Learn R Programming

Analysis, visualisation and simulation of digital PCR experiments.

Installation

dpcR is available on CRAN, so installation is as simple as:

install.packages("dpcR")

You can install the latest development version of the code using the devtools R package.

# Install devtools, if you haven't already.
install.packages("devtools")

library(devtools)
install_github("michbur/dpcR")

dpcReport - web server and standalone GUI

Our web server dpcReport allows analysis of dPCR data without installing the package. It may be also downloaded as a standalone application (does not require prior installation of R) from SourceForge.

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Version

Install

install.packages('dpcR')

Monthly Downloads

124

Version

0.5

License

GPL-3

Issues

Pull Requests

Stars

Forks

Last Published

February 3rd, 2019

Functions in dpcR (0.5)

dPCRmethyl

Methylated human gDNA
BioradCNV

Copy number variation experiment
dpcr_density_gui

Digital PCR Density Graphical User Interface
create_dpcr

Create dpcR object
read_amp

Read digital PCR amplitude raw data
read_QX200

Read QX200
count_test

Class "count_test"
White

Digitalized Data from a Fluidigm Array
dpcr_density_table

Calculate Density of Multiple dPCR runs
show-methods

Methods for Function show
dpcR-package

Digital PCR Analysis
sim_dpcr

Simulate Droplet Digital PCR
many_peaks

Artificial data set with many peaks
dpcReport

Digital PCR Report Graphical User Interface
dpcr-class

Class "dpcr" - general digital PCR
qpcr_analyser

qPCR Analyser
limit_cq

Limit Cy0 values
moments-methods

Calculate Moments of Poisson Distribution
qpcr2pp

qPCR to Poisson Process
bind_dpcr-methods

Bind dpcr objects
num2int

Convert numeric to integer
rename_dpcr

Rename object
plot.qdpcr

Plot qdpcr objects
rtadpcr-class

Class "rtadpcr" - real-time array digital PCR experiments
plot_panel

Plot Panel
sim_adpcr

Simulate Array Digital PCR
test_counts_gui

Compare digital PCR runs - interactive presentation
ddpcRquant

Quantify droplets
extract_dpcr

Extract Assays or Experiments
test_panel

Dispersion Test for Spatial Point Pattern in Array dPCR Based on Quadrat Counts
read_dpcr

Read digital PCR data
extract_run

Extract Digital PCR Run
bioamp

A function to analyze plot the raw data from a Bio-Rad droplet digital PCR experiment
six_panels

Simulated Digital PCR data
test_peaks

Peak Test
plot_vic_fam

Amplitude Plot VIC and FAM Channels of a Droplet Digital PCR Experiment
test_pooled

Compare pooled digital PCR
dpcr2df-methods

Convert dpcr object to data frame
qdpcr-class

Class "qdpcr"
read_redf

Read digital PCR raw data
dpcr_density

Calculate Density of Single dPCR Run
summary-methods

Methods for Function summary
read_BioMark

Read BioMark
test_counts

Test counts
read_QX100

Read QX100
adpcr2panel

Convert adpcr object to array
adpcr-class

Class "adpcr" - end-point array digital PCR experiments
calc_coordinates

Calculate Array Coordinates
adpcr2ppp

Convert adpcr to ppp
compare_dens

Plot and Compare Densities
binarize

Binarize digital PCR data
df2dpcr

Convert data.frame to dpcr object
pds

Plasmid dilution series results
pds_raw

Plasmid dilution series raw data