TraRe-package	TraRe
createModuleSummary	createModuleSummary
create_html_summary	create_html_summary
generatecliques	generatecliques
generategraph	generatecliques
gen_heatmap	runrewiring
heatmapplot	plot_igraph
html_from_graph	html_from_graph
LINKER_corrClust	LINKER_runPhase1
LINKER_EvaluateTestSet	LINKER_runPhase1
LINKER_extract_modules	LINKER_runPhase1
LINKER_init	LINKER_runPhase1
LINKER_LearnRegulatoryPrograms	LINKER_runPhase1
LINKER_ReassignGenesToClusters	LINKER_runPhase1
LINKER_run	LINKER_run
LINKER_runPhase1	LINKER_runPhase1
LINKER_runPhase2	LINKER_runPhase2
NET_compute_graph_all_LASSO1se	NET_run
NET_compute_graph_all_LASSOmin	NET_run
NET_compute_graph_all_LM	NET_run
NET_compute_graph_all_VBSR	NET_run
NET_run	NET_run
orderGraphWeights	plot_igraph
plotcliques	generatecliques
plot_correlation_row	plot_igraph
plot_expression_row	plot_igraph
plot_gene_pair_scatter	plot_igraph
plot_gene_pair_scatter_by_class	plot_igraph
plot_igraph	plot_igraph
preparedata	generatecliques
preparerewiring	preparerewiring
rawsummary	runrewiring
return_layout	plot_igraph
return_layout_phenotype	plot_igraph
rewiring_gene_level	rewiring_gene_level
rewiring_regulon_level	rewiring_regulon_level
rewiring_test	rewiring_test
rewiring_test_pair_detail	rewiring_test
runrewiring	runrewiring
selectmethod	generatecliques
TraRe	TraRe
