torchcell.graph

Gene graphs for S. cerevisiae. SCerevisiaeGraph assembles the Gene Ontology DAG, SGD physical and genetic interaction networks, regulatory networks and STRING networks over the genes of a genome; GeneGraph and GeneMultiGraph wrap the resulting NetworkX graphs as named, typed containers that the cell datasets consume. The filter_* functions prune the GO DAG (by annotation date, by contained genes, by evidence code, and by redundant terms).

Classes

SCerevisiaeGraph	Lazy builder of SGD, STRING, TFLink, and GO gene graphs for S.
GeneGraph	Graph with genes as nodes, wrapping an nx.Graph.
GeneMultiGraph	Collection of GeneGraph objects stored in a SortedDict.

Functions

filter_go_IGI	Return a new graph with gene annotations derived from IGI experiments removed.
filter_by_date	Return a new graph with nodes having annotations after cutoff_date removed.
filter_by_contained_genes	Return a new graph with nodes removed that contain fewer than n genes.
filter_redundant_terms	Return a new graph with redundant GO terms removed.
build_gene_multigraph	Build a GeneMultiGraph from the requested graph names.