Files in hyginn/ekplektoR
Network Analysis for Cell- and Systems Biology
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/aaa.R
R/annotate.R
R/combineSNV_CNA.R
R/data.R
R/diffuseV3.R
R/externalData.R
R/fastMap.R
R/fastMapGenerate.R
R/fastMapSanity.R
R/fastMapUpdate.R
R/findSub.R
R/gGtools.R
R/importFilterHypermutators.R
R/importM.COSMIC.R
R/importNet.STRING.R
R/importSNV.TCGA.R
R/isHGNCsymbol.R
R/logTools.R
R/multiply.R
R/nonEqSim.R
R/utils.R
R/zzz.R
README
inst/extdata/HGNCsymbols.RDS
inst/extdata/STRINGprototype.txt
inst/extdata/devCNA.txt
inst/extdata/devPPI.txt
inst/extdata/devSNV.maf
inst/extdata/fastMapCosmic.rds
inst/extdata/fastMapENSP.rds
inst/extdata/fastMapUniProt.rds
inst/hotnet2-example/README-hotnet2.md
inst/hotnet2-example/README.md
inst/hotnet2-example/configs/consensus.config
inst/hotnet2-example/configs/delta.config
inst/hotnet2-example/configs/heat.config
inst/hotnet2-example/configs/influence_matrix.config
inst/hotnet2-example/configs/influence_matrix2.config
inst/hotnet2-example/configs/run.config
inst/hotnet2-example/configs/significance.config
inst/hotnet2-example/configs/simple.config
inst/hotnet2-example/configs/simple2.config
inst/hotnet2-example/configs/website.config
inst/hotnet2-example/example.cna
inst/hotnet2-example/example.dname
inst/hotnet2-example/example.dscore
inst/hotnet2-example/example.heat
inst/hotnet2-example/example.snv
inst/hotnet2-example/example_edgelist.txt
inst/hotnet2-example/example_edgelist2.txt
inst/hotnet2-example/example_gene_index.txt
inst/hotnet2-example/influence_matrices/example_edge_list
inst/hotnet2-example/influence_matrices/example_index_genes
inst/hotnet2-example/influence_matrices/example_ppr_0.6.h5
inst/hotnet2-example/influence_matrices/permuted/1/example_edge_list
inst/hotnet2-example/influence_matrices/permuted/1/example_index_genes
inst/hotnet2-example/influence_matrices/permuted/1/example_ppr_0.6.h5
inst/hotnet2-example/influence_matrices/permuted/10/example_edge_list
inst/hotnet2-example/influence_matrices/permuted/10/example_index_genes
inst/hotnet2-example/influence_matrices/permuted/10/example_ppr_0.6.h5
inst/hotnet2-example/influence_matrices/permuted/2/example_edge_list
inst/hotnet2-example/influence_matrices/permuted/2/example_index_genes
inst/hotnet2-example/influence_matrices/permuted/2/example_ppr_0.6.h5
inst/hotnet2-example/influence_matrices/permuted/3/example_edge_list
inst/hotnet2-example/influence_matrices/permuted/3/example_index_genes
inst/hotnet2-example/influence_matrices/permuted/3/example_ppr_0.6.h5
inst/hotnet2-example/influence_matrices/permuted/4/example_edge_list
inst/hotnet2-example/influence_matrices/permuted/4/example_index_genes
inst/hotnet2-example/influence_matrices/permuted/4/example_ppr_0.6.h5
inst/hotnet2-example/influence_matrices/permuted/5/example_edge_list
inst/hotnet2-example/influence_matrices/permuted/5/example_index_genes
inst/hotnet2-example/influence_matrices/permuted/5/example_ppr_0.6.h5
inst/hotnet2-example/influence_matrices/permuted/6/example_edge_list
inst/hotnet2-example/influence_matrices/permuted/6/example_index_genes
inst/hotnet2-example/influence_matrices/permuted/6/example_ppr_0.6.h5
inst/hotnet2-example/influence_matrices/permuted/7/example_edge_list
inst/hotnet2-example/influence_matrices/permuted/7/example_index_genes
inst/hotnet2-example/influence_matrices/permuted/7/example_ppr_0.6.h5
inst/hotnet2-example/influence_matrices/permuted/8/example_edge_list
