fungenomics/cytobox
A toolbox for analyzing single cell RNA-seq data

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Files in fungenomics/cytobox
A toolbox for analyzing single cell RNA-seq data

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
R/cell_cycle.R R/comparisons_with_markers.R R/cytobox.R R/data.R R/expression_correlation.R R/feature_plots.R R/genes.R R/rf_marker_selection.R R/summarise.R R/utils.R R/utils_plotting.R R/utils_tidyeval.R R/visualization.R README.md
cytobox.Rproj
data-raw/get_cell_cycle_whitfield_2002.R data-raw/get_data.R data-raw/get_data_abcam_neuronal_markers.R
data/abcam.neuronal.markers.rda
data/cell.cycle.genes.whitfield.2002.rda
data/cell.cycle.genes.whitfield.2012.rda
data/hg.genes.rda
data/hg2mm.genes.rda
data/markers_pbmc.rda
data/mm.genes.rda
data/mm2hg.genes.rda
data/pbmc.rda
docs/LICENSE-text.html
docs/articles/cytobox.html
docs/articles/cytobox_files/figure-html/dashboard-1.png
docs/articles/cytobox_files/figure-html/dashboard-2.png
docs/articles/cytobox_files/figure-html/feature-1.png
docs/articles/cytobox_files/figure-html/feature-2.png
docs/articles/cytobox_files/figure-html/feature_indiv-1.png
docs/articles/cytobox_files/figure-html/feature_indiv-2.png
docs/articles/cytobox_files/figure-html/feature_indiv-3.png
docs/articles/cytobox_files/figure-html/heatmapPercentMarkerOverlap-1.png
docs/articles/cytobox_files/figure-html/heatmapPercentMarkerOverlap-2.png
docs/articles/cytobox_files/figure-html/heatmapPercentMarkerOverlap-3.png
docs/articles/cytobox_files/figure-html/heatmapPercentMarkerOverlap-4.png
docs/articles/cytobox_files/figure-html/heatmapPercentMarkerOverlap-5.png
docs/articles/cytobox_files/figure-html/heatmap_both-1.png
docs/articles/cytobox_files/figure-html/highlight-1.png
docs/articles/cytobox_files/figure-html/highlight-2.png
docs/articles/cytobox_files/figure-html/highlight-3.png
docs/articles/cytobox_files/figure-html/highlight-4.png
docs/articles/cytobox_files/figure-html/highlight-5.png
docs/articles/cytobox_files/figure-html/highlight-6.png
docs/articles/cytobox_files/figure-html/pariwiseVln-1.png
docs/articles/cytobox_files/figure-html/tsne-1.png
docs/articles/cytobox_files/figure-html/tsne-2.png
docs/articles/cytobox_files/figure-html/tsne-3.png
docs/articles/cytobox_files/figure-html/tsneByMeanMarkerExpression-1.png
docs/articles/cytobox_files/figure-html/tsneByPercentilesMarkerExpression-1.png
docs/articles/cytobox_files/figure-html/tsneByPercentilesMarkerExpression-2.png
docs/articles/cytobox_files/figure-html/tsneByPercentilesMarkerExpression-3.png
docs/articles/cytobox_files/figure-html/tsne_nUMI-1.png
docs/articles/cytobox_files/figure-html/tsne_nUMI_select-1.png
docs/articles/cytobox_files/figure-html/tsne_res.1-1.png
docs/articles/cytobox_files/figure-html/undetected-1.png
docs/articles/cytobox_files/figure-html/vln-1.png
docs/articles/cytobox_files/figure-html/vln-2.png
docs/articles/cytobox_files/figure-html/vlnGrid-1.png
docs/articles/cytobox_files/figure-html/vlnGrid-2.png
docs/articles/cytobox_files/figure-html/vlnGrid-3.png
docs/articles/extra/feature_plots.html
docs/articles/index.html
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/abcam.neuronal.markers.html
docs/reference/addEmbedding.html
docs/reference/addLabels.html
docs/reference/cell.cycle.genes.whitfield.2002.html
docs/reference/cellCyclePlot.html
docs/reference/clusterCenters.html
docs/reference/computeCC.html
docs/reference/constrainScale.html
docs/reference/convertGenesBetweenSpeciesHomologs.html
docs/reference/convertGenesBetweenSymbolsAndID.html
docs/reference/correlateExpression.html
docs/reference/cytobox.html
