├── .Rbuildignore ├── .Rhistory ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── ImportData.R ├── biaxial_plot.R ├── clusKNN.R ├── clusSignificancePlot.R ├── contourPlot.R ├── density_plot.R ├── diffClust.R ├── diffExpression.R ├── diffPlot.R ├── downsampleByVar.R ├── imc_rank.R ├── markerEnrichment.R ├── markerExpression.R ├── markerExpressionPerCluster.R ├── markerExpressionPerSample.R ├── mdsplot.R ├── medianHeatmap.R ├── metadataPlot.R ├── performTSNE.R ├── performUMAP.R ├── plotAbundance.R ├── plotClusters.R ├── plotSignatures.R ├── processFCS.R ├── runFlowSOM.R ├── runPhenograph.R ├── save_pheatmap_pdf.R ├── setClusterIdents.R ├── stat_test_clust.R ├── stat_test_expression.R ├── subsetSCE.R ├── subset_sce_metadata.R ├── volcanoPlot.R ├── writeToFlowSet.R └── write_sce_to_fcs.R ├── README.Rmd ├── README.md ├── README_files └── figure-gfm │ ├── abundance test-1.png │ ├── activation markers-1.png │ ├── bar plot-1.png │ ├── cell annotations-1.png │ ├── density plot-1.png │ ├── diagnostic heatmap-1.png │ ├── final heatmap-1.png │ ├── marker test-1.png │ ├── mds_plot-1.png │ ├── merge clusters-1.png │ ├── sample heatmap-1.png │ ├── unnamed-chunk-2-1.png │ └── viz flowSOM-1.png ├── immunoCluster.Rproj ├── man ├── biaxial_plot.Rd ├── density_plot.Rd ├── imc_rank.Rd ├── markerExpression.Rd ├── mdsplot.Rd ├── performTSNE.Rd ├── performUMAP.Rd ├── plotAbundance.Rd ├── processFCS.Rd ├── runFlowSOM.Rd ├── runPhenograph.Rd ├── setClusterIdents.Rd ├── stat_test_clust.Rd ├── stat_test_expression.Rd ├── subset_sce_metadata.Rd ├── volcanoPlot.Rd └── write_sce_to_fcs.Rd └── readme_bib.bib /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.Rhistory: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user 2 | -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/LICENSE -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/NAMESPACE -------------------------------------------------------------------------------- /R/ImportData.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/ImportData.R -------------------------------------------------------------------------------- /R/biaxial_plot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/biaxial_plot.R -------------------------------------------------------------------------------- /R/clusKNN.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/clusKNN.R -------------------------------------------------------------------------------- /R/clusSignificancePlot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/clusSignificancePlot.R -------------------------------------------------------------------------------- /R/contourPlot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/contourPlot.R -------------------------------------------------------------------------------- /R/density_plot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/density_plot.R -------------------------------------------------------------------------------- /R/diffClust.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/diffClust.R -------------------------------------------------------------------------------- /R/diffExpression.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/diffExpression.R -------------------------------------------------------------------------------- /R/diffPlot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/diffPlot.R -------------------------------------------------------------------------------- /R/downsampleByVar.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/downsampleByVar.R -------------------------------------------------------------------------------- /R/imc_rank.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/imc_rank.R -------------------------------------------------------------------------------- /R/markerEnrichment.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/markerEnrichment.R -------------------------------------------------------------------------------- /R/markerExpression.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/markerExpression.R -------------------------------------------------------------------------------- /R/markerExpressionPerCluster.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/markerExpressionPerCluster.R -------------------------------------------------------------------------------- /R/markerExpressionPerSample.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/markerExpressionPerSample.R -------------------------------------------------------------------------------- /R/mdsplot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/mdsplot.R -------------------------------------------------------------------------------- /R/medianHeatmap.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/medianHeatmap.R -------------------------------------------------------------------------------- /R/metadataPlot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/metadataPlot.R -------------------------------------------------------------------------------- /R/performTSNE.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/performTSNE.R -------------------------------------------------------------------------------- /R/performUMAP.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/performUMAP.R -------------------------------------------------------------------------------- /R/plotAbundance.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/plotAbundance.R -------------------------------------------------------------------------------- /R/plotClusters.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/plotClusters.R -------------------------------------------------------------------------------- /R/plotSignatures.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/plotSignatures.R -------------------------------------------------------------------------------- /R/processFCS.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/processFCS.R -------------------------------------------------------------------------------- /R/runFlowSOM.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/runFlowSOM.R -------------------------------------------------------------------------------- /R/runPhenograph.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/runPhenograph.R -------------------------------------------------------------------------------- /R/save_pheatmap_pdf.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/save_pheatmap_pdf.R -------------------------------------------------------------------------------- /R/setClusterIdents.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/setClusterIdents.R -------------------------------------------------------------------------------- /R/stat_test_clust.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/stat_test_clust.R -------------------------------------------------------------------------------- /R/stat_test_expression.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/stat_test_expression.R -------------------------------------------------------------------------------- /R/subsetSCE.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/subsetSCE.R -------------------------------------------------------------------------------- /R/subset_sce_metadata.