Analysis and Visualization of Droplet Digital PCR in R and on the Web

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Documentation for package ‘ddpcr’ version 1.15

Help Pages

analysis_complete Is the analysis complete?
analyze Run analysis on a ddPCR plate
clusters Potential droplet clusters for a plate type
custom_thresholds Plate type: custom thresholds
ddpcr Analysis and visualization of Droplet Digital PCR data.
ddpcr_plate Plate type: ddPCR plate
fam_positive_pnpp Plate type: FAM-positive PNPP
hex_positive_pnpp Plate type: HEX-positive PNPP
launch Run the interactive analysis tool (Shiny app) in a web browser
load_plate Load a previously saved ddPCR plate
name Plate name
name<- Plate name
new_plate Create a new ddPCR plate
next_step Run the next step in an analysis
params Plate parameters
params<- Plate parameters
plate_data Plate data (droplets data)
plate_meta Plate metadata
plate_types Supported plate types
plot.custom_thresholds Plot a ddPCR plate of type custom thresholds
plot.ddpcr_plate Plot a ddPCR plate
plot.wildtype_mutant_pnpp Plot a ddPCR plate of type wildtype/mutant PNPP
pnpp_experiment Plate type: PNPP experiment
reset Reset a plate
sample_data Get sample data
sample_data_dir Get sample data
sample_data_file Get sample data
sample_plate Get sample data
sample_results_file Get sample data
save_plate Save a ddPCR plate
set_default_params Reset plate parameters to their defaults
set_thresholds Get/set the thresholds
steps Analysis steps of a ddPCR plate
subset.ddpcr_plate Subsetting a ddPCR plate
thresholds Get/set the thresholds
thresholds<- Get/set the thresholds
type Plate type
wells_failed Get successful/failed wells
wells_mutant Get mutant wells
wells_negative Get negative wells
wells_positive Get positive wells
wells_success Get successful/failed wells
wells_used Get wells used in a ddPCR plate
wells_wildtype Get wildtype wells
well_info Get metadata info of a well
wildtype_mutant_pnpp Plate type: wildtype/mutant PNPP
x_threshold Get/set the X threshold
x_threshold<- Get/set the X threshold
x_var Get/set the X/Y variable (dye name)
x_var<- Get/set the X/Y variable (dye name)
y_threshold Get/set the Y threshold
y_threshold<- Get/set the Y threshold
y_var Get/set the X/Y variable (dye name)
y_var<- Get/set the X/Y variable (dye name)