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_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) |