Package: ddpcr 1.15.2.9000

ddpcr: Analysis and Visualization of Droplet Digital PCR in R and on the Web

An interface to explore, analyze, and visualize droplet digital PCR (ddPCR) data in R. This is the first non-proprietary software for analyzing two-channel ddPCR data. An interactive tool was also created and is available online to facilitate this analysis for anyone who is not comfortable with using R.

Authors:Dean Attali [aut, cre]

ddpcr_1.15.2.9000.tar.gz
ddpcr_1.15.2.9000.zip(r-4.5)ddpcr_1.15.2.9000.zip(r-4.4)ddpcr_1.15.2.9000.zip(r-4.3)
ddpcr_1.15.2.9000.tgz(r-4.4-any)ddpcr_1.15.2.9000.tgz(r-4.3-any)
ddpcr_1.15.2.9000.tar.gz(r-4.5-noble)ddpcr_1.15.2.9000.tar.gz(r-4.4-noble)
ddpcr_1.15.2.9000.tgz(r-4.4-emscripten)ddpcr_1.15.2.9000.tgz(r-4.3-emscripten)
ddpcr.pdf |ddpcr.html✨
ddpcr/json (API)
NEWS

# Install 'ddpcr' in R:
install.packages('ddpcr', repos = c('https://daattali.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/daattali/ddpcr/issues

On CRAN:

126 exports 60 stars 9.25 score 95 dependencies 1 dependents 3 mentions 136 scripts 539 downloads

Last updated 6 months agofrom:7646a8509f. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 22 2024
R-4.5-winNOTESep 22 2024
R-4.5-linuxNOTESep 22 2024
R-4.4-winNOTESep 22 2024
R-4.4-macNOTESep 22 2024
R-4.3-winNOTESep 22 2024
R-4.3-macNOTESep 22 2024

Exports:%>%%btwn%analysis_completeanalyzebind_df_endscalc_negative_freq_simplecalculate_concentrationcalculate_concentration_singlecalculate_neg_freq_singlecalculate_negative_freqscapitalizecat0check_stepclassify_dropletsclassify_droplets_singleclassify_thresholdsclustercluster_nameclusterscol_to_numdefine_clustersdefine_paramsdefine_stepserr_msgget_colget_empty_cutoffget_filled_borderget_filled_dropsget_outlier_cutoffget_rowget_single_wellget_wells_btwnhas_signif_negative_clusterhas_stepis_diris_dirtyis_empty_plateis_fileis_rangeis_well_successlaunchload_platelocal_maximalocal_minimalol_to_dfmark_clustersmerge_dfs_overwrite_colmeta_var_namemove_backmove_frontmsgnamename<-named_vec_to_dfnegative_namenegative_name<-new_platenext_stepnormalize_to_rdsnum_to_colnum_to_rowother_dimparamsparams<-parent_plate_typeplate_dataplate_data<-plate_metaplate_meta<-plate_typespoint2dpositive_dimpositive_dim_varpositive_dim<-positive_namepositive_name<-quietrange_list_to_vecrange_to_endpointsrange_to_seqreclassify_dropletsreclassify_droplets_singleremove_emptyremove_failuresremove_outliersresetrow_to_numsample_data_dirsample_data_filesample_platesample_results_filesave_plateset_default_paramsset_thresholdsstatusstatus<-stepstep_beginstep_endstep_namestepsthresholdsthresholds<-typeunanalyzed_clustersvariable_dimvariable_dim_varvariable_dim<-warn_msgWELL_ID_REGEXwell_infowells_failedwells_mutantwells_negativewells_positivewells_successwells_usedwells_wildtypex_thresholdx_threshold<-x_varx_var<-y_thresholdy_threshold<-y_vary_var<-

Dependencies:askpassbackportsbase64encbitbit64bslibcachemcheckmateclicliprcolorspacecommonmarkcpp11crayoncrosstalkcurldata.tabledigestdplyrDTevaluatefansifarverfastmapfontawesomefsgenericsggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonlitekernlabknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemixtoolsmunsellnlmeopensslpillarpkgconfigplotlyplyrprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppreadrrlangrmarkdownsassscalessegmentedshinyshinydisconnectshinyjssourcetoolsstringistringrsurvivalsystibbletidyrtidyselecttinytextzdbutf8vctrsviridisLitevroomwithrxfunxtableyaml

Algorithms in ddpcr analysis

Dean Attali

Rendered fromalgorithm.Rmdusingknitr::rmarkdownon Sep 22 2024.

Last update: 2023-04-01
Started: 2015-08-28

Extending ddpcr by adding new plate types

Dean Attali

Rendered fromextend.Rmdusingknitr::rmarkdownon Sep 22 2024.

Last update: 2016-07-29
Started: 2015-08-28

Implementation technical details

Dean Attali

Rendered fromtechnical_details.Rmdusingknitr::rmarkdownon Sep 22 2024.

Last update: 2016-05-08
Started: 2016-05-08

Package ddpcr

Dean Attali

Rendered fromoverview.Rmdusingknitr::rmarkdownon Sep 22 2024.

Last update: 2023-08-19
Started: 2015-08-26

Readme and manuals

Help Manual

Help pageTopics
Is the analysis complete?analysis_complete
Run analysis on a ddPCR plateanalyze
Potential droplet clusters for a plate typeclusters
Plate type: custom thresholdscustom_thresholds
Plate type: ddPCR plateddpcr_plate
Plate type: FAM-positive PNPPfam_positive_pnpp
Plate type: HEX-positive PNPPhex_positive_pnpp
Run the interactive analysis tool (Shiny app) in a web browserlaunch
Load a previously saved ddPCR plateload_plate
Plate namename name<-
Create a new ddPCR platenew_plate
Run the next step in an analysisnext_step
Plate parametersparams params<-
Plate data (droplets data)plate_data
Plate metadataplate_meta
Supported plate typesplate_types
Plot a ddPCR plate of type custom thresholdsplot.custom_thresholds
Plot a ddPCR plateplot.ddpcr_plate
Plot a ddPCR plate of type wildtype/mutant PNPPplot.wildtype_mutant_pnpp
Plate type: PNPP experimentpnpp_experiment
Reset a platereset
Get sample datasample_data sample_data_dir sample_data_file sample_plate sample_results_file
Save a ddPCR platesave_plate
Reset plate parameters to their defaultsset_default_params
Analysis steps of a ddPCR platesteps
Subsetting a ddPCR platesubset.ddpcr_plate
Get/set the thresholdsset_thresholds thresholds thresholds<-
Plate typetype
Get metadata info of a wellwell_info
Get mutant wellswells_mutant
Get negative wellswells_negative
Get positive wellswells_positive
Get successful/failed wellswells_failed wells_success
Get wells used in a ddPCR platewells_used
Get wildtype wellswells_wildtype
Plate type: wildtype/mutant PNPPwildtype_mutant_pnpp
Get/set the X thresholdx_threshold x_threshold<-
Get/set the X/Y variable (dye name)x_var x_var<- y_var y_var<-
Get/set the Y thresholdy_threshold y_threshold<-