This is the released version of MAPFX; for the devel version, see MAPFX.
MAssively Parallel Flow cytometry Xplorer (MAPFX): A Toolbox for Analysing Data from the Massively-Parallel Cytometry ExperimentsBioconductor version: Release (3.21)
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 âmissingâ 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] ORCID: 0000-0002-9586-1246 , Agus Salim [ctb], infinityFlow [ctb]
Maintainer: Hsiao-Chi Liao <chelsea.acad at gmail.com>
Citation (from within R, entercitation("MAPFX")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MAPFX")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MAPFX")Follow Installation instructions to use this package in your R session.
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