Files in campbio/celda
CEllular Latent Dirichlet Allocation
.Rbuildignore
.github/.gitignore
.github/workflows/BioC-check.yaml
.github/workflows/check-standard.yaml
.gitignore
CONDUCT.md
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
NOTICE
R/RcppExports.R
R/aaa.R
R/accessors.R
R/celdaGridSearch.R
R/celdaProbabilityMap.R
R/celdaUMAP.R
R/celda_C.R
R/celda_CG.R
R/celda_G.R
R/celda_functions.R
R/celda_heatmap.R
R/celdatSNE.R
R/celdatosce.R
R/clusterProbability.R
R/data.R
R/decon.R
R/elbow.R
R/factorizeMatrix.R
R/featureModuleLookup.R
R/geneSetEnrich.R
R/initialize_clusters.R
R/loglikelihood.R
R/matrixSums.R
R/misc.R
R/moduleHeatmap.R
R/perplexity.R
R/plotHeatmap.R
R/plot_decontx.R
R/plot_dr.R
R/recursiveSplit.R
R/reorderCelda.R
R/reports.R
R/selectFeatures.R
R/semi_pheatmap.R
R/simulateCells.R
R/splitModule.R
R/split_clusters.R
R/topRank.R
README.md
_pkgdown.yml
data/celdaCGGridSearchRes.rda
data/celdaCGMod.rda
data/celdaCGSim.rda
data/celdaCMod.rda
data/celdaCSim.rda
data/celdaGMod.rda
data/celdaGSim.rda
data/contaminationSim.rda
data/sampleCells.rda
data/sceCeldaC.rda
data/sceCeldaCG.rda
data/sceCeldaCGGridSearch.rda
data/sceCeldaG.rda
docs/404.html
docs/CONDUCT.html
docs/LICENSE-text.html
docs/articles/articles/celda_pbmc3k.html
docs/articles/articles/celda_pbmc3k_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/articles/celda_pbmc3k_files/figure-html/celdaProbabilityMap-1.png
docs/articles/articles/celda_pbmc3k_files/figure-html/cell_clusters-1.png
docs/articles/articles/celda_pbmc3k_files/figure-html/cell_identities-1.png
docs/articles/articles/celda_pbmc3k_files/figure-html/cell_marker_umap-1.png
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docs/articles/articles/celda_pbmc3k_files/figure-html/cell_split_perplexity-2.png
docs/articles/articles/celda_pbmc3k_files/figure-html/diffExp_plot-1.png
docs/articles/articles/celda_pbmc3k_files/figure-html/diffExp_plot-2.png
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docs/articles/articles/celda_pbmc3k_files/kePrint-0.0.1/kePrint.js
docs/articles/articles/celda_pbmc3k_files/lightable-0.0.1/lightable.css
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docs/articles/articles/decontX_pbmc4k_files/figure-html/UMAP_Clusters-1.png
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docs/articles/celda.html
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docs/articles/celda_files/figure-html/celda_heatmap-1.png
docs/articles/celda_files/figure-html/module_heatmap-1.png
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docs/articles/celda_pbmc3k.html
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docs/articles/celda_pbmc3k_files/figure-html/celdaProbabilityMap-1.png
docs/articles/celda_pbmc3k_files/figure-html/cell_clusters-1.png
docs/articles/celda_pbmc3k_files/figure-html/cell_identities-1.png
docs/articles/celda_pbmc3k_files/figure-html/cell_marker_umap-1.png
docs/articles/celda_pbmc3k_files/figure-html/cell_split_perplexity-1.png
docs/articles/celda_pbmc3k_files/figure-html/cell_split_perplexity-2.png
docs/articles/celda_pbmc3k_files/figure-html/diffExp_plot-1.png
docs/articles/celda_pbmc3k_files/figure-html/module_Tcell_prolif-1.png
docs/articles/celda_pbmc3k_files/figure-html/module_Tcell_prolif-2.png
docs/articles/celda_pbmc3k_files/figure-html/module_heatmap-1.png
docs/articles/celda_pbmc3k_files/figure-html/module_heatmap_topcells-1.png
docs/articles/celda_pbmc3k_files/figure-html/module_heatmap_with_display-1.png
docs/articles/celda_pbmc3k_files/figure-html/module_split_perplexity-1.png
docs/articles/celda_pbmc3k_files/figure-html/module_split_rpc-1.png
docs/articles/celda_pbmc3k_files/figure-html/module_umaps-1.png
docs/articles/celda_pbmc3k_files/figure-html/module_umaps_grid-1.png
docs/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-1.png
docs/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-2.png
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docs/articles/celda_pbmc3k_files/figure-html/violin-1.png
docs/articles/celda_pbmc3k_files/kePrint-0.0.1/kePrint.js
