dpcR: Digital PCR Analysis

Analysis, visualisation and simulation of digital polymerase chain reaction (dPCR).

Author
Michal Burdukiewicz [cre, aut], Stefan Roediger [aut], Bart Jacobs [aut], Piotr Sobczyk [ctb]
Date of publication
2016-03-15 12:35:24
Maintainer
Michal Burdukiewicz <michalburdukiewicz@gmail.com>
License
GPL-3
Version
0.3
URLs

View on CRAN

Man pages

adpcr2panel
Convert adpcr object to array
adpcr2ppp
Convert adpcr to ppp
adpcr-class
Class '"adpcr"' - end-point array digital PCR experiments
analyze_pooled
Pooled digital PCR analysis
binarize
Binarize digital PCR data
bind_dpcr-methods
Bind dpcr objects
bioamp
A function to analyze plot the raw data from a BioRad droplet...
BioradCNV
Copy number variation experiment
calc_coordinates
Calculate Array Coordinates
compare_dens
Plot and Compare Densities
count_test-class
Class '"count_test"'
create_dpcr
Create dpcR object
ddpcr-class
Class '"ddpcr"'
dpcr-class
Class '"dpcr"' - general digital PCR
dpcr_density
Calculate Density of Single dPCR Run
dpcr_density_gui
Digital PCR Density Graphical User Interface
dpcr_density_table
Calculate Density of Multiple dPCR runs
dpcReport
Digital PCR Report Graphical User Interface
dPCRmethyl
Methylated human gDNA
dpcR-package
Digital PCR Analysis
extract_dpcr
Extract Digital PCR Experiment
limit_cq
Limit Cy0 values
many_peaks
Artificial data set with many peaks
moments-methods
Calculate Moments of Poisson Distribution
num2int
Convert numeric to integer
pds
Plasmid dilution series results
pds_raw
Plasmid dilution series raw data
plot_panel
Plot Panel
plot.qdpcr
Plot 'qdpcr' objects
plot_vic_fam
Amplitude Plot VIC and FAM Channels of a Droplet Digital PCR...
qdpcr-class
Class '"qdpcr"'
qpcr2pp
qPCR to Poisson Process
qpcr_analyser
qPCR Analyser
read_BioMark
Read BioMark
read_dpcr
Read digital PCR data
read_QX100
Read QX100
read_raw
Read digital PCR raw data
rename_dpcr
Rename object
rtadpcr-class
Class '"rtadpcr"' - real-time array digital PCR experiments
show-methods
Methods for Function 'show'
sim_adpcr
Simulate Array Digital PCR
sim_ddpcr
Simulate Droplet Digital PCR
six_panels
Simulated Digital PCR data
summary-methods
Methods for Function 'summary'
test_counts
Test counts
test_counts_gui
Compare digital PCR runs - interactive presentation
test_panel
Dispersion Test for Spatial Point Pattern in Array dPCR Based...
test_peaks
Peak Test
test_ratio
Rate ratio test
White
Digitalized Data from a Fluidigm Array

