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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 - standalone GUI

The dpcReport GUI may be downloaded a standalone application (does not require prior installation of R) from SourceForge.

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Version

Install

install.packages('dpcR')

Monthly Downloads

117

Version

0.3

License

GPL-3

Issues

0

Pull Requests

0

Stars

9

Forks

2

Maintainer

Michal Burdukiewicz

Last Published

March 15th, 2016

Functions in dpcR (0.3)

num2int

Convert numeric to integer
calc_coordinates

Calculate Array Coordinates
BioradCNV

Copy number variation experiment
adpcr-class

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

Plasmid dilution series results
dpcr-class

Class "dpcr" - general digital PCR
analyze_pooled

Pooled digital PCR analysis
compare_dens

Plot and Compare Densities
dpcr_density_gui

Digital PCR Density Graphical User Interface
read_dpcr

Read digital PCR data
binarize

Binarize digital PCR data
ddpcr-class

Class "ddpcr"
plot_panel

Plot Panel
dPCRmethyl

Methylated human gDNA
bind_dpcr-methods

Bind dpcr objects
count_test

Class "count_test"
bioamp

A function to analyze plot the raw data from a BioRad droplet digital PCR experiment
rtadpcr-class

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

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

Rate ratio test
adpcr2ppp

Convert adpcr to ppp
qpcr2pp

qPCR to Poisson Process
summary-methods

Methods for Function summary
many_peaks

Artificial data set with many peaks
show-methods

Methods for Function show
test_counts_gui

Compare digital PCR runs - interactive presentation
test_peaks

Peak Test
dpcr_density_table

Calculate Density of Multiple dPCR runs
read_BioMark

Read BioMark
White

Digitalized Data from a Fluidigm Array
six_panels

Simulated Digital PCR data
read_QX100

Read QX100
dpcReport

Digital PCR Report Graphical User Interface
test_counts

Test counts
rename_dpcr

Rename object
adpcr2panel

Convert adpcr object to array
create_dpcr

Create dpcR object
extract_dpcr

Extract Digital PCR Experiment
plot.qdpcr

Plot qdpcr objects
dpcr_density

Calculate Density of Single dPCR Run
moments-methods

Calculate Moments of Poisson Distribution
dpcR-package

Digital PCR Analysis
sim_ddpcr

Simulate Droplet Digital PCR
qdpcr-class

Class "qdpcr"
read_raw

Read digital PCR raw data
sim_adpcr

Simulate Array Digital PCR
pds_raw

Plasmid dilution series raw data
test_panel

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

Limit Cy0 values
qpcr_analyser

qPCR Analyser