Man pages for sjessa/cytokit
A toolkit for analyzing single cell RNA-seq data
| abcam.neuronal.markers | A dataframe containing the abcam neuronal marker genes... |
| addEmbedding | addEmbedding |
| addLabels | Add cluster labels to a tSNE ggplot2 plot |
| annotateMarkers | Annotate cluster markers computed by Seurat |
| cell.cycle.genes.whitfield.2002 | A dataframe containing the gene symbols for each phase of the... |
| cellCyclePlot | cellCyclePlot |
| clusterCenters | clusterCenters |
| constrainScale | Constrain the scale of the plot to the dimensionality... |
| convertGenesBetweenSpeciesHomologs | convertGenesBetweenSpeciesHomologs |
| convertGenesBetweenSymbolsAndID | Convert between gene symbols and ENSEMBL gene IDs |
| correlateExpression | Correlate expression |
| cytokit | cytokit: A toolkit for analyzing single cell RNA-seq data |
| drLims | Get the limits of a the first two dimensions in a... |
| ensembl2symbols | Convert ENSEMBL gene IDs to gene symbols |
| fetchData | fetchData |
| filterGenesSample | filterGenesSample |
| findGenes | findGenes |
| geneName | geneName |
| getAllMarkers | Title |
| getClusterColours | Get a vector of cluster colours, optionally highlighting... |
| getVarianceExplained | getVarianceExplained |
| ggColours | Get default ggplot2/Seurat colours |
| heatmapPercentMarkerOverlap | Compute a heatmap of marker overlap between samples |
| hg2mm | hg2mm |
| highlight | Highlight select clusters on a tSNE plot |
| labelTSNEClusters | labelTSNEClusters |
| meanClusterExpression | meanClusterExpression |
| meanGeneExpression | meanGeneExpression |
| meanMarkerExpressionPerCell | meanMarkerExpression |
| mm2hg | mm2hg |
| noLegend | Remove the legend in a ggplot |
| noTicks | Remove axis ticks and tick labels from a ggplot |
| pairwiseVln | pairwiseVln |
| pbmc | pbmc |
| percentilesMarkerExpression | perecentilesMarkerExpression |
| percentMarkerOverlap | percentMarkerOverlap |
| plotDR | Plot a reduced dimensionality embedding for a dataset |
| rotateX | Rotate the x axis labels in a ggplot |
| selectMarkersRF | Title |
| seurat_to_monocle | Converts a Seurat object to a Monocle object. |
| symbols2ensembl | Convert gene symbols to ENSEMBL gene IDs |
| theme_min | Apply a clean theme to a ggplot2 object |
| tidyeval | Tidy eval helpers |
| tsneByMeanMarkerExpression | Colour cells in t-SNE or PCA space by gene expression |
| tsneByPercentileMarkerExpression | Colour cells in t-SNE space by percentile gene expression |
| tsne_plot_clusters_highlighted | Draws a tSNE plot highlighting the selected clusters. |
| tsne_plot_clusters_highlighted_with_pseudotime | Draws a tSNE plot with a pseudotime gradient in the selected... |
| vln | Generate violin plots of gene expression in each cluster |
| vlnGrid | Generate a grid of tiny violins of gene expression in each... |
| whichCells | Retrieve cells in specified clusters |
