KEGGlincs: Visualize all edges within a KEGG pathway and overlay LINCS data [option]

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See what is going on 'under the hood' of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.

Author
Shana White
Date of publication
None
Maintainer
Shana White <vandersm@mail.uc.edu>
License
GPL-3
Version
1.0.0

View on Bioconductor

Man pages

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...
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
KEGGlincs
KEGGlincs: an R package designed to explore the edges in KEGG...
KEGG_lincs
Combines all other package functions for one-step pathway...
node_mapping_info
Prepare nodes for mapping
overlap_info
Get overlap information for pairs of gene knock-outs from...
path_genes_by_cell_type
See how many pathway gene knock-outs are available from data
refine_mappings
Refine pathway by cell type
toCytoscape
cyREST utility functions

Files in this package

KEGGlincs/DESCRIPTION
KEGGlincs/NAMESPACE
KEGGlincs/NEWS
KEGGlincs/R
KEGGlincs/R/KEGG_lincs.R
KEGGlincs/R/KEGGlincs.R
KEGGlincs/R/add_edge_data.R
KEGGlincs/R/cyto_vis.R
KEGGlincs/R/edge_mapping_info.R
KEGGlincs/R/expand_KEGG_edges.R
KEGGlincs/R/expand_KEGG_mappings.R
KEGGlincs/R/from_cyREST.R
KEGGlincs/R/generate_mappings.R
KEGGlincs/R/get_KGML.R
KEGGlincs/R/get_fisher_info.R
KEGGlincs/R/get_graph_object.R
KEGGlincs/R/node_mapping_info.R
KEGGlincs/R/overlap_info.R
KEGGlincs/R/path_genes_by_cell_type.R
KEGGlincs/R/refine_mappings.R
KEGGlincs/build
KEGGlincs/build/vignette.rds
KEGGlincs/inst
KEGGlincs/inst/doc
KEGGlincs/inst/doc/Cytoscape_formatting.R
KEGGlincs/inst/doc/Cytoscape_formatting.Rmd
KEGGlincs/inst/doc/Cytoscape_formatting.html
KEGGlincs/inst/doc/Example-workflow.R
KEGGlincs/inst/doc/Example-workflow.Rmd
KEGGlincs/inst/doc/Example-workflow.html
KEGGlincs/man
KEGGlincs/man/KEGG_lincs.Rd
KEGGlincs/man/KEGGlincs.Rd
KEGGlincs/man/add_edge_data.Rd
KEGGlincs/man/cyto_vis.Rd
KEGGlincs/man/edge_mapping_info.Rd
KEGGlincs/man/expand_KEGG_edges.Rd
KEGGlincs/man/expand_KEGG_mappings.Rd
KEGGlincs/man/generate_mappings.Rd
KEGGlincs/man/get_KGML.Rd
KEGGlincs/man/get_fisher_info.Rd
KEGGlincs/man/get_graph_object.Rd
KEGGlincs/man/node_mapping_info.Rd
KEGGlincs/man/overlap_info.Rd
KEGGlincs/man/path_genes_by_cell_type.Rd
KEGGlincs/man/refine_mappings.Rd
KEGGlincs/man/toCytoscape.Rd
KEGGlincs/vignettes
KEGGlincs/vignettes/Cytoscape_formatting.Rmd
KEGGlincs/vignettes/Example-workflow.Rmd
KEGGlincs/vignettes/image_files
KEGGlincs/vignettes/image_files/KEGGlincs_overview.jpeg
KEGGlincs/vignettes/image_files/color_1.svg
KEGGlincs/vignettes/image_files/color_2.svg
KEGGlincs/vignettes/image_files/find_box.jpg
KEGGlincs/vignettes/image_files/fit_content.jpg
KEGGlincs/vignettes/image_files/foxo_ID_conversion.jpeg
KEGGlincs/vignettes/image_files/foxo_no_IDconversion.jpeg
KEGGlincs/vignettes/image_files/hsa04068.png
KEGGlincs/vignettes/image_files/p53_HA1E.jpeg
KEGGlincs/vignettes/image_files/p53_HA1E_vignette.jpeg
KEGGlincs/vignettes/image_files/p53_PC3.jpeg
KEGGlincs/vignettes/image_files/p53_PC3_vignette.jpeg
KEGGlincs/vignettes/image_files/p53_coverage_graph.png
KEGGlincs/vignettes/image_files/p53_default.jpeg
KEGGlincs/vignettes/image_files/random_KO_info.jpeg
KEGGlincs/vignettes/image_files/select_style_tab.jpg