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/subset_sce_metadata.R -------------------------------------------------------------------------------- /R/volcanoPlot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/volcanoPlot.R -------------------------------------------------------------------------------- /R/writeToFlowSet.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/writeToFlowSet.R -------------------------------------------------------------------------------- /R/write_sce_to_fcs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/R/write_sce_to_fcs.R -------------------------------------------------------------------------------- /README.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/README.Rmd -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/README.md -------------------------------------------------------------------------------- /README_files/figure-gfm/abundance test-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/README_files/figure-gfm/abundance test-1.png -------------------------------------------------------------------------------- /README_files/figure-gfm/activation markers-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/README_files/figure-gfm/activation markers-1.png -------------------------------------------------------------------------------- /README_files/figure-gfm/bar plot-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/README_files/figure-gfm/bar plot-1.png -------------------------------------------------------------------------------- /README_files/figure-gfm/cell annotations-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/README_files/figure-gfm/cell annotations-1.png -------------------------------------------------------------------------------- /README_files/figure-gfm/density plot-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/README_files/figure-gfm/density plot-1.png -------------------------------------------------------------------------------- /README_files/figure-gfm/diagnostic heatmap-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/README_files/figure-gfm/diagnostic heatmap-1.png -------------------------------------------------------------------------------- /README_files/figure-gfm/final heatmap-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/README_files/figure-gfm/final heatmap-1.png -------------------------------------------------------------------------------- /README_files/figure-gfm/marker test-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/README_files/figure-gfm/marker test-1.png -------------------------------------------------------------------------------- /README_files/figure-gfm/mds_plot-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/README_files/figure-gfm/mds_plot-1.png -------------------------------------------------------------------------------- /README_files/figure-gfm/merge clusters-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/README_files/figure-gfm/merge clusters-1.png -------------------------------------------------------------------------------- /README_files/figure-gfm/sample heatmap-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/README_files/figure-gfm/sample heatmap-1.png -------------------------------------------------------------------------------- /README_files/figure-gfm/unnamed-chunk-2-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/README_files/figure-gfm/unnamed-chunk-2-1.png -------------------------------------------------------------------------------- /README_files/figure-gfm/viz flowSOM-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/README_files/figure-gfm/viz flowSOM-1.png -------------------------------------------------------------------------------- /immunoCluster.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/immunoCluster.Rproj -------------------------------------------------------------------------------- /man/biaxial_plot.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/man/biaxial_plot.Rd -------------------------------------------------------------------------------- /man/density_plot.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/man/density_plot.Rd -------------------------------------------------------------------------------- /man/imc_rank.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/man/imc_rank.Rd -------------------------------------------------------------------------------- /man/markerExpression.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/man/markerExpression.Rd -------------------------------------------------------------------------------- /man/mdsplot.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/man/mdsplot.Rd -------------------------------------------------------------------------------- /man/performTSNE.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/man/performTSNE.Rd -------------------------------------------------------------------------------- /man/performUMAP.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/man/performUMAP.Rd -------------------------------------------------------------------------------- /man/plotAbundance.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/man/plotAbundance.Rd -------------------------------------------------------------------------------- /man/processFCS.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/man/processFCS.Rd -------------------------------------------------------------------------------- /man/runFlowSOM.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/man/runFlowSOM.Rd -------------------------------------------------------------------------------- /man/runPhenograph.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/man/runPhenograph.Rd -------------------------------------------------------------------------------- /man/setClusterIdents.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/man/setClusterIdents.Rd -------------------------------------------------------------------------------- /man/stat_test_clust.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/man/stat_test_clust.Rd -------------------------------------------------------------------------------- /man/stat_test_expression.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/man/stat_test_expression.Rd -------------------------------------------------------------------------------- /man/subset_sce_metadata.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/man/subset_sce_metadata.Rd -------------------------------------------------------------------------------- /man/volcanoPlot.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/man/volcanoPlot.Rd -------------------------------------------------------------------------------- /man/write_sce_to_fcs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/man/write_sce_to_fcs.Rd -------------------------------------------------------------------------------- /readme_bib.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kordastilab/ImmunoCluster/HEAD/readme_bib.bib --------------------------------------------------------------------------------