docs/articles/celda_pbmc3k_files/lightable-0.0.1/lightable.css
docs/articles/decontX.html
docs/articles/decontX_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/decontX_files/figure-html/UMAP_Clusters-1.png
docs/articles/decontX_files/figure-html/barplotBoth-1.png
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docs/articles/decontX_files/figure-html/barplotDecontCounts-1.png
docs/articles/decontX_files/figure-html/newDecontX-1.png
docs/articles/decontX_files/figure-html/plotDecontXMarkerExpression-1.png
docs/articles/decontX_files/figure-html/plot_decon-1.png
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docs/articles/decontX_pbmc4k.html
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docs/articles/decontX_pbmc4k_files/figure-html/UMAP_Clusters-1.png
docs/articles/decontX_pbmc4k_files/figure-html/barplotBoth-1.png
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docs/articles/index.html
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docs/articles/installation_files/accessible-code-block-0.0.1/empty-anchor.js
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Rplot001.png
docs/reference/Rplot002.png
docs/reference/Rplot003.png
docs/reference/Rplot004.png
docs/reference/Rplot005.png
docs/reference/Rplot006.png
docs/reference/appendCeldaList.html
docs/reference/availableModels.html
docs/reference/bestLogLikelihood.html
docs/reference/celda.html
docs/reference/celdaCGGridSearchRes.html
docs/reference/celdaCGMod.html
docs/reference/celdaCGSim.html
docs/reference/celdaCMod.html
docs/reference/celdaCSim.html
docs/reference/celdaClusters.html
docs/reference/celdaGMod.html
docs/reference/celdaGSim.html
docs/reference/celdaGridSearch.html
docs/reference/celdaHeatmap.html
docs/reference/celdaModel.html
docs/reference/celdaModules.html
docs/reference/celdaPerplexity-celdaList-method.html
docs/reference/celdaPerplexity.html
docs/reference/celdaProbabilityMap-1.png
docs/reference/celdaProbabilityMap.html
docs/reference/celdaTsne.html
docs/reference/celdaUmap.html
docs/reference/celda_C.html
docs/reference/celda_CG.html
docs/reference/celda_G.html
docs/reference/celdatosce.html
docs/reference/clusterProbability.html
docs/reference/compareCountMatrix.html
docs/reference/contaminationSim.html
docs/reference/countChecksum-celdaList-method.html
docs/reference/countChecksum.html
docs/reference/decontX-1.png
docs/reference/decontX-2.png
docs/reference/decontX-3.png
docs/reference/decontX-4.png
docs/reference/decontX-5.png
docs/reference/decontX-6.png
docs/reference/decontX.html
docs/reference/decontXcounts.html
docs/reference/distinctColors.html
docs/reference/eigenMatMultInt.html
docs/reference/eigenMatMultNumeric.html
docs/reference/factorizeMatrix.html
docs/reference/fastNormProp.html
docs/reference/fastNormPropLog.html
docs/reference/fastNormPropSqrt.html
docs/reference/featureModuleLookup.html
docs/reference/featureModuleTable.html
docs/reference/geneSetEnrich.html
docs/reference/index.html
docs/reference/logLikelihood.html
docs/reference/logLikelihoodHistory.html
docs/reference/matrixNames.html
docs/reference/moduleHeatmap-1.png
docs/reference/moduleHeatmap.html
docs/reference/nonzero.html
docs/reference/normalizeCounts.html
docs/reference/params.html
docs/reference/perplexity.html
docs/reference/plotCeldaViolin-1.png
docs/reference/plotCeldaViolin-2.png
docs/reference/plotCeldaViolin.html
docs/reference/plotDecontXContamination.html
docs/reference/plotDecontXMarkerExpression.html
docs/reference/plotDecontXMarkerPercentage.html
docs/reference/plotDimReduceCluster-1.png
docs/reference/plotDimReduceCluster-2.png
docs/reference/plotDimReduceCluster.html
docs/reference/plotDimReduceFeature-1.png
docs/reference/plotDimReduceFeature-2.png
docs/reference/plotDimReduceFeature.html
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docs/reference/plotDimReduceGrid-2.png
docs/reference/plotDimReduceGrid.html
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docs/reference/plotDimReduceModule-2.png
