Package: dPCP 2.0.1
dPCP: Automated Analysis of Multiplex Digital PCR Data
The automated clustering and quantification of the digital PCR data is based on the combination of 'DBSCAN' (Hahsler et al. (2019) <doi:10.18637/jss.v091.i01>) and 'c-means' (Bezdek et al. (1981) <doi:10.1007/978-1-4757-0450-1>) algorithms. The analysis is independent of multiplexing geometry, dPCR system, and input amount. The details about input data and parameters are available in the vignette.
Authors:
dPCP_2.0.1.tar.gz
dPCP_2.0.1.zip(r-4.5)dPCP_2.0.1.zip(r-4.4)dPCP_2.0.1.zip(r-4.3)
dPCP_2.0.1.tgz(r-4.4-any)dPCP_2.0.1.tgz(r-4.3-any)
dPCP_2.0.1.tar.gz(r-4.5-noble)dPCP_2.0.1.tar.gz(r-4.4-noble)
dPCP_2.0.1.tgz(r-4.4-emscripten)dPCP_2.0.1.tgz(r-4.3-emscripten)
dPCP.pdf |dPCP.html✨
dPCP/json (API)
NEWS
| # Install 'dPCP' in R: |
| install.packages('dPCP', repos = c('https://alfodefalco.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/alfodefalco/dpcp/issues
Last updated 1 years agofrom:514b1985eb. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 08 2024 |
| R-4.5-win | OK | Sep 08 2024 |
| R-4.5-linux | OK | Sep 08 2024 |
| R-4.4-win | OK | Sep 08 2024 |
| R-4.4-mac | OK | Sep 08 2024 |
| R-4.3-win | OK | Sep 08 2024 |
| R-4.3-mac | OK | Sep 08 2024 |
Exports:centers_datacmeans_clusdbscan_combinationdPCPexport_csvmanual_correctionrain_reclusread_referenceread_sampleread_sampleTablereference_dbscanreplicates_quantreport_dPCPtarget_quant
Dependencies:abindbackportsbase64encbootbriobroombslibcachemcallrcarcarDataclasscliclustercolorspacecommonmarkcorrplotcowplotcpp11crayondata.tabledbscanDerivdescdiffobjdigestdoBydplyre1071evaluateexactcifansifarverfastmapfontawesomefsgenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehtmltoolshttpuvisobandjquerylibjsonlitelabelinglaterlatticelifecyclelme4magrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnumDerivpbkrtestpillarpkgbuildpkgconfigpkgloadpolynompraiseprocessxpromisesproxypspurrrquantregR6rappdirsrasterRColorBrewerRcppRcppEigenrematch2rlangrlistrprojrootrstatixsassscalesshinyshinyjssourcetoolsspSparseMssanvstringistringrsurvivalterratestthattibbletidyrtidyselectutf8vctrsviridisLitewaldowithrXMLxtableyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Prediction of clusters centroid position | centers_data plot.centers_data |
| Cluster analysis with fuzzy c-means algorithm | cmeans_clus plot.cmeans_clus |
| Test eps and minPts combinations for DBSCAN analysis | dbscan_combination |
| Automated analysis of digital PCR data | dPCP plot.dPCP |
| Export dPCP analysis results to a csv file | export_csv |
| Manual correction of dPCP cluster analysis | manual_correction |
| Identification and clustering of "rain" data | plot.rain_reclus rain_reclus |
| Read reference files | read_reference |
| Read sample files | read_sample |
| Read sample table | read_sampleTable |
| Find the empty partitions and single target clusters in the reference sample | plot.reference_dbscan reference_dbscan |
| Calculation of targets concentration, pooling the sample replicates | replicates_quant |
| Export dPCP analysis results to a pdf report | report_dPCP |
| Calculation of targets concentration. | target_quant |
