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MAssively Parallel Flow cytometry Xplorer (MAPFX): A Toolbox for Analysing Data from the Massively-Parallel Cytometry Experiments

Bioconductor version: Release (3.19)

MAPFX is an end-to-end toolbox that pre-processes the raw data from MPC experiments (e.g., BioLegend's LEGENDScreen and BD Lyoplates assays), and further imputes the ‘missing’ infinity markers in the wells without those measurements. The pipeline starts by performing background correction on raw intensities to remove the noise from electronic baseline restoration and fluorescence compensation by adapting a normal-exponential convolution model. Unwanted technical variation, from sources such as well effects, is then removed using a log-normal model with plate, column, and row factors, after which infinity markers are imputed using the informative backbone markers as predictors. The completed dataset can then be used for clustering and other statistical analyses. Additionally, MAPFX can be used to normalise data from FFC assays as well.

Author: Hsiao-Chi Liao [aut, cre] , Agus Salim [ctb], infinityFlow [ctb]

Maintainer: Hsiao-Chi Liao <chelsea.acad at>

Citation (from within R, enter citation("MAPFX")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

MAPFX: MAssively Parallel Flow cytometry Xplorer HTML R Script
Reference Manual PDF


biocViews CellBasedAssays, Clustering, FlowCytometry, Proteomics, SingleCell, Software
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License GPL-2
Depends R (>= 4.4.0)
Imports flowCore, Biobase, stringr, uwot, iCellR, igraph, ggplot2, RColorBrewer, Rfast, ComplexHeatmap, circlize, glmnetUtils, e1071, xgboost, parallel, pbapply, reshape2, gtools, utils, stats, cowplot, methods, grDevices, graphics
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Source Package MAPFX_1.0.0.tar.gz
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macOS Binary (x86_64) MAPFX_1.0.0.tgz
macOS Binary (arm64) MAPFX_1.0.0.tgz
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