GitHub - sara-sousi/CANCER.GENOMICS: Integrated tools for the discovery of driver features in cancers

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 1,038 Commits
BACKUP.SCRIPTS		BACKUP.SCRIPTS
BLOG		BLOG
PIPELINE		PIPELINE
RESULTS		RESULTS
011215.BAYES.REF.ALT.TYPE.FEAT.REP.TIME.jpeg		011215.BAYES.REF.ALT.TYPE.FEAT.REP.TIME.jpeg
052815.DS.1.R		052815.DS.1.R
060315.F.R		060315.F.R
080615.F.R		080615.F.R
080615.R		080615.R
083015.R		083015.R
090715.F.R		090715.F.R
090715.R		090715.R
092115.RUN.ICGC.1.R		092115.RUN.ICGC.1.R
1000G.TRIMER.PHASTCON.ASSIGN.sh		1000G.TRIMER.PHASTCON.ASSIGN.sh
165.py		165.py
CHEN.REPLICATION.GENE.ASSIGN.sh		CHEN.REPLICATION.GENE.ASSIGN.sh
DEEP.ANALYSIS.1.R		DEEP.ANALYSIS.1.R
DEEP.ITER.1.R		DEEP.ITER.1.R
DEEP.ITER.2.R		DEEP.ITER.2.R
DEEP_TUTORIAL.ipynb		DEEP_TUTORIAL.ipynb
DESPRAT.REPLICATION.GENE.ASSIGN.sh		DESPRAT.REPLICATION.GENE.ASSIGN.sh
Drug_feature_functions.R		Drug_feature_functions.R
Function.053015.DS.2.R		Function.053015.DS.2.R
Function.053015.DS.3.R		Function.053015.DS.3.R
Function.053015.DS.4.R		Function.053015.DS.4.R
Function.053015.DS.5.R		Function.053015.DS.5.R
Function.072715.SCRIPT.R		Function.072715.SCRIPT.R
Function.072815.SCRIPT.R		Function.072815.SCRIPT.R
Function.072915.SCRIPT.R		Function.072915.SCRIPT.R
Function.080415.SCRIPT.R		Function.080415.SCRIPT.R
Function.081415.SCRIPT.R		Function.081415.SCRIPT.R
Function.BAYESIAN.MAIN.R		Function.BAYESIAN.MAIN.R
Function.BIOGRID.PROCESSING.R		Function.BIOGRID.PROCESSING.R
Function.Background.SAMPLE.WILCOX.R		Function.Background.SAMPLE.WILCOX.R
Function.DEEP.LEARNING.1.R		Function.DEEP.LEARNING.1.R
Function.DIFF.EXP.MR.R		Function.DIFF.EXP.MR.R
Function.EQTL.MAF.EXP.WITHIN.R		Function.EQTL.MAF.EXP.WITHIN.R
Function.EXP.CNV.LINKAGE.NC.R		Function.EXP.CNV.LINKAGE.NC.R
Function.EXP.MATRIX.MI.R		Function.EXP.MATRIX.MI.R
Function.EXP.MUT.LINKAGE.NC.R		Function.EXP.MUT.LINKAGE.NC.R
Function.EXP.MUT.LINKAGE.R		Function.EXP.MUT.LINKAGE.R
Function.EXP.MUT.POS.LINKAGE.NC.R		Function.EXP.MUT.POS.LINKAGE.NC.R
Function.EXP.MUT.POS.LINKAGE.R		Function.EXP.MUT.POS.LINKAGE.R
Function.Exp.Normal.Matrix.R		Function.Exp.Normal.Matrix.R
Function.Gene.Met.Enrich.R		Function.Gene.Met.Enrich.R
Function.HOO.ROC.OPTIM.R		Function.HOO.ROC.OPTIM.R
Function.MAF.BMR.R		Function.MAF.BMR.R
