hgmd.__main__

hgmd.__main__.init_parser(parser)

Initialize parser args.

hgmd.__main__.main()

Hypergeometric marker detection. Finds markers identifying a cluster.

Reads in data from single-cell RNA sequencing. Data is in the form of 3 CSVs: gene expression data by gene by cell, 2-D tSNE data by cell, and the clusters of interest by cell. Creates a list of genes and a list of gene pairs (including complements), ranked by hypergeometric and t-test significance. The highest ranked marker genes generally best identify the cluster of interest. Saves these lists to CSV and creates gene expression visualizations.

hgmd.__main__.read_data(cls_path, tsne_path, marker_path)

Reads in cluster series, tsne data, marker expression without complements at given paths.