inst/hotnet2-example/influence_matrices/permuted/8/example_index_genes
inst/hotnet2-example/influence_matrices/permuted/8/example_ppr_0.6.h5
inst/hotnet2-example/influence_matrices/permuted/9/example_edge_list
inst/hotnet2-example/influence_matrices/permuted/9/example_index_genes
inst/hotnet2-example/influence_matrices/permuted/9/example_ppr_0.6.h5
inst/hotnet2-example/influence_matrices2/example2_edge_list
inst/hotnet2-example/influence_matrices2/example2_index_genes
inst/hotnet2-example/influence_matrices2/example2_ppr_0.6.h5
inst/hotnet2-example/influence_matrices2/permuted/1/example2_edge_list
inst/hotnet2-example/influence_matrices2/permuted/1/example2_index_genes
inst/hotnet2-example/influence_matrices2/permuted/1/example2_ppr_0.6.h5
inst/hotnet2-example/influence_matrices2/permuted/10/example2_edge_list
inst/hotnet2-example/influence_matrices2/permuted/10/example2_index_genes
inst/hotnet2-example/influence_matrices2/permuted/10/example2_ppr_0.6.h5
inst/hotnet2-example/influence_matrices2/permuted/2/example2_edge_list
inst/hotnet2-example/influence_matrices2/permuted/2/example2_index_genes
inst/hotnet2-example/influence_matrices2/permuted/2/example2_ppr_0.6.h5
inst/hotnet2-example/influence_matrices2/permuted/3/example2_edge_list
inst/hotnet2-example/influence_matrices2/permuted/3/example2_index_genes
inst/hotnet2-example/influence_matrices2/permuted/3/example2_ppr_0.6.h5
inst/hotnet2-example/influence_matrices2/permuted/4/example2_edge_list
inst/hotnet2-example/influence_matrices2/permuted/4/example2_index_genes
inst/hotnet2-example/influence_matrices2/permuted/4/example2_ppr_0.6.h5
inst/hotnet2-example/influence_matrices2/permuted/5/example2_edge_list
inst/hotnet2-example/influence_matrices2/permuted/5/example2_index_genes
inst/hotnet2-example/influence_matrices2/permuted/5/example2_ppr_0.6.h5
inst/hotnet2-example/influence_matrices2/permuted/6/example2_edge_list
inst/hotnet2-example/influence_matrices2/permuted/6/example2_index_genes
inst/hotnet2-example/influence_matrices2/permuted/6/example2_ppr_0.6.h5
inst/hotnet2-example/influence_matrices2/permuted/7/example2_edge_list
inst/hotnet2-example/influence_matrices2/permuted/7/example2_index_genes
inst/hotnet2-example/influence_matrices2/permuted/7/example2_ppr_0.6.h5
inst/hotnet2-example/influence_matrices2/permuted/8/example2_edge_list
inst/hotnet2-example/influence_matrices2/permuted/8/example2_index_genes
inst/hotnet2-example/influence_matrices2/permuted/8/example2_ppr_0.6.h5
inst/hotnet2-example/influence_matrices2/permuted/9/example2_edge_list
inst/hotnet2-example/influence_matrices2/permuted/9/example2_index_genes
inst/hotnet2-example/influence_matrices2/permuted/9/example2_ppr_0.6.h5
inst/hotnet2-example/output/simple/delta_0.0260452711285/components.txt
inst/hotnet2-example/output/simple/delta_0.0260452711285/heat.json
inst/hotnet2-example/output/simple/delta_0.0260452711285/results.json
inst/hotnet2-example/output/simple/delta_0.0260452711285/significance.txt
inst/hotnet2-example/output/simple/delta_0.0298581562389/components.txt
inst/hotnet2-example/output/simple/delta_0.0298581562389/heat.json
inst/hotnet2-example/output/simple/delta_0.0298581562389/results.json
inst/hotnet2-example/output/simple/delta_0.0298581562389/significance.txt
inst/hotnet2-example/output/simple/delta_0.0463290678437/components.txt
inst/hotnet2-example/output/simple/delta_0.0463290678437/heat.json
inst/hotnet2-example/output/simple/delta_0.0463290678437/results.json
inst/hotnet2-example/output/simple/delta_0.0463290678437/significance.txt
