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 (3.21)
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 ‘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] (ORCID:
Maintainer: Hsiao-Chi Liao <chelsea.acad at gmail.com>
citation("MAPFX")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | CellBasedAssays, Clustering, FlowCytometry, Proteomics, SingleCell, Software |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (0.5 years) |
| 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 |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MAPFX_1.3.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |