Transcriptional Rewiring

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Documentation for package ‘TraRe’ version 1.6.3

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

Help Pages

createModuleSummary	Create module summary
create_html_summary	Create HTML summary
generatecliques	Cliques generation and plot displaying.
generategraph	Cliques generation and plot displaying.
gen_heatmap	GRN Modules Rewiring Method.
heatmapplot	Plotting functions for Gene Regulatory Network.
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_correlation_row	Plotting functions for Gene Regulatory Network.
plot_expression_row	Plotting functions for Gene Regulatory Network.
plot_gene_pair_scatter	Plotting functions for Gene Regulatory Network.
plot_gene_pair_scatter_by_class	Plotting functions for Gene Regulatory Network.
plot_igraph	Plotting functions for Gene Regulatory Network.
preparedata	Cliques generation and plot displaying.
preparerewiring	Prepare rewiring data for running the method.
rawsummary	GRN Modules Rewiring Method.
return_layout	Plotting functions for Gene Regulatory Network.
return_layout_phenotype	Plotting functions for Gene Regulatory Network.
rewiring_gene_level	Perform the rewiring at the gene level
rewiring_regulon_level	Perform the rewiring at the regulon level
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.