dpcR: Digital PCR Analysis
Version 0.4

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.

Browse man pages Browse package API and functions Browse package files

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
URL https://github.com/michbur/dpcR
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("dpcR")

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

AUCtest Source code
BioradCNV Man page
White Man page
adpcr Man page
adpcr-class Man page
adpcr2panel Man page Source code
adpcr2ppp Man page Source code
amp2dpcr Source code
analyze_qpcR Source code
binarize Man page Source code
bind_dpcr Man page Source code
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
bind_factor Source code
bioamp Man page Source code
calc_bars Source code
calc_breaks Source code
calc_coordinates Man page Source code
calc_deltaF Source code
calc_lambda Source code
calc_moms Source code
cbind_dpcr Source code
coef,count_test-method Man page
compare_dens Man page Source code
construct_dpcr Source code
count_test Man page
count_test-class Man page
create_adpcr Source code
create_dpcr Man page Source code
create_ppp Source code
dPCRmethyl Man page
ddpcRquant Man page Source code
deal.ties Source code
df2dpcr Man page Source code
dpcR Man page
dpcR-package Man page
dpcReport Man page Source code
dpcr Man page
dpcr-class Man page
dpcr2df Man page Source code
dpcr2df,adpcr-method Man page
dpcr2df,dpcr-method Man page
dpcr2df-methods Man page
dpcr_calculator Source code
dpcr_density Man page Source code
dpcr_density_gui Man page Source code
dpcr_density_table Man page Source code
empir_moms Source code
extract_dpcr Man page Source code
extract_run Man page Source code
fit_adpcr Source code
fit_single_adpcr Source code
fl Source code
get_k_n Source code
get_runs_ids Source code
hsm Source code
limit_cq Man page Source code
many_peaks Man page
moments Man page Source code
moments,dpcr-method Man page
moments,matrix-method Man page
moments,numeric-method Man page
moments-methods Man page
moms Source code
num2int Man page Source code
pds Man page
pds_raw Man page
plot,count_test,ANY-method Man page
plot,count_test-method Man page
plot,qdpcr,ANY-method Man page
plot,qdpcr-method Man page
plot.count_test Man page
plot.qdpcr Man page
plot_conf_int Source code
plot_distr Source code
plot_panel Man page Source code
plot_vf_circ Source code
plot_vic_fam Man page Source code
print_summary Source code
qdpcr Man page
qdpcr-class Man page
qpcr2pp Man page Source code
qpcr_analyser Man page Source code
qpcr_analyser,adpcr-method Man page
qpcr_analyser,data.frame-method Man page
qpcr_analyser,modlist-method Man page
qpcr_analyser-methods Man page
read_BioMark Man page Source code
read_QX100 Man page Source code
read_QX200 Man page Source code
read_amp Man page Source code
read_dpcr Man page Source code
read_input Source code
read_redf Man page Source code
read_zipped_amps Source code
rename_dpcr Man page Source code
rtadpcr Man page
rtadpcr-class Man page
safe_efficiency Source code
show Man page
show,count_test-method Man page
show,dpcr-method Man page
show,qdpcr-method Man page
show-methods Man page
show.qdpcr Man page
sim_adpcr Man page Source code
sim_dpcr Man page Source code
sim_dpcr_dube Source code
sim_dpcr_fluo Source code
sim_dpcr_multi Source code
sim_dpcr_raw Source code
six_panels Man page
summary Man page
summary,adpcr-method Man page
summary,count_test-method Man page
summary,dpcr-method Man page
summary,qdpcr-method Man page
summary-methods Man page
summary.adpcr Man page
summary.dpcr Man page
summary.qdpcr Man page
test_counts Man page Source code
test_counts_gui Man page Source code
test_panel Man page Source code
test_peaks Man page Source code
test_peaks,adpcr-method Man page
test_peaks,numeric-method Man page
test_peaks-methods Man page
test_pooled Man page Source code
valid_amp Source code
y_val_conf Source code

