rmarkdownon Mar 21 2025.

Last update: 2022-02-22
Started: 2022-02-04