Files in pcahan1/cancerCellNet
CellNet, for cancer
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/.DS_Store
R/ModifiedRandomize.R
R/addRandToSampTab.R
R/aggregate_scProfiles.R
R/avgGeneCat.R
R/barPlotGene.R
R/broadClass_predict.R
R/broadClass_train.R
R/ccn_classAssess.R
R/ccn_hmClass.R
R/compareGenePairs.R
R/conversionList.R
R/findClassyGenes.R
R/grn_construction.R
R/grn_status.R
R/grn_tfScores.R
R/grn_utils.R
R/hm_gpa_sel.R
R/makeClassifier.R
R/makeGeneCompareTab.R
R/makeSubClassifier.R
R/plotGeneComparison.R
R/plot_class_PRs.R
R/ptGetTop.R
R/query_transform.R
R/randomize.R
R/rf_classPredict.R
R/sampR_to_pattern.R
R/sdGeneCat.R
R/splitCommon.R
R/splitCommon_proportion.R
R/statTab.R
R/subClassQuery_transform.R
R/subClass_predict.R
R/subClass_train.R
R/testPattern.R
R/trans_prop.R
R/utils_convertToGeneSymbols.R
R/utils_loadObject.R
R/utils_matchSampTab.R
R/weighted_down.R
README.md
cancerCellNet.Rproj
data/conversionList.rda
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/GEP_makeMean.html
docs/reference/ModifiedRandomize.html
docs/reference/addRandToSampTab.html
docs/reference/avgGeneCat.html
docs/reference/barPlotGene.html
docs/reference/broadClass_ensemblePredict.html
docs/reference/broadClass_ensembleTrain.html
docs/reference/broadClass_predict.html
docs/reference/broadClass_train.html
docs/reference/ccn_classAssess.html
docs/reference/ccn_hmClass.html
docs/reference/cn_HmClass.html
docs/reference/cn_clPerf.html
docs/reference/cn_correctZmat.html
docs/reference/cn_eval.html
docs/reference/compareGenePairs.html
docs/reference/conversionList.html
docs/reference/downSampleW.html
docs/reference/findBestPairs.html
docs/reference/findClassyGenes.html
docs/reference/find_genes_byGo.html
docs/reference/gene_expr_sum.html
docs/reference/getClassGenes.html
docs/reference/gnrAll.html
docs/reference/gnrBP.html
docs/reference/hm_gpa_sel.html
docs/reference/index.html
docs/reference/makeClassifier.html
docs/reference/makeGeneCompareTab.html
docs/reference/makePairTab.html
docs/reference/makeSubClassifier.html
docs/reference/pair_transform.html
docs/reference/plotGeneComparison.html
docs/reference/plot_class_PRs.html
docs/reference/ptGetTop.html
docs/reference/ptSmall.html
docs/reference/query_transform.html
docs/reference/randomize.html
docs/reference/rf_classPredict.html
docs/reference/sc_compAlpha.html
docs/reference/sc_compMu.html
docs/reference/sc_cov.html
docs/reference/sc_fano.html
docs/reference/sc_filterCells.html
docs/reference/sc_filterGenes.html
docs/reference/sc_sampR_to_pattern.html
docs/reference/sc_statTab.html
docs/reference/sc_testPattern.html
docs/reference/sdGeneCat.html
docs/reference/splitCommon.html
docs/reference/subClassQuery_transform.html
docs/reference/subClass_hmClass.html
docs/reference/subClass_predict.html
docs/reference/subClass_train.html
docs/reference/trans_prop.html
docs/reference/utils_convertLongTab.html
docs/reference/utils_convertToGeneSymbols.html
docs/reference/utils_loadObject.html
docs/reference/utils_matchSampTab.html
docs/reference/utils_myDate.html
docs/reference/utils_myDist.html
docs/reference/utils_strip_fname.html
docs/reference/utils_stripwhite.html
docs/reference/weighted_down.html
man/.DS_Store
man/ModifiedRandomize.Rd
man/addRandToSampTab.Rd
man/aggregate_scProfiles.Rd
man/avgGeneCat.Rd
man/barPlotGene.Rd
man/broadClass_predict.Rd
man/broadClass_train.Rd
man/calc_normTfScore.Rd
man/calc_tfScores.Rd
man/ccn_MakeTLs.Rd
man/ccn_classAssess.Rd
man/ccn_extractRegsDF.Rd
man/ccn_extract_SN_DF.Rd
man/ccn_findSpecGenes.Rd
man/ccn_getRawGRN.Rd
man/ccn_get_targets.Rd
man/ccn_hmClass.Rd
man/ccn_makeGRN.Rd
man/ccn_make_tVals.Rd
man/ccn_make_tVals_predict.Rd
man/ccn_netScores.Rd
man/ccn_normalizeScores.Rd
man/ccn_queryGRNstatus.Rd
man/ccn_rawScore.Rd
man/ccn_reduceMatLarge.Rd
man/ccn_sampR_to_pattern.Rd
man/ccn_score.Rd
man/ccn_specGRNs.Rd
man/ccn_specGenesAll.Rd
man/ccn_testPattern.Rd
man/ccn_tfScores.Rd
man/ccn_trainNorm.Rd
man/ccn_zscoreVect.Rd
man/cn_clPerf.Rd
man/cn_eval.Rd
man/compareGenePairs.Rd
man/conversionList.Rd
man/downSampleW.Rd
man/findBestPairs.Rd
man/findClassyGenes.Rd
man/find_tfs.Rd
man/geneScores.Rd
man/getClassGenes.Rd
man/gnrAll.Rd
man/grn_corr_round.Rd
man/grn_zscores.Rd
man/hm_gpa_sel.Rd
man/ig_tabToIgraph.Rd
man/logRank.Rd
man/makeClassifier.Rd
man/makeGeneCompareTab.Rd
man/makePairTab.Rd
man/makeSubClassifier.Rd
man/mat_zscores.Rd
man/meanTraining.Rd
man/minDif.Rd
man/parallel_quickPairs.Rd
man/plotGeneComparison.Rd
man/plot_class_PRs.Rd
man/processImportance.Rd
man/ptGetTop.Rd
man/ptSmall.Rd
man/query_transform.Rd
man/randomize.Rd
man/rf_classPredict.Rd
man/sc_compAlpha.Rd
man/sc_compMu.Rd
man/sc_cov.Rd
man/sc_fano.Rd
man/sc_filterGenes.Rd
man/sc_sampR_to_pattern.Rd
man/sc_statTab.Rd
man/sc_testPattern.Rd
man/sdGeneCat.Rd
man/splitCommon.Rd
man/splitCommon_proportion.Rd
man/subClassQuery_transform.Rd
man/subClass_predict.Rd
man/subClass_train.Rd
man/trans_prop.Rd
man/utils_convertToGeneSymbols.Rd
man/utils_loadObject.Rd
man/utils_matchSampTab.Rd
man/utils_reduceMat.Rd
man/weighted_down.Rd
man/zscore.Rd
md_img/CCL_classification.png
md_img/GRN_status_CCLs.png
md_img/PR_curves.png
md_img/TF_scoreMatrix.PNG
md_img/broadValidation_general.png
md_img/classificationgene_heatmap.png
md_img/genepair_heatmap.png
md_img/generalClassificationWsplit.png
md_img/grn_status.png
md_img/new_UCEC_sub_val.png
md_img/sc_aggregate.png
md_img/subClass_Val_PR.png
md_img/subClass_heatmap_CCLs.png
md_img/subClass_validationHeatmap.png
md_img/val_PR_UCEC.png
