Package: MAPFX
Title: MAssively Parallel Flow cytometry Xplorer (MAPFX): A Toolbox for
        Analysing Data from the Massively-Parallel Cytometry
        Experiments
Version: 1.7.1
Authors@R: 
	c(person("Hsiao-Chi", "Liao", email = "chelsea.acad@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9586-1246")),
	  person("Agus", "Salim", role = c("ctb")), person("infinityFlow", role = c("ctb")))
Description: 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.
Depends: R (>= 4.4.0)
License: GPL-2
Encoding: UTF-8
RoxygenNote: 7.3.1
Roxygen: list(markdown = TRUE)
biocViews: Software, FlowCytometry, CellBasedAssays, SingleCell,
        Proteomics, Clustering
Imports: flowCore, Biobase, stringr, uwot, iCellR, igraph, ggplot2,
        RColorBrewer, Rfast, ComplexHeatmap, circlize, glmnetUtils,
        e1071, xgboost (>= 3.0.0), parallel, pbapply, reshape2, gtools,
        utils, stats, cowplot, methods, grDevices, graphics
Suggests: BiocStyle, knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
URL: https://github.com/HsiaoChiLiao/MAPFX
BugReports: https://github.com/HsiaoChiLiao/MAPFX/issues
Config/pak/sysreqs: cmake libglpk-dev make libhdf5-dev libicu-dev
        libpng-dev libxml2-dev libssl-dev perl zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-12-20 01:36:19 UTC
RemoteUrl: https://github.com/bioc/MAPFX
RemoteRef: HEAD
RemoteSha: 158ad54992df13e0226eaf9a96b6b191ec290d87
Packaged: 2025-12-20 03:58:33 UTC; root
Author: Hsiao-Chi Liao [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-9586-1246>),
  Agus Salim [ctb],
  infinityFlow [ctb]
Maintainer: Hsiao-Chi Liao <chelsea.acad@gmail.com>
Built: R 4.6.0; ; 2025-12-20 04:01:00 UTC; windows