Files in this package

dpcR
dpcR/inst
dpcR/inst/dpcr_density_gui
dpcR/inst/dpcr_density_gui/ui.R
dpcR/inst/dpcr_density_gui/server.R
dpcR/inst/CITATION
dpcR/inst/dpcReport
dpcR/inst/dpcReport/ui.R
dpcR/inst/dpcReport/server.R
dpcR/inst/dpcReport/www
dpcR/inst/dpcReport/www/copy_csv_xls.swf
dpcR/inst/dpcReport/test_counts
dpcR/inst/dpcReport/test_counts/test_counts_res.R
dpcR/inst/dpcReport/test_counts/test_counts1.md
dpcR/inst/dpcReport/test_counts/test_counts3.md
dpcR/inst/dpcReport/test_counts/test_counts_plot.R
dpcR/inst/dpcReport/test_counts/test_counts_group.R
dpcR/inst/dpcReport/test_counts/test_counts2.md
dpcR/inst/dpcReport/data_summary
dpcR/inst/dpcReport/data_summary/summary_input.R
dpcR/inst/dpcReport/data_summary/data_summary_table1.md
dpcR/inst/dpcReport/r_code_gen.R
dpcR/inst/dpcReport/server_data.R
dpcR/inst/dpcReport/summary_plots
dpcR/inst/dpcReport/summary_plots/summary_plot.R
dpcR/inst/dpcReport/summary_plots/data_summary_scatterchart2.md
dpcR/inst/dpcReport/summary_plots/data_summary_scatterchart1.md
dpcR/inst/dpcReport/summary_plots/summary_exprep_plot.R
dpcR/inst/dpcReport/report.css
dpcR/inst/dpcReport/report_template.Rmd
dpcR/inst/dpcReport/about.md
dpcR/inst/dpcReport/plot_panel
dpcR/inst/dpcReport/plot_panel/plot_panel.R
dpcR/inst/dpcReport/plot_panel/subpanel_summary.R
dpcR/inst/dpcReport/plot_panel/plot_panel1.md
dpcR/inst/dpcReport/plot_panel/test_panel.R
dpcR/inst/dpcReport/plot_panel/plot_panel2.md
dpcR/inst/dpcReport/plot_panel/plot_panel0.md
dpcR/inst/dpcReport/dpcR_logo.png
dpcR/inst/dpcReport/input_file2.md
dpcR/inst/dpcReport/about.Rmd
dpcR/inst/dpcReport/dpcr.bib
dpcR/inst/dpcReport/prob_distr
dpcR/inst/dpcReport/prob_distr/prob_distr3.md
dpcR/inst/dpcReport/prob_distr/get_kn.R
dpcR/inst/dpcReport/prob_distr/prob_distr1.md
dpcR/inst/dpcReport/prob_distr/single_run_moments.R
dpcR/inst/dpcReport/prob_distr/plot_density.R
dpcR/inst/dpcReport/prob_distr/prob_distr2.md
dpcR/inst/dpcReport/prob_distr/prob_distr4.md
dpcR/inst/dpcReport/input_file1.md
dpcR/inst/dpcReport/download_report1.md
dpcR/inst/test_counts_gui
dpcR/inst/test_counts_gui/ui.R
dpcR/inst/test_counts_gui/server.R
dpcR/inst/test_counts_gui/readme.md
dpcR/inst/doc
dpcR/inst/doc/overview.R
dpcR/inst/doc/overview.html
dpcR/inst/doc/overview.Rmd
dpcR/NAMESPACE
dpcR/CHANGELOG
dpcR/data
dpcR/data/six_panels.rda
dpcR/data/BioradCNV.rda
dpcR/data/pds.rda
dpcR/data/dPCRmethyl.rda
dpcR/data/datalist
dpcR/data/White.rda
dpcR/data/pds_raw.rda
dpcR/data/many_peaks.rda
dpcR/R
dpcR/R/test_counts.R
dpcR/R/classes.R
dpcR/R/White.R
dpcR/R/plot_distr.R
dpcR/R/dPCRmethyl.R
