Analysis Tools#

Differential Gene Expression#

A menubar plugin to compute differential gene expression for two subsets.

This plugin is normally invoked with a GUI but the core logic can be invoked as get_gene_diff_exp.

get_gene_diff_exp(subset1, subset2, data)

Get differential gene expression for two subsets over a dataset

DifferentialGeneExpressionListener(subset1, ...)

A Listener that updates the differential gene expression SynComponent(s) when the underlying subsets are changed.

Gene Subset Summary#

Calculate a summary statistic for cells based on genesubset

This menubar plugin in normally invoked through a dialog which not only does the initial calculation and stores the summary is a new component in the target dataset, but sets up a Listener to keep that new component up-to-date when changes are made to the gene subset.

do_calculation_over_gene_subset(...[, ...])

Calculate a summary statistic for cells based on genesubset

GeneSummaryListener(genesubset, basename, key)

A Listener to keep the new components in target_dataset up-to-date with any changes in the genesubset.

Enrich Gene Subset#

A menubar plugin to do Gene Set Enrichment Analysis on a set of genes.