README.md

fcsjanitor

Automate cleanup of CyTOF fcs files using the algorithm as outined in Fluidigm techincal note PN 400248 B1 "Approach to Bivariate Analysis of Data Acquired Using the Maxpar Direct Immune Profiling Assay"

Install

Requires Python 3.10+

pip install git+https://github.com/milescsmith/fcsjanitor

Usage

Usage: janitor [OPTIONS]                                                                                                                                                                           
                                                                                                                                                                                                    
 Clean one or more CyTOF FCS files.                                                                                                                                                                 
                                                                                                                                                                                                    
 *  --input    -i      PATH           Either a list of input files or directories in which to look for FCS files
                                      [default: None]
                                      [required]
    --output   -o      PATH           Location to write cleaned FCS files
                                      [default: /Users/milessmith/workspace/fcsjanitor]
    --method   -m      TEXT           Method to use when filtering events
                                      [default: FilterMethod.sd]
    --suffix   -s      TEXT           Suffix to append to the new files
                                      [default: None]
    --format   -f      [anndata|fcs]  Save the cleaned data as an FCS or AnnData object?
                                      [default: OutputFormat.fcs]
    --verbose  -v
    --version
    --help                            Show this message and exit.