Files

inst
inst/dpcr_density_gui
inst/dpcr_density_gui/ui.R
inst/dpcr_density_gui/server.R
inst/CITATION
inst/dpcReport
inst/dpcReport/ui.R
inst/dpcReport/server.R
inst/dpcReport/www
inst/dpcReport/www/copy_csv_xls.swf
inst/dpcReport/test_counts
inst/dpcReport/test_counts/test_counts_res.R
inst/dpcReport/test_counts/test_counts1.md
inst/dpcReport/test_counts/test_counts3.md
inst/dpcReport/test_counts/test_counts_plot.R
inst/dpcReport/test_counts/test_counts_group.R
inst/dpcReport/test_counts/test_counts2.md
inst/dpcReport/data_summary
inst/dpcReport/data_summary/summary_input.R
inst/dpcReport/data_summary/data_summary_table1.md
inst/dpcReport/r_code_gen.R
inst/dpcReport/server_data.R
inst/dpcReport/summary_plots
inst/dpcReport/summary_plots/summary_plot.R
inst/dpcReport/summary_plots/data_summary_scatterchart2.md
inst/dpcReport/summary_plots/data_summary_scatterchart1.md
inst/dpcReport/summary_plots/summary_exprep_plot.R
inst/dpcReport/report.css
inst/dpcReport/report_template.Rmd
inst/dpcReport/about.md
inst/dpcReport/plot_panel
inst/dpcReport/plot_panel/plot_panel.R
inst/dpcReport/plot_panel/subpanel_summary.R
inst/dpcReport/plot_panel/plot_panel1.md
inst/dpcReport/plot_panel/test_panel.R
inst/dpcReport/plot_panel/plot_panel2.md
inst/dpcReport/plot_panel/plot_panel0.md
inst/dpcReport/ga.js
inst/dpcReport/dpcR_logo.png
inst/dpcReport/input_file2.md
inst/dpcReport/about.Rmd
inst/dpcReport/dpcr.bib
inst/dpcReport/prob_distr
inst/dpcReport/prob_distr/prob_distr3.md
inst/dpcReport/prob_distr/get_kn.R
inst/dpcReport/prob_distr/prob_distr1.md
inst/dpcReport/prob_distr/single_run_moments.R
inst/dpcReport/prob_distr/plot_density.R
inst/dpcReport/prob_distr/prob_distr2.md
inst/dpcReport/prob_distr/prob_distr4.md
inst/dpcReport/input_file1.md
inst/dpcReport/download_report1.md
inst/test_counts_gui
inst/test_counts_gui/ui.R
inst/test_counts_gui/server.R
inst/test_counts_gui/readme.md
inst/doc
inst/doc/overview.R
inst/doc/overview.html
inst/doc/overview.Rmd
NAMESPACE
CHANGELOG
data
data/six_panels.rda
data/BioradCNV.rda
data/pds.rda
data/dPCRmethyl.rda
data/White.rda
data/pds_raw.rda
data/many_peaks.rda
R
R/test_counts.R
R/classes.R
R/White.R
R/plot_distr.R
R/dPCRmethyl.R
R/fit_adpcr.R
R/rtadpcr.R
R/sim_ddpcr_bkm.R
R/df2dpcr.R
R/plot_panel.R
R/qpcr_analyser.R
R/modlist.R
R/read_amp.R
R/print_summary.R
R/moments.R
R/test_counts_gui.R
R/calc_lambda.R
R/valid_amp.R
R/num2int.R
R/calc_coordinates.R
R/test_peaks.R
R/qpcr2pp.R
R/sim_adpcr.R
R/test_panel.R
R/compare_dens.R
R/BioradCNV.R
R/bind_dpcr.R
R/dpcr_density_table.R
R/binarize.R
R/y_val_conf.R
R/dpcReport_gui.R
R/dpcr_calculator.R
R/ddpcRquant.R
R/plot_vf_circ.R
R/dpcr2df.R
R/adpcr2ppp.R
R/plot_vic_fam.R
R/many_peaks.R
R/safe_efficiency.R
R/dpcr_density_gui.R
R/pds_raw.R
R/rename_dpcr.R
R/calc_breaks.R
R/create_dpcr.R
R/adpcr2panel.R
R/summary_dpcr.R
R/get_k_n.R
R/pds.R
R/six_panels.R
R/fl.R
R/dpcr_density.R
R/extract_run.R
R/hsm.R
R/qdpcr.R
R/simulations.R
R/bioamp.R
R/dpcR-package.R
R/AUCtest.R
R/count_test-class.R
R/show_dpcr.R
R/limit_cq.R
R/read_dpcr.R
R/sim_dpcr.R
R/test_pooled.R
vignettes
vignettes/workflow.svg
vignettes/adpcr_comp.RData
vignettes/overview.Rmd
vignettes/vig.RData
vignettes/coverage_poster.RData
vignettes/dpcR_logo.png
vignettes/dpcr.bib
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/plot_panel.Rd
man/read_dpcr.Rd
man/dpcr-class.Rd
man/summary-methods.Rd
man/dpcr_density.Rd
man/bind_dpcr-methods.Rd
man/read_amp.Rd
man/num2int.Rd
man/dpcr_density_gui.Rd
man/compare_dens.Rd
man/sim_adpcr.Rd
man/adpcr2panel.Rd
man/test_pooled.Rd
man/moments-methods.Rd
man/read_QX200.Rd
man/read_redf.Rd
man/limit_cq.Rd
man/dPCRmethyl.Rd
man/read_QX100.Rd
man/count_test-class.Rd
man/df2dpcr.Rd
man/qpcr2pp.Rd
man/test_panel.Rd
man/sim_dpcr.Rd
man/rename_dpcr.Rd
man/dpcr2df-methods.Rd
man/binarize.Rd
man/qpcr_analyser.Rd
man/test_peaks.Rd
man/White.Rd
man/ddpcRquant.Rd
man/bioamp.Rd
man/plot_vic_fam.Rd
man/pds_raw.Rd
man/dpcr_density_table.Rd
man/BioradCNV.Rd
man/read_BioMark.Rd
man/dpcReport.Rd
man/plot.qdpcr.Rd
man/calc_coordinates.Rd
man/rtadpcr-class.Rd
man/adpcr2ppp.Rd
man/six_panels.Rd
man/test_counts.Rd
man/extract_run.Rd
man/many_peaks.Rd
man/adpcr-class.Rd
man/qdpcr-class.Rd
man/extract_dpcr.Rd
man/create_dpcr.Rd
man/test_counts_gui.Rd
man/dpcR-package.Rd
man/pds.Rd
man/show-methods.Rd
dpcR documentation built on May 19, 2017, 12:52 p.m.