# Cytometry dATa anALYSis Tools

## Documentation for package ‘CATALYST’ version 1.1.1

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

## Help Pages

applyCutoffs | Single-cell debarcoding (2)
applyCutoffs-method | Single-cell debarcoding (2)
assignPrelim | Single-cell debarcoding (1)
assignPrelim-method | Single-cell debarcoding (1)
bc_ids | Extraction and replacement methods for objects of class 'dbFrame'
bc_ids-method | Extraction and replacement methods for objects of class 'dbFrame'
bc_key | Extraction and replacement methods for objects of class 'dbFrame'
bc_key-method | Extraction and replacement methods for objects of class 'dbFrame'
compCytof | Compensate CyTOF experiment
compCytof-method | Compensate CyTOF experiment
computeSpillmat | Compute spillover matrx
computeSpillmat-method | Compute spillover matrx
concatFCS | FCS file concatination
concatFCS-method | FCS file concatination
counts | Extraction and replacement methods for objects of class 'dbFrame'
counts-method | Extraction and replacement methods for objects of class 'dbFrame'
data | Example data sets
dbFrame | Debarcoding frame class
dbFrame-class | Debarcoding frame class
dbFrame-methods | Extraction and replacement methods for objects of class 'dbFrame'
deltas | Extraction and replacement methods for objects of class 'dbFrame'
deltas-method | Extraction and replacement methods for objects of class 'dbFrame'
estCutoffs | Estimation of distance separation cutoffs
estCutoffs-method | Estimation of distance separation cutoffs
estTrim | Estimation of optimal trim value
estTrim-method | Estimation of optimal trim value
exprs | Extraction and replacement methods for objects of class 'dbFrame'
exprs-method | Extraction and replacement methods for objects of class 'dbFrame'
mhl_cutoff | Extraction and replacement methods for objects of class 'dbFrame'
mhl_cutoff-method | Extraction and replacement methods for objects of class 'dbFrame'
mhl_cutoff<- | Extraction and replacement methods for objects of class 'dbFrame'
mhl_cutoff<--method | Extraction and replacement methods for objects of class 'dbFrame'
mhl_dists | Extraction and replacement methods for objects of class 'dbFrame'
mhl_dists-method | Extraction and replacement methods for objects of class 'dbFrame'
mp_cells | Example data sets
normCytof | Bead-based normalization
normCytof-method | Bead-based normalization
normed_bcs | Extraction and replacement methods for objects of class 'dbFrame'
normed_bcs-method | Extraction and replacement methods for objects of class 'dbFrame'
outFCS | Write population-wise FCS files
outFCS-method | Write population-wise FCS files
plotEvents | Event plot
plotEvents-method | Event plot
plotMahal | Biaxial plot
plotMahal-method | Biaxial plot
plotSpillmat | Spillover matrix heat map
plotYields | Yield plot
plotYields-method | Yield plot
raw_data | Example data sets
sample_ff | Example data sets
sample_key | Example data sets
sep_cutoffs | Extraction and replacement methods for objects of class 'dbFrame'
sep_cutoffs-method | Extraction and replacement methods for objects of class 'dbFrame'
sep_cutoffs<- | Extraction and replacement methods for objects of class 'dbFrame'
sep_cutoffs<--method | Extraction and replacement methods for objects of class 'dbFrame'
ss_exp | Example data sets
yields | Extraction and replacement methods for objects of class 'dbFrame'
yields-method | Extraction and replacement methods for objects of class 'dbFrame'