# Visualize all edges within a KEGG pathway and overlay LINCS data

## Documentation for package ‘KEGGlincs’ version 1.20.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

KEGGlincs-package | KEGGlincs: an R package designed to explore the edges in KEGG pathways
add_edge_data | Annotate KEGG edge mappings with user data
cyto_vis | Send graph to Cytoscape via CyREST
edge_mapping_info | Prepare edges for mapping
expand_KEGG_edges | Get detailed KEGG mapping information for each relation [edge] documented in KEGG
expand_KEGG_mappings | Get detailed KEGG mapping information for each map entity
generate_mappings | The 'boilerplate' for this package's desired graph style
get_fisher_info | Perform Fisher's Exact test for edges in pathway
get_graph_object | Generate graph object from nodes and edges
get_KGML | Download and parse KGML file
keggerize_edges | Add in edges to map documented in other pathways
KEGGlincs | KEGGlincs: an R package designed to explore the edges in KEGG pathways
KEGG_lincs | Combines all other package functions for one-step pathway visualization
KL_compare | Combines all other package functions for one-step cell line comparison
mapAttributes | cyREST utility functions
node_mapping_info | Prepare nodes for mapping
overlap_info | Get overlap information for pairs of gene knock-outs from LINCS data
path_genes_by_cell_type | See how many pathway gene knock-outs are available from data
refine_mappings | Refine pathway by cell type
tidy_edge | Tidy up pathway by combining edges inside of edge_mapping_info
toCytoscape | cyREST utility functions