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

## Documentation for package ‘MAPFX’ version 1.9.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

bkc_bkb | Background correction for the backbone markers
bkc_pe | Background correction for the well-specific markers (PE)
cluster.analysis | Cluster analysis with normalised backbone measurements and the complete dataset
cluster.analysis.bkbOnly | Cluster analysis with normalised backbone measurements
fcs_to_rds | Converting FCS files to RDS files
fcs_to_rds_bkb | Converting FCS files to RDS files (for the case without exploratory markers)
imputation_bkb.predictors | Imputing the unmeasured well-specific markers with regression models
initM | Initial biological clusters
MapfxFFC | Normalising data from the Fluorescence Flow Cytometry (FFC) Experiments with mapfx.norm
MapfxMPC | MAssively Parallel Flow cytometry Xplorer (MAPFX)
mkImputeMT | Making the input for imputation
ord.fcs.raw.meta.df.out_ffc | Metadata of the example MPC data
ord.fcs.raw.meta.df.out_mpc | Metadata of the example FFC data
ord.fcs.raw.mt_ffc | Subset of the single-cell murine lung data at steady state from an MPC experiment
ord.fcs.raw.mt_mpc | Subset of the sorted CD4+ and CD8+ T cells from mice splenocytes from an FFC experiment
rmBatchEffect | Removing batch effect from the data (FFC)
rmWellEffect | Removing well effect from the data