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

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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("KEGGlincs")
AuthorShana White
Bioconductor views CellBiology DataRepresentation GeneExpression GraphAndNetwork KEGG Network NetworkInference Pathways ThirdPartyClient
Date of publicationNone
MaintainerShana White <vandersm@mail.uc.edu>
LicenseGPL-3
Version1.0.0

View on Bioconductor

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.