cellphoneDB_plot directory: plot CellPhoneDB results, see cpdbPlot.html for details.

compare.R: Calculate intersect and difference of two strings.

exportSeurat.R: Export Seurat object data and metadata as flat txt files.

export_cellphonedb.R: Export Seurat object for use with CellPhoneDB.

markerDescription.R: Takes a dataframe with a 'gene' column containing HGNC gene IDs (i.e. Seurat::FindAllMarkers() output) and returns it with added Entrez ID, Gene name (description), Cluster occurrences, Summary columns.

markerDescription_ens97.R: Version that works with the latest Ensembl database.

pdt_heatmap.R: Plot a heatmap from results of https://github.com/haniffalab/scRNA-seq_analysis/tree/master/pipelines/13_pseudotime.

plot3D.R: Interactive 3D dimensionality reduction (t-SNE) plot.

plotCircles.R: Plot circles for use in figures.

plotData.R: Dotplot for use in https://github.com/veghp/Sequencing.

plotGenes.R: Save feature plots of specified genes.

read10xsummary.R: Reads 10x Cell Ranger metrics_summary.csv or web_summary.html files into a matrix (see https://github.com/veghp/Sequencing).