rnalysis.enrichment

Description

This module can perform enrichment analyses on a given set of genomic features and visualize their intersections. These include gene ontology/tissue/phenotype enrichment, enrichment for user-defined attributes, set visualization ,etc. Results of enrichment analyses can be saved to .csv files.

Classes

FeatureSet([gene_set, set_name])	Receives a filtered gene set and the set's name (optional) and preforms various enrichment analyses on them.
RankedSet(ranked_genes[, set_name])	Receives a ranked gene set, sorted by any biologically-meaningful value (expression level, fold-change, etc) and preforms various enrichment analyses on them.

Functions

enrichment_bar_plot(results_table_path[, ...])	Generate an enrichment bar-plot based on an enrichment results table.
gene_ontology_graph(aspect, results_table_path)	Generate a GO enrichment ontology graph based on an enrichment results table.
kegg_pathway_graph(pathway_id, marked_genes)	Generate a KEGG Pathway graph.
upset_plot(objs[, set_colors, title, ...])	Generate an UpSet plot of 2 or more sets, FeatureSets or attributes from the Attribute Reference Table.
venn_diagram(objs[, title, ...])	Generate a Venn diagram of 2 to 3 sets, FeatureSets or attributes from the Attribute Reference Table.