Package index • icWGCNA

Main icWGCNA Function

icwgcna(): Iterative Correcting Weighted Gene Co-expression Network Analysis

Downstream/Enrichment Functions

Functions to run on icWGCNA results

compute_panglaoDB_enrichment(): Compute Cell Type Enrichments Using panglaoDB Cell Markers

compute_MSigDB_enrichment(): Compute MSigDB Collection Enrichments for each community

compute_xCell_enrichment(): Compute Cell Type Enrichments Using xCell Cell Markers

compute_eigengene_matrix(): Compute community signatures (eigengenes)

make_network_umap(): Display UMAP of Community Membership with text overlays

display_top_genes(): Identify Top Genes and Values of Communities

find_unique_top_genes(): Identify Top Gene of Communities that are unique (only belong to one community)

map_eigengenes_on_seurat(): Map Eigengenes on a Seurat Object

Utility Functions

expression_compression(): Expression Dataset Conversion Between Two Sets of Gene IDs

eigenMapMatMult(): Faster Matrix Multiplication

RfastTOMdist(): RfastTOMdist

fastTOMwrapper(): fastTOMwrapper

pangDB_link: Current link used to connect to panglaoDB cell markers

prolif_names: Current list of proliferation genes to check