docs/reference/drLims.html
docs/reference/ensembl2symbols.html
docs/reference/fetchData.html
docs/reference/filterGenesSample.html
docs/reference/findGenes.html
docs/reference/geneName.html
docs/reference/getAllMarkers.html
docs/reference/getClusterColours.html
docs/reference/getVarianceExplained.html
docs/reference/ggColours.html
docs/reference/heatmapPercentMarkerOverlap-1.png
docs/reference/heatmapPercentMarkerOverlap.html
docs/reference/hg2mm.html
docs/reference/highlight-1.png
docs/reference/highlight-2.png
docs/reference/highlight-3.png
docs/reference/highlight-4.png
docs/reference/highlight-5.png
docs/reference/highlight.html
docs/reference/index.html
docs/reference/meanClusterExpression.html
docs/reference/meanGeneExpression.html
docs/reference/meanMarkerExpressionPerCell.html
docs/reference/mm2hg.html
docs/reference/noLegend.html
docs/reference/noTicks.html
docs/reference/pairwiseVln-1.png
docs/reference/pairwiseVln.html
docs/reference/pbmc.html
docs/reference/percentMarkerOverlap.html
docs/reference/percentilesMarkerExpression.html
docs/reference/plot_dr-1.png
docs/reference/plot_dr-2.png
docs/reference/plot_dr-3.png
docs/reference/plot_dr-4.png
docs/reference/plot_dr-5.png
docs/reference/plot_dr.html
docs/reference/rotateX.html
docs/reference/selectMarkersRF.html
docs/reference/seurat_to_monocle.html
docs/reference/symbols2ensembl.html
docs/reference/theme_min.html
docs/reference/tidyeval.html
docs/reference/tsneByMeanMarkerExpression-1.png
docs/reference/tsneByMeanMarkerExpression-2.png
docs/reference/tsneByMeanMarkerExpression-3.png
docs/reference/tsneByMeanMarkerExpression.html
docs/reference/tsneByPercentileMarkerExpression-1.png
docs/reference/tsneByPercentileMarkerExpression-2.png
docs/reference/tsneByPercentileMarkerExpression-3.png
docs/reference/tsneByPercentileMarkerExpression.html
docs/reference/tsne_plot_clusters_highlighted_with_pseudotime.html
docs/reference/vln-1.png
docs/reference/vln-2.png
docs/reference/vln-3.png
docs/reference/vln.html
docs/reference/vlnGrid-1.png
docs/reference/vlnGrid-2.png
docs/reference/vlnGrid-3.png
docs/reference/vlnGrid-4.png
docs/reference/vlnGrid.html
docs/reference/whichCells.html
man/abcam.neuronal.markers.Rd man/addEmbedding.Rd man/addLabels.Rd man/cell.cycle.genes.whitfield.2002.Rd man/cellCyclePlot.Rd man/clusterCenters.Rd man/computeCC.Rd man/constrainScale.Rd man/convertGenesBetweenSpeciesHomologs.Rd man/convertGenesBetweenSymbolsAndID.Rd man/correlateExpression.Rd man/cytobox.Rd man/drLims.Rd man/ensembl2symbols.Rd man/fetchData.Rd man/filterGenesSample.Rd man/findGenes.Rd man/geneName.Rd man/getAllMarkers.Rd man/getClusterColours.Rd man/getVarianceExplained.Rd man/ggColours.Rd man/heatmapPercentMarkerOverlap.Rd man/hg2mm.Rd man/highlight.Rd man/meanClusterExpression.Rd man/meanGeneExpression.Rd man/meanMarkerExpressionPerCell.Rd man/mm2hg.Rd man/noLegend.Rd man/noTicks.Rd man/pairwiseVln.Rd man/pbmc.Rd man/percentMarkerOverlap.Rd man/percentilesMarkerExpression.Rd man/plot_dr.Rd man/rotateX.Rd man/selectMarkersRF.Rd man/symbols2ensembl.Rd man/theme_min.Rd man/tidyeval.Rd man/tsneByMeanMarkerExpression.Rd man/tsneByPercentileMarkerExpression.Rd man/vln.Rd man/vlnGrid.Rd man/whichCells.Rd tests/testthat.R tests/testthat/test-comparisons.R tests/testthat/test-correlation.R tests/testthat/test-genes.R tests/testthat/test-plotting_utils.R tests/testthat/test-summarise.R tests/testthat/test-utils.R
vignettes/.gitignore
vignettes/cytobox.Rmd vignettes/extra/feature_plots.Rmd
fungenomics/cytobox documentation built on Feb. 13, 2020, 10:51 a.m.

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