dpcR/R/fit_adpcr.R
dpcR/R/rtadpcr.R
dpcR/R/sim_ddpcr_bkm.R
dpcR/R/plot_panel.R
dpcR/R/qpcr_analyser.R
dpcR/R/modlist.R
dpcR/R/print_summary.R
dpcR/R/moments.R
dpcR/R/test_counts_gui.R
dpcR/R/test_ratio.R
dpcR/R/calc_lambda.R
dpcR/R/valid_amp.R
dpcR/R/num2int.R
dpcR/R/calc_coordinates.R
dpcR/R/test_peaks.R
dpcR/R/qpcr2pp.R
dpcR/R/sim_adpcr.R
dpcR/R/test_panel.R
dpcR/R/compare_dens.R
dpcR/R/BioradCNV.R
dpcR/R/bind_dpcr.R
dpcR/R/dpcr_density_table.R
dpcR/R/binarize.R
dpcR/R/y_val_conf.R
dpcR/R/dpcReport_gui.R
dpcR/R/dpcr_calculator.R
dpcR/R/extract_dpcr.R
dpcR/R/plot_vf_circ.R
dpcR/R/adpcr2ppp.R
dpcR/R/plot_vic_fam.R
dpcR/R/many_peaks.R
dpcR/R/safe_efficiency.R
dpcR/R/dpcr_density_gui.R
dpcR/R/analyze_pooled.R
dpcR/R/pds_raw.R
dpcR/R/rename_dpcr.R
dpcR/R/calc_breaks.R
dpcR/R/create_dpcr.R
dpcR/R/sim_ddpcr.R
dpcR/R/adpcr2panel.R
dpcR/R/summary_dpcr.R
dpcR/R/get_k_n.R
dpcR/R/pds.R
dpcR/R/six_panels.R
dpcR/R/fl.R
dpcR/R/dpcr_density.R
dpcR/R/qdpcr.R
dpcR/R/simulations.R
dpcR/R/bioamp.R
dpcR/R/dpcR-package.R
dpcR/R/AUCtest.R
dpcR/R/count_test-class.R
dpcR/R/show_dpcr.R
dpcR/R/limit_cq.R
dpcR/R/read_dpcr.R
dpcR/vignettes
dpcR/vignettes/adpcr_comp.RData
dpcR/vignettes/overview.Rmd
dpcR/vignettes/vig.RData
dpcR/vignettes/coverage_poster.RData
dpcR/vignettes/dpcR_logo.png
dpcR/vignettes/dpcr.bib
dpcR/README.md
dpcR/MD5
dpcR/build
dpcR/build/vignette.rds
dpcR/DESCRIPTION
dpcR/man
dpcR/man/plot_panel.Rd
dpcR/man/read_dpcr.Rd
dpcR/man/dpcr-class.Rd
dpcR/man/summary-methods.Rd
dpcR/man/dpcr_density.Rd
dpcR/man/bind_dpcr-methods.Rd
dpcR/man/num2int.Rd
dpcR/man/dpcr_density_gui.Rd
dpcR/man/ddpcr-class.Rd
dpcR/man/compare_dens.Rd
dpcR/man/sim_adpcr.Rd
dpcR/man/read_raw.Rd
dpcR/man/adpcr2panel.Rd
dpcR/man/moments-methods.Rd
dpcR/man/limit_cq.Rd
dpcR/man/dPCRmethyl.Rd
dpcR/man/read_QX100.Rd
dpcR/man/count_test-class.Rd
dpcR/man/qpcr2pp.Rd
dpcR/man/test_panel.Rd
dpcR/man/rename_dpcr.Rd
dpcR/man/binarize.Rd
dpcR/man/qpcr_analyser.Rd
dpcR/man/test_peaks.Rd
dpcR/man/White.Rd
dpcR/man/sim_ddpcr.Rd
dpcR/man/test_ratio.Rd
dpcR/man/bioamp.Rd
dpcR/man/plot_vic_fam.Rd
dpcR/man/pds_raw.Rd
dpcR/man/dpcr_density_table.Rd
dpcR/man/BioradCNV.Rd
dpcR/man/read_BioMark.Rd
dpcR/man/dpcReport.Rd
dpcR/man/plot.qdpcr.Rd
dpcR/man/calc_coordinates.Rd
dpcR/man/rtadpcr-class.Rd
dpcR/man/adpcr2ppp.Rd
dpcR/man/six_panels.Rd
dpcR/man/test_counts.Rd
dpcR/man/many_peaks.Rd
dpcR/man/adpcr-class.Rd
dpcR/man/qdpcr-class.Rd
dpcR/man/extract_dpcr.Rd
dpcR/man/create_dpcr.Rd
dpcR/man/test_counts_gui.Rd
dpcR/man/dpcR-package.Rd
dpcR/man/pds.Rd
dpcR/man/show-methods.Rd
dpcR/man/analyze_pooled.Rd