Files in EngeLab/CIMseq.publication

The CIMseq.publication package reproduces the figures associated with the CIMseq publication

R/CIMseq.publication-package.R R/data.R R/funToCheckKnownResults.R R/palette.R R/plotting.R R/renamingAndOrdering.R R/swarmOnPlatform.R R/syntheticMultipletsFromCounts.R R/utils.R README.Rmd README.md inst/analysis/MGA.analysis_SI20/analysis/analysis.Rmd inst/analysis/MGA.analysis_SI20/scripts/CIMseqData_subset.R inst/analysis/MGA.analysis_SI20/scripts/CIMseqSwarm.R inst/analysis/MGA.analysis_colon20/analysis/analysis.Rmd inst/analysis/MGA.analysis_colon20/scripts/CIMseqData_subset.R inst/analysis/MGA.analysis_colon20/scripts/CIMseqSwarm.R inst/analysis/MGA.analysis_colon20/scripts/seuratDE.R inst/analysis/MGA.analysis_enge20/analysis/analysis.Rmd inst/analysis/MGA.analysis_enge20/scripts/CIMseqData.R inst/analysis/MGA.analysis_enge20/scripts/CIMseqSwarm.R inst/analysis/SCM.analysis/analysis/analysis.Rmd inst/analysis/SCM.analysis/scripts/script.R inst/analysis/deconvoluteSingletsMouse/analysis/analysis.Rmd inst/analysis/deconvoluteSingletsMouse/scripts/CIMseqSwarm.R inst/analysis/methodSchematic/scripts/schematicCode.R inst/analysis/multipletCellNrDist/analysis/analysis.Rmd inst/analysis/runAnalysis.R inst/analysis/visualizingPoissonAlgo/analysis/analysis.Rmd inst/analysis/visualizingPoissonAlgo/scripts/script.R inst/analysis/visualizingSolutionSpace/analysis/analysis.Rmd inst/analysis/visualizingSolutionSpace/scripts/script.R inst/data/Mouse.gut.architecture_MGA.R inst/data/Sorted.cell.line.multiplets_SCM.R inst/data/data.R man/CIMseq.publication-package.Rd man/checkResults.Rd man/classOrder.MGA.Rd man/convertCountsToMatrix.Rd man/detectERCCreads.Rd man/detectLowQualityCells.ERCCfrac.Rd man/detectLowQualityCells.housekeeping.Rd man/detectLowQualityCells.totalCounts.Rd man/detectLowQualityGenes.Rd man/detectNonGenes.Rd man/filterCountsData.Rd man/getCountsDataViaLinks.Rd man/getMetadataViaLink.Rd man/labelSingletsAndMultiplets.Rd man/moveGenesToRownames.Rd man/palette.Rd man/plotPDF.Rd man/plotRmarkdown.Rd man/printResults.Rd man/removeHTSEQsuffix.Rd man/renameClasses.MGA.Rd man/renameClasses.SCM.Rd man/renameMgfpSamples.Rd man/resultsInPlate.Rd man/runSwarmMultiprocess.Rd man/runSwarmUppmax.Rd man/saveRDA.Rd man/setupPlate.Rd man/seuratToCIMseq.Rd man/syntheticMultipletsFromCounts.Rd man/syntheticSinglets.Rd man/viewAsPlate.Rd tests/testthat.R tests/testthat/test_funToCheckKnownResults.R tests/testthat/test_permutationFunctions.R