dkainer/RWRtoolkit
Random Walk with Restart Tool Suite

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Random Walk with Restart Tool Suite

.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md .github/pull_request_template.md
.gitignore
DESCRIPTION
LICENSE.md
NAMESPACE
R/RWR_CV.R R/RWR_LOE.R R/RWR_make_multiplex.R R/RWR_netstats.R R/RWR_network_aggregation.R R/RWR_shortestpaths.R R/utils.R README.Rmd README.md
inst/example_data/flist.tsv
inst/example_data/geneset1.tsv
inst/example_data/geneset2.tsv
inst/example_data/layers/automated_textmining.tsv
inst/example_data/layers/coexpression.tsv
inst/example_data/layers/combined_score.tsv
inst/example_data/layers/database_annotated.tsv
inst/example_data/layers/experimentally_determined_interaction.tsv
inst/example_data/layers/gene_fusion.tsv
inst/example_data/layers/homology.tsv
inst/example_data/layers/neighborhood_on_chromosome.tsv
inst/example_data/layers/phylogenetic_cooccurrence.tsv
inst/example_data/netstat/combined_score-random-gold.tsv
inst/example_data/netstat/combined_score-random-test.tsv
inst/example_data/string_interactions.Rdata
inst/scripts/run_cv.R inst/scripts/run_loe.R inst/scripts/run_make_multiplex.R inst/scripts/run_netstats.R inst/scripts/run_network_aggregation.R inst/scripts/run_shortestpaths.R man/RWR_CV.Rd man/RWR_LOE.Rd man/RWR_ShortestPaths.Rd man/RWR_make_multiplex.Rd man/RWR_netstats.Rd man/RWR_network_aggregation.Rd man/basic_statistics_multiplex.Rd man/calculate_basic_statistics.Rd man/calculate_tau.Rd man/compare_networks.Rd man/exclusivity.Rd man/extract_highest_scoring_path.Rd man/get_name.Rd man/jaccard_score_edges.Rd man/load_flist.Rd man/load_network.Rd man/make_dummy_multiplex.Rd man/merged_with_all_edges.Rd man/merged_with_edgecounts.Rd man/overlap_many_pairwise.Rd man/overlap_many_vs_reference.Rd man/overlap_pair.Rd man/overlap_score.Rd
man/styles/Cytoscape_Comprehensive_Athal_Style.xml
tests/testFlists/abc_flist.txt
tests/testFlists/testFlist.txt
tests/testFlists/testFlist_badPaths.txt
tests/testFlists/testFlist_heterogeneous.txt
tests/testFlists/testFlist_heterogeneous_badGrouping.txt
tests/testFlists/test_flist_2cols.tsv
tests/testFlists/test_flist_5cols.tsv
tests/testGenesets/testGeneset1.csv
tests/testGenesets/testGeneset1.tsv
tests/testGenesets/testGeneset1_weighted.tsv
tests/testGenesets/testGeneset2.tsv
tests/testGenesets/testGeneset3.tsv
tests/testGenesets/testGeneset_Bad_oneColumn.tsv
tests/testGenesets/test_abc_genesetA.tsv
tests/testGenesets/test_abc_genesetAC.tsv
tests/testGenesets/test_abc_genesetC.tsv
tests/testGenesets/test_abc_genesetG.tsv
tests/testGenesets/test_circular_geneset_1.tsv
tests/testGenesets/test_circular_geneset_2.tsv
tests/testGenesets/test_geneset_5_cols.tsv
tests/testMultiplex/abc_multiplex.Rdata
tests/testMultiplex/circular_network.Rdata
tests/testMultiplex/network.Rdata
tests/testMultiplex/unitTestMultiplex.Rdata
tests/testNetworks/abc_layer1.tsv
tests/testNetworks/abc_layer1_extra_columns.tsv
tests/testNetworks/abc_layer1_noweight.tsv
tests/testNetworks/abc_layer2.tsv
tests/testNetworks/abc_layer3.tsv
tests/testNetworks/graphNonNormalHeaders.txt
tests/testNetworks/i1.txt
tests/testNetworks/m1.txt
tests/testNetworks/m1_noHeader.txt
tests/testNetworks/m1_noweights.txt
tests/testNetworks/m1_tabDelim.txt
tests/testNetworks/m2.txt
tests/testNetworks/m2_noHeader.txt
tests/testNetworks/m2_tabDelim.txt
tests/testNetworks/n1.txt
tests/testNetworks/network_m1m2.rdata
tests/testSTRINGDB/README.md
tests/testSTRINGDB/flist.tsv
tests/testSTRINGDB/geneset.tsv
tests/testSTRINGDB/geneset1.tsv
tests/testSTRINGDB/geneset2.tsv
tests/testSTRINGDB/genesetLong.tsv
tests/testSTRINGDB/layers/automated_textmining.tsv
tests/testSTRINGDB/layers/coexpression.tsv
tests/testSTRINGDB/layers/combined_score-random-gold.tsv
tests/testSTRINGDB/layers/combined_score-random-test.tsv
tests/testSTRINGDB/layers/combined_score.tsv
tests/testSTRINGDB/layers/database_annotated.tsv
tests/testSTRINGDB/layers/experimentally_determined_interaction.tsv
tests/testSTRINGDB/layers/gene_fusion.tsv
tests/testSTRINGDB/layers/homology.tsv
tests/testSTRINGDB/layers/neighborhood_on_chromosome.tsv
tests/testSTRINGDB/layers/phylogenetic_cooccurrence.tsv
tests/testSTRINGDB/netstat/combined_score-random-gold.tsv
tests/testSTRINGDB/netstat/combined_score-random-test.tsv
tests/testSTRINGDB/netstat/refgenes.tsv
tests/testSTRINGDB/string_interactions.Rdata
tests/testSTRINGDB/string_interactions.tsv
tests/testthat/testRWR_CV.R tests/testthat/testRWR_LOE.R tests/testthat/testRWR_inst_scripts.R tests/testthat/testRWR_make_multiplex.R tests/testthat/testRWR_netstats.R tests/testthat/testRWR_network_aggregation.R tests/testthat/testRWR_shortestpaths.R tests/testthat/testUtils.R
vignettes/.gitignore
vignettes/rwr-cv-example.Rmd vignettes/rwr-cv-network-validation.Rmd vignettes/rwr-loe-gwas-example.Rmd vignettes/rwr-loe-knockout-example.Rmd vignettes/rwr-makemultiplex-example.Rmd vignettes/rwr-netstats-example.Rmd vignettes/rwr-network-aggrigation-example.Rmd vignettes/rwr-shortestpaths-example.Rmd
dkainer/RWRtoolkit documentation built on Jan. 11, 2025, 3:26 a.m.

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