inst/hotnet2-example/output/simple/delta_0.0900611409683/components.txt
inst/hotnet2-example/output/simple/delta_0.0900611409683/heat.json
inst/hotnet2-example/output/simple/delta_0.0900611409683/results.json
inst/hotnet2-example/output/simple/delta_0.0900611409683/significance.txt
inst/hotnet2-example/output/simple/viz/index.html
inst/hotnet2-example/output/simple/viz/subnetworks.json
inst/hotnet2-example/output/simple2/delta_0.0401620285399/components.txt
inst/hotnet2-example/output/simple2/delta_0.0401620285399/heat.json
inst/hotnet2-example/output/simple2/delta_0.0401620285399/results.json
inst/hotnet2-example/output/simple2/delta_0.0401620285399/significance.txt
inst/hotnet2-example/output/simple2/delta_0.0465311609617/components.txt
inst/hotnet2-example/output/simple2/delta_0.0465311609617/heat.json
inst/hotnet2-example/output/simple2/delta_0.0465311609617/results.json
inst/hotnet2-example/output/simple2/delta_0.0465311609617/significance.txt
inst/hotnet2-example/output/simple2/delta_0.0470540865706/components.txt
inst/hotnet2-example/output/simple2/delta_0.0470540865706/heat.json
inst/hotnet2-example/output/simple2/delta_0.0470540865706/results.json
inst/hotnet2-example/output/simple2/delta_0.0470540865706/significance.txt
inst/hotnet2-example/output/simple2/delta_0.090225313719/components.txt
inst/hotnet2-example/output/simple2/delta_0.090225313719/heat.json
inst/hotnet2-example/output/simple2/delta_0.090225313719/results.json
inst/hotnet2-example/output/simple2/delta_0.090225313719/significance.txt
inst/hotnet2-example/output/simple2/viz/index.html
inst/hotnet2-example/output/simple2/viz/subnetworks.json
inst/hotnet2-example/tested_genes.txt
inst/hotnet2-example/tested_samples.txt
inst/scripts/buildGeneDataList.R
inst/scripts/functionTemplate.R
inst/scripts/generateHGNCtable.R
man/NOSUCH.maf.Rd
man/annotateGraph.Rd
man/combineSNV_CNA.Rd
man/devCNA.txt.Rd
man/devPPI.txt.Rd
man/devSNV.maf.Rd
man/diffuseV3.Rd
man/fastMap.Rd
man/fastMapGenerate.Rd
man/fastMapSanity.Rd
man/fastMapUpdate.Rd
man/findUUID.Rd
man/findsub.Rd
man/getProvenance.Rd
man/getUUID.Rd
man/importFilterHypermutators.Rd
man/importM.COSMIC.Rd
man/importNet.STRING.Rd
man/isHGNCsymbol.Rd
man/logEvent.Rd
man/logFileName.Rd
man/logMessage.Rd
man/multiply.Rd
rete.Rproj
tests/testthat.R
tests/testthat/dataSTRING.txt
tests/testthat/devCNA.rds
tests/testthat/devSNV.rds
tests/testthat/hgnc_subset.txt
tests/testthat/hgnc_with_conflict.txt
tests/testthat/importSNV_input_corr_file.maf
tests/testthat/importSNV_input_test_file.maf
tests/testthat/importSNV_output_test_file
tests/testthat/testAnnotate.R
tests/testthat/testCombine.R
tests/testthat/testCosmicCNA.tsv
tests/testthat/testCosmicCNAEmpty.tsv
tests/testthat/testCosmicCNA_columns.tsv
tests/testthat/testCosmicCNA_gene_name_has_NA.tsv
tests/testthat/testCosmicCNA_gene_name_has_N_A.tsv
tests/testthat/testCosmicCNA_gene_name_has_dash.tsv
tests/testthat/testCosmicCNA_sample_string.tsv
tests/testthat/testCosmicCNA_totalCN_negative.tsv
tests/testthat/testCosmicCNA_totalCN_string.tsv
tests/testthat/testCosmicCNA_tumour_string.tsv
tests/testthat/testDiffuseV3.R
tests/testthat/testDummy.R
tests/testthat/testFastMap.R
tests/testthat/testFilter.R
tests/testthat/testFindSub.R
tests/testthat/testImport.R
tests/testthat/testImportM.COSMIC.R
tests/testthat/testImportSNV.TCGA.R
tests/testthat/testIsHGNCsymbol.R
tests/testthat/testLogTools.R
tests/testthat/testMultiply.R
tests/testthat/testUtils.R
