dpcR: Digital PCR Analysis

Analysis, visualisation and simulation of digital polymerase chain reaction (dPCR). Supports data formats of commerical systems (Bio-Rad QX100 and QX200; Fluidigm BioMark) and other systems.

AuthorMichal Burdukiewicz [cre, aut], Stefan Roediger [aut], Bart Jacobs [aut], Piotr Sobczyk [ctb]
Date of publication2017-01-03 16:30:54
MaintainerMichal Burdukiewicz <michalburdukiewicz@gmail.com>
LicenseGPL-3
Version0.4
https://github.com/michbur/dpcR

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

binarize: Binarize digital PCR data

bind_dpcr-methods: Bind dpcr objects

bioamp: A function to analyze plot the raw data from a Bio-Rad...

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

ddpcRquant: Quantify droplets

df2dpcr: Convert data.frame to dpcr object

dpcr2df-methods: Convert dpcr object to data frame

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 Assays or Experiments

extract_run: Extract Digital PCR Run

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_amp: Read digital PCR amplitude raw data

read_BioMark: Read BioMark

read_dpcr: Read digital PCR data

read_QX100: Read QX100

read_QX200: Read QX200

read_redf: 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_dpcr: 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_pooled: Compare pooled digital PCR

White: Digitalized Data from a Fluidigm Array

Functions

adpcr Man page
adpcr2panel Man page
adpcr2ppp Man page
adpcr-class Man page
binarize Man page
bind_dpcr Man page
bind_dpcr,adpcr Man page
bind_dpcr,adpcr-method Man page
bind_dpcr,dpcr Man page
bind_dpcr,dpcr-method Man page
bind_dpcr,list Man page
bind_dpcr,list-method Man page
bind_dpcr-methods Man page
bioamp Man page
BioradCNV Man page
calc_coordinates Man page
coef,count_test-method Man page
compare_dens Man page
count_test Man page
count_test-class Man page
create_dpcr Man page
ddpcRquant Man page
df2dpcr Man page
dpcr Man page
dpcR Man page
dpcr2df Man page
dpcr2df,adpcr-method Man page
dpcr2df,dpcr-method Man page
dpcr2df-methods Man page
dpcr-class Man page
dpcr_density Man page
dpcr_density_gui Man page
dpcr_density_table Man page
dpcReport Man page
dPCRmethyl Man page
dpcR-package Man page
extract_dpcr Man page
extract_run Man page
limit_cq Man page
many_peaks Man page
moments Man page
moments,dpcr-method Man page
moments,matrix-method Man page
moments-methods Man page
moments,numeric-method Man page
num2int Man page
pds Man page
pds_raw Man page
plot.count_test Man page
plot,count_test,ANY-method Man page
plot,count_test-method Man page
plot_panel Man page
plot.qdpcr Man page
plot,qdpcr,ANY-method Man page
plot,qdpcr-method Man page
plot_vic_fam Man page
qdpcr Man page
qdpcr-class Man page
qpcr2pp Man page
qpcr_analyser Man page
qpcr_analyser,adpcr-method Man page
qpcr_analyser,data.frame-method Man page
qpcr_analyser-methods Man page
qpcr_analyser,modlist-method Man page
read_amp Man page
read_BioMark Man page
read_dpcr Man page
read_QX100 Man page
read_QX200 Man page
read_redf Man page
rename_dpcr Man page
rtadpcr Man page
rtadpcr-class Man page
show Man page
show,count_test-method Man page
show,dpcr-method Man page
show-methods Man page
show.qdpcr Man page
show,qdpcr-method Man page
sim_adpcr Man page
sim_dpcr Man page
six_panels Man page
summary Man page
summary.adpcr Man page
summary,adpcr-method Man page
summary,count_test-method Man page
summary.dpcr Man page
summary,dpcr-method Man page
summary-methods Man page
summary.qdpcr Man page
summary,qdpcr-method Man page
test_counts Man page
test_counts_gui Man page
test_panel Man page
test_peaks Man page
test_peaks,adpcr-method Man page
test_peaks-methods Man page
test_peaks,numeric-method Man page
test_pooled Man page
White Man page

Files

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/ga.js
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/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/df2dpcr.R dpcR/R/plot_panel.R dpcR/R/qpcr_analyser.R dpcR/R/modlist.R dpcR/R/read_amp.R dpcR/R/print_summary.R dpcR/R/moments.R dpcR/R/test_counts_gui.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/ddpcRquant.R dpcR/R/plot_vf_circ.R dpcR/R/dpcr2df.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/pds_raw.R dpcR/R/rename_dpcr.R dpcR/R/calc_breaks.R dpcR/R/create_dpcr.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/extract_run.R dpcR/R/hsm.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/R/sim_dpcr.R dpcR/R/test_pooled.R
dpcR/vignettes
dpcR/vignettes/workflow.svg
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/read_amp.Rd dpcR/man/num2int.Rd dpcR/man/dpcr_density_gui.Rd dpcR/man/compare_dens.Rd dpcR/man/sim_adpcr.Rd dpcR/man/adpcr2panel.Rd dpcR/man/test_pooled.Rd dpcR/man/moments-methods.Rd dpcR/man/read_QX200.Rd dpcR/man/read_redf.Rd dpcR/man/limit_cq.Rd dpcR/man/dPCRmethyl.Rd dpcR/man/read_QX100.Rd dpcR/man/count_test-class.Rd dpcR/man/df2dpcr.Rd dpcR/man/qpcr2pp.Rd dpcR/man/test_panel.Rd dpcR/man/sim_dpcr.Rd dpcR/man/rename_dpcr.Rd dpcR/man/dpcr2df-methods.Rd dpcR/man/binarize.Rd dpcR/man/qpcr_analyser.Rd dpcR/man/test_peaks.Rd dpcR/man/White.Rd dpcR/man/ddpcRquant.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/extract_run.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

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