docs/reference/plotDimReduceModule.html
docs/reference/plotGridSearchPerplexity-1.png
docs/reference/plotGridSearchPerplexity-2.png
docs/reference/plotGridSearchPerplexity.html
docs/reference/plotHeatmap.html
docs/reference/plotRPC-1.png
docs/reference/plotRPC-2.png
docs/reference/plotRPC.html
docs/reference/recodeClusterY.html
docs/reference/recodeClusterZ.html
docs/reference/recursiveSplitCell-1.png
docs/reference/recursiveSplitCell-2.png
docs/reference/recursiveSplitCell-3.png
docs/reference/recursiveSplitCell-4.png
docs/reference/recursiveSplitCell.html
docs/reference/recursiveSplitModule-1.png
docs/reference/recursiveSplitModule-2.png
docs/reference/recursiveSplitModule.html
docs/reference/reorderCelda.html
docs/reference/reportceldaCG.html
docs/reference/resList.html
docs/reference/resamplePerplexity-1.png
docs/reference/resamplePerplexity-2.png
docs/reference/resamplePerplexity.html
docs/reference/retrieveFeatureIndex.html
docs/reference/runParams.html
docs/reference/sampleCells.html
docs/reference/sampleLabel.html
docs/reference/sceCeldaC.html
docs/reference/sceCeldaCG.html
docs/reference/sceCeldaCGGridSearch.html
docs/reference/sceCeldaG.html
docs/reference/selectBestModel.html
docs/reference/selectFeatures.html
docs/reference/semiPheatmap.html
docs/reference/simulateCells.html
docs/reference/simulateContamination.html
docs/reference/splitModule.html
docs/reference/subsetCeldaList.html
docs/reference/topRank.html
docs/sitemap.xml
inst/rmarkdown/CeldaCG_PlotResults.Rmd
inst/rmarkdown/CeldaCG_Run.Rmd
man/appendCeldaList.Rd
man/availableModels.Rd
man/bestLogLikelihood.Rd
man/celda.Rd
man/celdaCGGridSearchRes.Rd
man/celdaCGMod.Rd
man/celdaCGSim.Rd
man/celdaCMod.Rd
man/celdaCSim.Rd
man/celdaClusters.Rd
man/celdaGMod.Rd
man/celdaGSim.Rd
man/celdaGridSearch.Rd
man/celdaHeatmap.Rd
man/celdaModel.Rd
man/celdaModules.Rd
man/celdaPerplexity-celdaList-method.Rd
man/celdaPerplexity.Rd
man/celdaProbabilityMap.Rd
man/celdaTsne.Rd
man/celdaUmap.Rd
man/celda_C.Rd
man/celda_CG.Rd
man/celda_G.Rd
man/celdatosce.Rd
man/clusterProbability.Rd
man/compareCountMatrix.Rd
man/contaminationSim.Rd
man/countChecksum-celdaList-method.Rd
man/countChecksum.Rd
man/decontX.Rd
man/decontXcounts.Rd
man/distinctColors.Rd
man/eigenMatMultInt.Rd
man/eigenMatMultNumeric.Rd
man/factorizeMatrix.Rd
man/fastNormProp.Rd
man/fastNormPropLog.Rd
man/fastNormPropSqrt.Rd
man/featureModuleLookup.Rd
man/featureModuleTable.Rd
man/geneSetEnrich.Rd
man/logLikelihood.Rd
man/logLikelihoodHistory.Rd
man/matrixNames.Rd
man/moduleHeatmap.Rd
man/nonzero.Rd
man/normalizeCounts.Rd
man/params.Rd
man/perplexity.Rd
man/plotCeldaViolin.Rd
man/plotDecontXContamination.Rd
man/plotDecontXMarkerExpression.Rd
man/plotDecontXMarkerPercentage.Rd
man/plotDimReduceCluster.Rd
man/plotDimReduceFeature.Rd
man/plotDimReduceGrid.Rd
man/plotDimReduceModule.Rd
man/plotGridSearchPerplexity.Rd
man/plotHeatmap.Rd
man/plotRPC.Rd
man/recodeClusterY.Rd
man/recodeClusterZ.Rd
man/recursiveSplitCell.Rd
man/recursiveSplitModule.Rd
man/reorderCelda.Rd
man/reportceldaCG.Rd
man/resList.Rd
man/resamplePerplexity.Rd
man/retrieveFeatureIndex.Rd
man/runParams.Rd
man/sampleCells.Rd
man/sampleLabel.Rd
man/sceCeldaC.Rd
man/sceCeldaCG.Rd
man/sceCeldaCGGridSearch.Rd
man/sceCeldaG.Rd
man/selectBestModel.Rd
man/selectFeatures.Rd
man/semiPheatmap.Rd
man/simulateCells.Rd
man/simulateContamination.Rd
man/splitModule.Rd
man/subsetCeldaList.Rd
man/topRank.Rd
src/DecontX.cpp
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/cG_calcGibbsProbY.cpp
src/eigenMatMultInt.cpp
src/matrixNorm.cpp
src/matrixSums.c
src/matrixSumsSparse.cpp
src/perplexity.c
tests/testthat.R
tests/testthat/test-celda-functions.R
tests/testthat/test-celda_C.R
tests/testthat/test-celda_CG.R
tests/testthat/test-celda_G.R
tests/testthat/test-decon.R
tests/testthat/test-intialize_cluster.R
tests/testthat/test-matrixSums.R
tests/testthat/test-with_seed.R
vignettes/articles/celda_pbmc3k.Rmd
vignettes/articles/decontX_pbmc4k.Rmd
vignettes/articles/installation.Rmd
vignettes/celda.Rmd
vignettes/decontX.Rmd
