Files in ubioinformat/TraRe
Transcriptional Rewiring
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS
R/cliques_generatecliques.R
R/compute_KL.R
R/html_from_graph.R
R/linker_html_summary.R
R/linker_html_summary_functions.R
R/linker_runlinker.R
R/linker_runlinkernet.R
R/linker_runphaseone.R
R/linker_runphasetwo.R
R/plot_functions.R
R/preprocessing.R
R/rewiring_create_module_summary.R
R/rewiring_gene_level.R
R/rewiring_html_summary.R
R/rewiring_html_summary_functions.R
R/rewiring_preparerewiring.R
R/rewiring_regulon_level.R
R/rewiring_runrewiring.R
R/rewiring_stats_functions.R
R/vbsr.R
R/zzz.R
README.md
inst/data-raw/gene_info.tsv
inst/extdata/VignetteFiles/1_SeObject_quickexample_vignette.rds
inst/extdata/VignetteFiles/1_TraReObj_quickexample_vignette.rds
inst/extdata/VignetteFiles/1_expression_quickexample_vignette.txt
inst/extdata/VignetteFiles/1_geneinfo_example_vignette.txt
inst/extdata/VignetteFiles/1_linkeroutput_quickexample_vignette.rds
inst/extdata/VignetteFiles/1_phenotype_rewiring_quickexample_vignette.txt
inst/extdata/VignetteFiles/1_preprew_quickexample_vignette.rds
inst/extdata/VignetteFiles/1_refinedsumm.rds
inst/extdata/VignetteFiles/2_TraReObj_rewiring_example.rds
inst/extdata/VignetteFiles/2_expression_rewiring_example.txt
inst/extdata/VignetteFiles/2_linkeroutput_rewiring_example.rds
inst/extdata/VignetteFiles/2_phenotype_rewiring_example.txt
inst/extdata/VignetteFiles/2_preprew_rewiring_example.rds
inst/extdata/VignetteFiles/3_TraReObj_rewiring_example_pheno.rds
inst/extdata/VignetteFiles/3_linkeroutput_50boots_example.rds
inst/extdata/VignetteFiles/3_rewired_modules_50boots.txt
inst/extdata/VignetteFiles/3_rewired_modules_50boots_fs_0.05.txt
inst/extdata/VignetteFiles/3_table_rewired_tfs.tsv
inst/extdata/VignetteFiles/4_graph_netrun_vignette.rds
inst/extdata/VignetteFiles/Html.png
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/clusters.rds
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/glossary.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/htmls/data_VBSR_1_mod_rewiring_scores.html
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/htmls/data_VBSR_1_sigmod_overlap.html
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/imgs/mod_sim.VBSR.1.dendro.pdf
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/imgs/mod_sim.VBSR.1.heatm.pdf
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/index.html
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/logfile.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/sorttable.js
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.1/htmls/data_VBSR_raw_edgesumm.html
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.1/htmls/data_VBSR_raw_nodesumm.html
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.1/index.html
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.1/txts/data_VBSR_raw_edgesumm.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.1/txts/data_VBSR_raw_nodesumm.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.2/glossary.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.2/htmls/data_VBSR_raw_edgesumm.html
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.2/htmls/data_VBSR_raw_nodesumm.html
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.2/htmls/data_VBSR_refined_edgesumm.html
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.2/htmls/data_VBSR_refined_nodesumm.html
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.2/htmls/refined_edges_table.html
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.2/imgs/igraphs.raw.full_graph.pdf
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.2/imgs/igraphs.refined.graphs.pdf
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.2/index.html
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.2/rawsumm.rds
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.2/refinedsumm.rds
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.2/sorttable.js
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.2/txts/data_VBSR_raw_edgesumm.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.2/txts/data_VBSR_raw_nodesumm.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.2/txts/data_VBSR_refined_edgesumm.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.2/txts/data_VBSR_refined_nodesumm.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.2/txts/refined_supermodule_edges.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.2/txts/refined_supermodule_summary.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.3/glossary.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.3/htmls/data_VBSR_raw_edgesumm.html
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.3/htmls/data_VBSR_raw_nodesumm.html
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.3/htmls/data_VBSR_refined_edgesumm.html
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.3/htmls/data_VBSR_refined_nodesumm.html
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.3/htmls/refined_edges_table.html
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.3/imgs/igraphs.raw.full_graph.pdf
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.3/imgs/igraphs.refined.graphs.pdf
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.3/index.html
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.3/rawsumm.rds
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.3/refinedsumm.rds
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.3/sorttable.js
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.3/txts/data_VBSR_raw_edgesumm.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.3/txts/data_VBSR_raw_nodesumm.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.3/txts/data_VBSR_refined_edgesumm.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.3/txts/data_VBSR_refined_nodesumm.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.3/txts/refined_supermodule_edges.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.3/txts/refined_supermodule_summary.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.4/glossary.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.4/htmls/data_VBSR_raw_edgesumm.html
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.4/htmls/data_VBSR_raw_nodesumm.html
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.4/htmls/data_VBSR_refined_edgesumm.html
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.4/htmls/data_VBSR_refined_nodesumm.html
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.4/htmls/refined_edges_table.html
