Package: ddPCRclust 1.32.0
Benedikt G. Brink
ddPCRclust: Clustering algorithm for ddPCR data
The ddPCRclust algorithm can automatically quantify the CPDs of non-orthogonal ddPCR reactions with up to four targets. In order to determine the correct droplet count for each target, it is crucial to both identify all clusters and label them correctly based on their position. For more information on what data can be analyzed and how a template needs to be formatted, please check the vignette.
Authors:
ddPCRclust_1.32.0.tar.gz
ddPCRclust_1.32.0.zip(r-4.7)ddPCRclust_1.32.0.zip(r-4.6)ddPCRclust_1.32.0.zip(r-4.5)
ddPCRclust_1.32.0.tgz(r-4.6-any)ddPCRclust_1.32.0.tgz(r-4.5-any)
ddPCRclust_1.32.0.tar.gz(r-4.7-any)ddPCRclust_1.32.0.tar.gz(r-4.6-any)
ddPCRclust_1.32.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ddPCRclust/json (API)
NEWS
| # Install 'ddPCRclust' in R: |
| install.packages('ddPCRclust', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bgbrink/ddpcrclust/issues
On BioConductor:ddPCRclust-1.33.0(bioc 3.24)ddPCRclust-1.32.0(bioc 3.23)
ddpcrclusteringbiological-data-analysis
Last updated from:ffa5b1c854 (on RELEASE_3_23). Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 175 | ||
| linux-devel-x86_64 | NOTE | 538 | ||
| source / vignettes | OK | 280 | ||
| linux-release-x86_64 | NOTE | 279 | ||
| macos-release-arm64 | NOTE | 208 | ||
| macos-oldrel-arm64 | NOTE | 168 | ||
| windows-devel | NOTE | 228 | ||
| windows-release | NOTE | 220 | ||
| windows-oldrel | NOTE | 201 | ||
| wasm-release | OK | 159 |
Exports:calculateCPDscreateEnsembleddPCRclustexportPlotsexportToCSVexportToExcelreadFilesreadTemplaterunDensityrunPeaksrunSam
Dependencies:abindbackportsBHBiobaseBiocGenericsbiocmakebitopsbootbroomcarcarDatacaToolscliclueclustercolorspacecowplotcpp11cytolibdeldirDerivdir.expirydoBydplyrfarverfilelockflowCoreflowDensityflowPeaksflowVizforecastFormulafracdiffgenericsggplot2gluegplotsgtablegtoolshexbinIDPmiscinterpisobandjpegKernSmoothlabelinglatticelatticeExtralifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmatrixStatsmgcvmicrobenchmarkminqamodelrnlmenloptrnnetnumDerivopenxlsxpbkrtestpillarpkgconfigplotrixpngpolyclippurrrquantregR.methodsS3R.ooR.utilsR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasRhdf5librlangRProtoBufLibS4VectorsS7SamSPECTRALscalesSparseMstringistringrsurvivaltibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithrzipzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculates the copies per droplet | calculateCPDs |
| Create a cluster ensemble | createEnsemble |
| ddPCRclust A package for automated quantification of multiplexed ddPCR data | ddPCRclust-package ddPCRclust |
| Plot the algorithms results with ggplot2 | exportPlots |
| Export the algorithms results to a csv file | exportToCSV |
| Export the algorithms results to an Excel file | exportToExcel |
| Read the csv files from your disk | readFiles |
| Read a template file from disk | readTemplate |
| Find the clusters using flowDensity | runDensity |
| Find the clusters using flowPeaks | runPeaks |
| Find the clusters using SamSPECTRAL | runSam |
| Correct for DNA shearing | shearCorrection |