Function.MAF.Decay.Fit.R		Function.MAF.Decay.Fit.R
Function.MAF.Predict.R		Function.MAF.Predict.R
Function.MET.DEEP.R		Function.MET.DEEP.R
Function.MET.HUB.INTER.NULL.R		Function.MET.HUB.INTER.NULL.R
Function.MET.PERSONALIZED.P.VAL.R		Function.MET.PERSONALIZED.P.VAL.R
Function.METABOLIC.COR.BACKGROUND.R		Function.METABOLIC.COR.BACKGROUND.R
Function.METABOLIC.COR.R		Function.METABOLIC.COR.R
Function.MI.CANCER.ANALYSIS.R		Function.MI.CANCER.ANALYSIS.R
Function.MUT.EXP.SOLVE.R		Function.MUT.EXP.SOLVE.R
Function.Parse.Exp.Matrices.R		Function.Parse.Exp.Matrices.R
Function.RNASEQ.DESEQ.R		Function.RNASEQ.DESEQ.R
Function.TEST.SIZE.WICOX.R		Function.TEST.SIZE.WICOX.R
Function.u.R		Function.u.R
Functions.R		Functions.R
Gee_Bor_Dex.R		Gee_Bor_Dex.R
Gee_Cis.R		Gee_Cis.R
Gee_Doc.R		Gee_Doc.R
Gee_Erl.R		Gee_Erl.R
PROPOSAL.R		PROPOSAL.R
README		README
TCGA.TRIMER.ASSIGN.sh		TCGA.TRIMER.ASSIGN.sh
TODO.R		TODO.R
TRAIN.SCRIPT.R		TRAIN.SCRIPT.R
ccle_pca_predict.R		ccle_pca_predict.R
ccle_pca_predict.py		ccle_pca_predict.py
ccle_pca_predict.sh		ccle_pca_predict.sh
ccle_pca_predict_preprocess.R		ccle_pca_predict_preprocess.R
cgp.cor.AUC_class_pred.py		cgp.cor.AUC_class_pred.py
cgp.cor.AUC_class_pred.sh		cgp.cor.AUC_class_pred.sh
cgp.cor.AUC_class_pred_plot.R		cgp.cor.AUC_class_pred_plot.R
cgp_1.sh		cgp_1.sh
cgp_all_feat_pca_mlp.2.cmd		cgp_all_feat_pca_mlp.2.cmd
cgp_all_feat_pca_mlp.2.py		cgp_all_feat_pca_mlp.2.py
cgp_all_feat_pca_mlp.cmd		cgp_all_feat_pca_mlp.cmd
cgp_all_feat_pca_mlp.py		cgp_all_feat_pca_mlp.py
cgp_all_feat_pca_train.py		cgp_all_feat_pca_train.py
cgp_all_feat_pca_train_tcga.py		cgp_all_feat_pca_train_tcga.py
cgp_all_feat_prep.R		cgp_all_feat_prep.R
cgp_baseline.R		cgp_baseline.R
cgp_baseline_mlp.R		cgp_baseline_mlp.R
cgp_baseline_mlp.cmd		cgp_baseline_mlp.cmd
cgp_baseline_mlp.py		cgp_baseline_mlp.py
cgp_baseline_mlp.sh		cgp_baseline_mlp.sh
cgp_baseline_mlp_plots.R		cgp_baseline_mlp_plots.R
cgp_baseline_mlp_predict.py		cgp_baseline_mlp_predict.py
cgp_encode.py		cgp_encode.py
cgp_exp_drugs_mlp.py		cgp_exp_drugs_mlp.py
cgp_exp_drugsbatch_mlp.py		cgp_exp_drugsbatch_mlp.py
cgp_exp_drugsbatch_mlpcv.py		cgp_exp_drugsbatch_mlpcv.py
cgp_exp_tcga_model.R		cgp_exp_tcga_model.R
cgp_mixed_class.cmd		cgp_mixed_class.cmd
cgp_mixed_class.py		cgp_mixed_class.py
cgp_mixed_class.sh		cgp_mixed_class.sh