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.4/imgs/igraphs.raw.full_graph.pdf
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.4/imgs/igraphs.refined.graphs.pdf
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.4/index.html
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.4/rawsumm.rds
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.4/refinedsumm.rds
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.4/sorttable.js
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.4/txts/data_VBSR_raw_edgesumm.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.4/txts/data_VBSR_raw_nodesumm.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.4/txts/data_VBSR_refined_edgesumm.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.4/txts/data_VBSR_refined_nodesumm.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.4/txts/refined_supermodule_edges.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/supermodule1.VBSR.4/txts/refined_supermodule_summary.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/txts/data_VBSR_1_mod_rewiring_scores.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/txts/data_VBSR_1_sigmod_overlap.txt
inst/extdata/VignetteFiles/Vignette_Rewiring_0.05/supermod_rewiring/txts/sigmodules_VBSR_1.txt
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/clusters.rds
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/glossary.txt
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/htmls/data_VBSR_1_mod_rewiring_scores.html
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/htmls/data_VBSR_1_sigmod_overlap.html
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/imgs/mod_sim.VBSR.1.dendro.pdf
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/imgs/mod_sim.VBSR.1.heatm.pdf
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/index.html
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/logfile.txt
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/sorttable.js
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.1/glossary.txt
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.1/htmls/data_VBSR_raw_edgesumm.html
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.1/htmls/data_VBSR_raw_nodesumm.html
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.1/htmls/data_VBSR_refined_edgesumm.html
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.1/htmls/data_VBSR_refined_nodesumm.html
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.1/htmls/refined_edges_table.html
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.1/imgs/igraphs.raw.full_graph.pdf
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.1/imgs/igraphs.refined.graphs.pdf
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.1/index.html
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.1/rawsumm.rds
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.1/refinedsumm.rds
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.1/sorttable.js
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.1/txts/data_VBSR_raw_edgesumm.txt
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.1/txts/data_VBSR_raw_nodesumm.txt
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.1/txts/data_VBSR_refined_edgesumm.txt
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.1/txts/data_VBSR_refined_nodesumm.txt
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.1/txts/refined_supermodule_edges.txt
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.1/txts/refined_supermodule_summary.txt
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.2/glossary.txt
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.2/htmls/data_VBSR_raw_edgesumm.html
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.2/htmls/data_VBSR_raw_nodesumm.html
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.2/htmls/data_VBSR_refined_edgesumm.html
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.2/htmls/data_VBSR_refined_nodesumm.html
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.2/htmls/refined_edges_table.html
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.2/imgs/igraphs.raw.full_graph.pdf
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.2/imgs/igraphs.refined.graphs.pdf
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.2/index.html
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.2/rawsumm.rds
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.2/refinedsumm.rds
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.2/sorttable.js
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.2/txts/data_VBSR_raw_edgesumm.txt
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.2/txts/data_VBSR_raw_nodesumm.txt
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.2/txts/data_VBSR_refined_edgesumm.txt
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.2/txts/data_VBSR_refined_nodesumm.txt
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.2/txts/refined_supermodule_edges.txt
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/supermodule1.VBSR.2/txts/refined_supermodule_summary.txt
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/txts/data_VBSR_1_mod_rewiring_scores.txt
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/txts/data_VBSR_1_sigmod_overlap.txt
inst/extdata/VignetteFiles/Vignette_quickexample_0.05/supermod_rewiring/txts/sigmodules_VBSR_1.txt
inst/extdata/VignetteFiles/igraphs.raw.full_graph.png
inst/extdata/VignetteFiles/igraphs.refined.graphs.png
inst/extdata/VignetteFiles/mod_sim.VBSR.1.dendro.png
inst/extdata/VignetteFiles/mod_sim.VBSR.1.heatm.png
inst/script/gene_info.R
inst/unitTests/cliquesgeneration_tests.R
inst/unitTests/excel_generation_tests.R
inst/unitTests/plot_tests.R
inst/unitTests/rewiring_tests.R
inst/unitTests/runlinker_testindex.R
inst/unitTests/runlinker_testmatrix.R
inst/unitTests/runlinkernet_testindex.R
inst/unitTests/runlinkernet_testmatrix.R
man/LINKER_run.Rd
man/LINKER_runPhase1.Rd
man/LINKER_runPhase2.Rd
man/NET_run.Rd
man/TraRe.Rd
man/createModuleSummary.Rd
man/create_html_summary.Rd
man/generatecliques.Rd
man/html_from_graph.Rd
man/plot_igraph.Rd
man/preparerewiring.Rd
man/rewiring_gene_level.Rd
man/rewiring_regulon_level.Rd
man/rewiring_test.Rd
man/runrewiring.Rd
man/trare_preprocessing.Rd
src/Makevars.win
src/RegisterDynamicSymbol.c
src/RegisterDynamicSymbol.o
src/TraRe.dll
src/vbsr.c
src/vbsr.h
src/vbsr.o
tests/runTests.R
vignettes/.gitignore
vignettes/TraRe.Rmd
vignettes/TraRe_files/MathJax.js.descarga
vignettes/Trare.png
