# Transcriptional Rewiring

## Documentation for package ‘TraRe’ version 1.5.0

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

## Help Pages

create_html_summary | Create HTML summary
generatecliques | Cliques generation and plot displaying.
generategraph | Cliques generation and plot displaying.
html_from_graph | Html generation
LINKER_corrClust | Phase I : module generation
LINKER_EvaluateTestSet | Phase I : module generation
LINKER_extract_modules | Phase I : module generation
LINKER_init | Phase I : module generation
LINKER_LearnRegulatoryPrograms | Phase I : module generation
LINKER_ReassignGenesToClusters | Phase I : module generation
LINKER_run | GRN inference via selected model.
LINKER_runPhase1 | Phase I : module generation
LINKER_runPhase2 | Phase II : bipartitive graphs generation
NET_compute_graph_all_LASSO1se | Single gene network approaches.
NET_compute_graph_all_LASSOmin | Single gene network approaches.
NET_compute_graph_all_LM | Single gene network approaches.
NET_compute_graph_all_VBSR | Single gene network approaches.
NET_run | Single gene network approaches.
orderGraphWeights | Plotting functions for Gene Regulatory Network.
plotcliques | Cliques generation and plot displaying.
plot_igraph | Plotting functions for Gene Regulatory Network.
preparedata | Cliques generation and plot displaying.
preparerewiring | Prepare rewiring data for running the method.
return_layout | Plotting functions for Gene Regulatory Network.
return_layout_phenotype | Plotting functions for Gene Regulatory Network.
rewiring_test | Generate stats for the rewiring method.
rewiring_test_pair_detail | Generate stats for the rewiring method.
runrewiring | GRN Modules Rewiring Method.
selectmethod | Cliques generation and plot displaying.