MAPFX

This is the development version of MAPFX; for the stable release version, see MAPFX.

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


Bioconductor version: Development (3.20)

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 gmail.com>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("MAPFX")

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

Documentation

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

browseVignettes("MAPFX")
MAPFX: MAssively Parallel Flow cytometry Xplorer HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CellBasedAssays, Clustering, FlowCytometry, Proteomics, SingleCell, Software
Version 1.1.0
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
System Requirements
URL https://github.com/HsiaoChiLiao/MAPFX
Bug Reports https://github.com/HsiaoChiLiao/MAPFX/issues
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Suggests BiocStyle, knitr, rmarkdown, testthat
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package MAPFX_1.1.0.tar.gz
Windows Binary MAPFX_1.1.0.zip (64-bit only)
macOS Binary (x86_64) MAPFX_1.1.0.tgz
macOS Binary (arm64) MAPFX_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MAPFX
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MAPFX
Bioc Package Browser https://code.bioconductor.org/browse/MAPFX/
Package Short Url https://bioconductor.org/packages/MAPFX/
Package Downloads Report Download Stats