All functions
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abcam.neuronal.markers
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A dataframe containing the abcam neuronal marker genes
abcam.neuronal.markers |
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addEmbedding()
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addEmbedding |
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addLabels()
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Add cluster labels to a tSNE ggplot2 plot |
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cell.cycle.genes.whitfield.2002
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A dataframe containing the gene symbols for each phase of the cell cycle.
cell.cycle.genes.whitfield.2002 |
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cellCyclePlot()
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cellCyclePlot |
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clusterCenters()
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clusterCenters |
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computeCC()
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computeCC |
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constrainScale()
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Constrain the scale of the plot to the dimensionality reduction limits |
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convertGenesBetweenSpeciesHomologs()
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convertGenesBetweenSpeciesHomologs |
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convertGenesBetweenSymbolsAndID()
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Convert between gene symbols and ENSEMBL gene IDs |
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correlateExpression()
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Correlate expression |
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cytobox
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cytobox: A toolbox for analyzing single cell RNA-seq data |
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drLims()
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Get the limits of a the first two dimensions in a dimensionality reduction |
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ensembl2symbols()
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Convert ENSEMBL gene IDs to gene symbols |
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fetchData()
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fetchData |
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filterGenesSample()
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filterGenesSample |
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findGenes()
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findGenes |
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geneName()
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geneName |
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getAllMarkers()
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Title |
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getClusterColours()
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Get a vector of cluster colours, optionally highlighting select clusters |
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getVarianceExplained()
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getVarianceExplained |
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ggColours()
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Get default ggplot2/Seurat colours |
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heatmapPercentMarkerOverlap()
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Compute a heatmap of marker overlap between samples |
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hg2mm()
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hg2mm |
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highlight()
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Highlight select clusters on a dimensionality reduction plot |
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meanClusterExpression()
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meanClusterExpression |
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meanGeneExpression()
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meanGeneExpression |
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meanMarkerExpressionPerCell()
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meanMarkerExpression |
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mm2hg()
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mm2hg |
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noLegend()
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Remove the legend in a ggplot |
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noTicks()
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Remove axis ticks and tick labels from a ggplot |
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pairwiseVln()
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pairwiseVln |
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pbmc
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pbmc |
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percentMarkerOverlap()
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percentMarkerOverlap |
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percentilesMarkerExpression()
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perecentilesMarkerExpression |
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plot_dr() tsne() pca() umap() phate()
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Plot a reduced dimensionality embedding for a Seurat object, colouring
by cluster or arbitrary variables. |
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rotateX()
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Rotate the x axis labels in a ggplot |
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selectMarkersRF()
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Title |
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symbols2ensembl()
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Convert gene symbols to ENSEMBL gene IDs |
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theme_min()
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Apply a clean theme to a ggplot2 object |
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tsneByMeanMarkerExpression() feature()
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Colour cells in t-SNE or PCA space by gene expression |
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tsneByPercentileMarkerExpression()
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Colour cells in t-SNE space by percentile gene expression |
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vln()
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Generate violin plots of gene expression in each cluster |
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vlnGrid()
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Generate a grid of tiny violins of gene expression in each cluster |
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whichCells()
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Retrieve cells in specified clusters |