Analysis and Visualization of Droplet Digital PCR in R and on the Web
Is the analysis complete?
Run analysis on a ddPCR plate
Helper function for move_front and move_back
Calculate negative frequency based on number of drops
Calculate concentration in a single well
Calculate template concentration
Calculate negative frequency of a single well
Calculate negative frequencies in whole plate
Capitalize the first letter of a string
Concatenate strings with no space between them
Ensure the plate's status is at the right step
Classify droplets in a well
Classify droplets in a well
Analysis step: Classify droplets
Analysis step: Classify droplets
Analysis step: Classify droplets
Get cluster name by ID
Get cluster ID by name
Potential droplet clusters for a plate type
Convert a plate column to a number
Plate type: custom thresholds
Plate type: ddPCR plate
ddpcr: Analysis and Visualization of Droplet Digital PCR in R and on t...
Define droplet clusters for custom thresholds plates
Define droplet clusters for default plates
Define droplet clusters for PNPP experiments
Define droplet clusters
Define plate type parameters for custom thresholds plates
Define plate type parameters for default plates
Define plate type parameters for FAM-positive PNPP
Define plate type parameters for HEX-positive PNPP
Define plate type parameters for PNPP experiments
Define plate type parameters
Define plate type parameters for wildtype/mutant PNPP
Define analysis steps for custom thresholds plates
Define analysis steps for default plates
Define analysis steps for PNPP experiments
Define analysis steps
Euclidean distance between two points
Show an error message
Plate type: FAM-positive PNPP
Get column from well ID
Get the cutoff for empty droplets in a well
Get the cutoff for empty droplets in a well
Get the cutoff for empty droplets in a well
Get border of filled droplets in PNPP experiment
Get filled droplets in PNPP experiment
Get the cutoff for outliers
Get the cutoff for outliers
Get row from well ID
Get droplet data from a well
Get all wells between two wells (assume a rectangle layout)
Determine if a numeric value is within a range
magrittr forward-pipe operator
Does a well have a statistically significant number of negative drople...
Does a ddPCR plate have a step with this name?
Plate type: HEX-positive PNPP
Determine if a given path is a valid directory
Is the plate object dirty (ie has changed since the analysis was run)?
Is a plate empty?
Determine if a given path is a valid file
Is the given parameter a range?
Determine if a well had a successful ddPCR run
Determine if a well had a successful ddPCR run
Determine if a well had a successful ddPCR run
Run the interactive analysis tool (Shiny app) in a web browser
Load a previously saved ddPCR plate
Get the indices of the local maxima in a list of numbers
Get the indices of the local minima in a list of numbers
Convert a list of lists returned from vapply to a dataframe
Mark the clusters of droplets only in certain wells to their assigned ...
Overwrite a column in a data.frame based on a matching column in anoth...
Name of variable in PNPP experiment metadata
Move columns to the back of a data.frame
Move columns to the front of a data.frame
Write a message to the user if the ddpcr.verbose option is on
Plate name
Convert a named vector returned from vapply to a dataframe
Create a new ddPCR plate
Run the next step in an analysis
Normalize a file name to .rds suffix
Convert a number to plate column
Convert a number to plate row
Given an axis (X or Y), return the other
Plate parameters
Parent plate type of default plates
Parent plate type of any plate
Parent plate type of FAM-positive PNPP
Parent plate type of HEX-positive PNPP
Parent plate type
Parent plate type of wildtype/mutant PNPP
Overwrite the plate data
Plate data (droplets data)
Overwrite the plate metadata
Plate metadata
Supported plate types
Plot a ddPCR plate of type custom thresholds
Plot a ddPCR plate
Plot a ddPCR plate of type PNPP experiment
Plot a ddPCR plate of type wildtype/mutant PNPP
Plate type: PNPP experiment
Representation of a 2D point
Name of dye in positive dimension in PNPP experiment
Positive dimension in a PNPP experiment
Name identifier for positive and negative droplets
Print info about a ddPCR plate
Suppress all output from an expression. Works cross-platform.
Convert a list of ranges to a vector of its individual components
Extract the two endpoints of a range
Convert a range to a vector of all elements between the endpoints
Reclassify droplets in a well
Reclassify droplets in a well
Analysis step: Reclassify droplets
Analysis step: Reclassify droplets
Analysis step: Remove empty droplets
Analysis step: Remove empty droplets
Analysis step: Remove empty droplets
Analysis step: Remove failed wells
Analysis step: Remove failed wells
Analysis Step: Remove outlier droplets
Analysis Step: Remove outlier droplets
Reset a plate
Convert a plate row to a number
Get sample data
Save a ddPCR plate
Reset plate parameters to their defaults
Plate status
Inform the user that an analysis step is starting
Inform the user that an analysis step finished
Get step name by ID
Get step ID by step name
Analysis steps of a ddPCR plate
Subsetting a ddPCR plate
Get/set the thresholds
Plate type
Get unanalyzed cluseter IDs
Name of dye in variable dimension in PNPP experiment
Variable dimension in a PNPP experiment
Show a warning message
regex for a well ID
Get metadata info of a well
Get mutant wells
Get negative wells
Get positive wells
Get successful/failed wells
Get wells used in a ddPCR plate
Get wildtype wells
Plate type: wildtype/mutant PNPP
Get/set the X threshold
Get/set the X/Y variable (dye name)
Get/set the Y threshold
An interface to explore, analyze, and visualize droplet digital PCR (ddPCR) data in R. This is the first non-proprietary software for analyzing two-channel ddPCR data. An interactive tool was also created and is available online to facilitate this analysis for anyone who is not comfortable with using R.
Useful links