# Cyanobacteria Population Identification for Flow Cytometry

## Documentation for package ‘cyanoFilter’ version 0.1.3

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

## Help Pages

cyanoFilter-package | cyanoFilter: A package to identify and/or assign indicators to BS4, BS5 cyanobacteria cells contained in water sample.
bs4_nc | gates out or assign indicators to Synechococcus cyanobacteria cells in the bottom right of the 2-D space.
bs5_nc | gates out or assign indicators to Synechococcus cyanobacteria cells in the top right of the 2-D space.
celldebris_emclustering | identifies Synechococcus cyanobacteria cells and Debris in a flowfile using an EM style algorithm.
celldebris_nc | gates out or assign indicators to Synechococcus cyanobacteria cells.
cellmargin | Removes or assign indicators to margin events.
cluster_plot | plots the expression matrix of a flowframe analysed with celldebris_emclustering.
cyanoFilter | cyanoFilter: A package to identify and/or assign indicators to BS4, BS5 cyanobacteria cells contained in water sample.
debris_inc | gates out or assign indicators to debris particle.
debris_nc | gates out or assign indicators to debris particle.
goodfcs | indicates if measurement from a flowfile is good or bad.
lnTrans | log transforms the expression matrix of a flowframe
mvnorm | multivariate normal density
nona | Removes NA values from the expression matrix of a flow cytometer file.
noneg | Removes negative values from the expression matrix
pair_plot | plots the expression matrix of a flowframe. Note that, it takes some time to display the plot.
retain | Decides if a file should be retiained or removed based on its status.