├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── .DS_Store ├── ModifiedRandomize.R ├── addRandToSampTab.R ├── aggregate_scProfiles.R ├── avgGeneCat.R ├── barPlotGene.R ├── broadClass_predict.R ├── broadClass_train.R ├── ccn_classAssess.R ├── ccn_hmClass.R ├── compareGenePairs.R ├── conversionList.R ├── findClassyGenes.R ├── grn_construction.R ├── grn_status.R ├── grn_tfScores.R ├── grn_utils.R ├── hm_gpa_sel.R ├── makeClassifier.R ├── makeGeneCompareTab.R ├── makeSubClassifier.R ├── plotGeneComparison.R ├── plot_class_PRs.R ├── ptGetTop.R ├── query_transform.R ├── randomize.R ├── rf_classPredict.R ├── sampR_to_pattern.R ├── sdGeneCat.R ├── splitCommon.R ├── splitCommon_proportion.R ├── statTab.R ├── subClassQuery_transform.R ├── subClass_predict.R ├── subClass_train.R ├── testPattern.R ├── trans_prop.R ├── utils_convertToGeneSymbols.R ├── utils_loadObject.R ├── utils_matchSampTab.R └── weighted_down.R ├── README.md ├── cancerCellNet.Rproj ├── data └── conversionList.rda ├── docs ├── authors.html ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml └── reference │ ├── GEP_makeMean.html │ ├── ModifiedRandomize.html │ ├── addRandToSampTab.html │ ├── avgGeneCat.html │ ├── barPlotGene.html │ ├── broadClass_ensemblePredict.html │ ├── broadClass_ensembleTrain.html │ ├── broadClass_predict.html │ ├── broadClass_train.html │ ├── ccn_classAssess.html │ ├── ccn_hmClass.html │ ├── cn_HmClass.html │ ├── cn_clPerf.html │ ├── cn_correctZmat.html │ ├── cn_eval.html │ ├── compareGenePairs.html │ ├── conversionList.html │ ├── downSampleW.html │ ├── findBestPairs.html │ ├── findClassyGenes.html │ ├── find_genes_byGo.html │ ├── gene_expr_sum.html │ ├── getClassGenes.html │ ├── gnrAll.html │ ├── gnrBP.html │ ├── hm_gpa_sel.html │ ├── index.html │ ├── makeClassifier.html │ ├── makeGeneCompareTab.html │ ├── makePairTab.html │ ├── makeSubClassifier.html │ ├── pair_transform.html │ ├── plotGeneComparison.html │ ├── plot_class_PRs.html │ ├── ptGetTop.html │ ├── ptSmall.html │ ├── query_transform.html │ ├── randomize.html │ ├── rf_classPredict.html │ ├── sc_compAlpha.html │ ├── sc_compMu.html │ ├── sc_cov.html │ ├── sc_fano.html │ ├── sc_filterCells.html │ ├── sc_filterGenes.html │ ├── sc_sampR_to_pattern.html │ ├── sc_statTab.html │ ├── sc_testPattern.html │ ├── sdGeneCat.html │ ├── splitCommon.html │ ├── subClassQuery_transform.html │ ├── subClass_hmClass.html │ ├── subClass_predict.html │ ├── subClass_train.html │ ├── trans_prop.html │ ├── utils_convertLongTab.html │ ├── utils_convertToGeneSymbols.html │ ├── utils_loadObject.html │ ├── utils_matchSampTab.html │ ├── utils_myDate.html │ ├── utils_myDist.html │ ├── utils_strip_fname.html │ ├── utils_stripwhite.html │ └── weighted_down.html ├── man ├── .DS_Store ├── ModifiedRandomize.Rd ├── addRandToSampTab.Rd ├── aggregate_scProfiles.Rd ├── avgGeneCat.Rd ├── barPlotGene.Rd ├── broadClass_predict.Rd ├── broadClass_train.Rd ├── calc_normTfScore.Rd ├── calc_tfScores.Rd ├── ccn_MakeTLs.Rd ├── ccn_classAssess.Rd ├── ccn_extractRegsDF.Rd ├── ccn_extract_SN_DF.Rd ├── ccn_findSpecGenes.Rd ├── ccn_getRawGRN.Rd ├── ccn_get_targets.Rd ├── ccn_hmClass.Rd ├── ccn_makeGRN.Rd ├── ccn_make_tVals.Rd ├── ccn_make_tVals_predict.Rd ├── ccn_netScores.Rd ├── ccn_normalizeScores.Rd ├── ccn_queryGRNstatus.Rd ├── ccn_rawScore.Rd ├── ccn_reduceMatLarge.Rd ├── ccn_sampR_to_pattern.Rd ├── ccn_score.Rd ├── ccn_specGRNs.Rd ├── ccn_specGenesAll.Rd ├── ccn_testPattern.Rd ├── ccn_tfScores.Rd ├── ccn_trainNorm.Rd ├── ccn_zscoreVect.Rd ├── cn_clPerf.Rd ├── cn_eval.Rd ├── compareGenePairs.Rd ├── conversionList.Rd ├── downSampleW.Rd ├── findBestPairs.Rd ├── findClassyGenes.Rd ├── find_tfs.Rd ├── geneScores.Rd ├── getClassGenes.Rd ├── gnrAll.Rd ├── grn_corr_round.Rd ├── grn_zscores.Rd ├── hm_gpa_sel.Rd ├── ig_tabToIgraph.Rd ├── logRank.Rd ├── makeClassifier.Rd ├── makeGeneCompareTab.Rd ├── makePairTab.Rd ├── makeSubClassifier.Rd ├── mat_zscores.Rd ├── meanTraining.Rd ├── minDif.Rd ├── parallel_quickPairs.Rd ├── plotGeneComparison.Rd ├── plot_class_PRs.Rd ├── processImportance.Rd ├── ptGetTop.Rd ├── ptSmall.Rd ├── query_transform.Rd ├── randomize.Rd ├── rf_classPredict.Rd ├── sc_compAlpha.Rd ├── sc_compMu.Rd ├── sc_cov.Rd ├── sc_fano.Rd ├── sc_filterGenes.Rd ├── sc_sampR_to_pattern.Rd ├── sc_statTab.Rd ├── sc_testPattern.Rd ├── sdGeneCat.Rd ├── splitCommon.Rd ├── splitCommon_proportion.Rd ├── subClassQuery_transform.Rd ├── subClass_predict.Rd ├── subClass_train.Rd ├── trans_prop.Rd ├── utils_convertToGeneSymbols.Rd ├── utils_loadObject.Rd ├── utils_matchSampTab.Rd ├── utils_reduceMat.Rd ├── weighted_down.Rd └── zscore.Rd └── md_img ├── CCL_classification.png ├── GRN_status_CCLs.png ├── PR_curves.png ├── TF_scoreMatrix.PNG ├── broadValidation_general.png ├── classificationgene_heatmap.png ├── genepair_heatmap.png ├── generalClassificationWsplit.png ├── grn_status.png ├── new_UCEC_sub_val.png 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