├── 1.Figure1 ├── 1.Model Construction.R ├── 2.Boxplot and ROC Curve.R └── ICI cohort gene pairs.qs ├── 2.Figure2 ├── 1.ROC curve analysis and multivariate regression in the Mariathasan cohort.R ├── 2.ROC curve analysis and multivariate regression in the Braun cohort.R ├── 3.ROC curve analysis and multivariate regression in the OAK cohort.R ├── 4.ROC curve analysis and multivariate regression in the Riaz cohort.R ├── 5.Shiny Web tool.R ├── OAK.Response-clinical.csv ├── RCC-Braun_2020.Response-clinical.tsv ├── Riaz.Response-clinical.csv └── all_res.rds ├── 3.Figure3 └── 1.Independent cohort validation.R ├── 4.Figure4 ├── 1.Identify genes associated with immune evasion based on CRISPR data.R ├── 2.Identify key genes associated with poor prognosis in high-risk groups using univariate Cox regression.R ├── ICI RNA-seq.qs └── crispr.Rdata ├── 5.Figure5 ├── 1.Flow cytometry data visualization.R ├── 2.Mouse tumor volume data visualization.R ├── 3.Mouse survival visualization.R └── 4.Mouse volumn visualization.R ├── DESCRIPTION ├── NAMESPACE ├── R ├── GA_train.R ├── basic_learner.R ├── basic_learner_predictor.R ├── gene_pair.R └── gene_pair_matrix.R ├── README.md ├── iMLGAM.Rproj └── man ├── GA_train.Rd ├── basic_learner.Rd ├── basic_learner_predictor.Rd ├── gene_pair.Rd └── gene_pair_matrix.Rd /1.Figure1/1.Model Construction.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Yelab1994/iMLGAM/HEAD/1.Figure1/1.Model Construction.R -------------------------------------------------------------------------------- /1.Figure1/2.Boxplot and ROC Curve.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Yelab1994/iMLGAM/HEAD/1.Figure1/2.Boxplot and ROC Curve.R -------------------------------------------------------------------------------- /1.Figure1/ICI cohort gene pairs.qs: 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-------------------------------------------------------------------------------- /2.Figure2/3.ROC curve analysis and multivariate regression in the OAK cohort.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Yelab1994/iMLGAM/HEAD/2.Figure2/3.ROC curve analysis and multivariate regression in the OAK cohort.R -------------------------------------------------------------------------------- /2.Figure2/4.ROC curve analysis and multivariate regression in the Riaz cohort.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Yelab1994/iMLGAM/HEAD/2.Figure2/4.ROC curve analysis and multivariate regression in the Riaz cohort.R -------------------------------------------------------------------------------- /2.Figure2/5.Shiny Web tool.R: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- /4.Figure4/2.Identify key genes associated with poor prognosis in high-risk groups using univariate Cox regression.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Yelab1994/iMLGAM/HEAD/4.Figure4/2.Identify key genes associated with poor prognosis in high-risk groups using univariate Cox regression.R -------------------------------------------------------------------------------- /4.Figure4/ICI RNA-seq.qs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Yelab1994/iMLGAM/HEAD/4.Figure4/ICI RNA-seq.qs -------------------------------------------------------------------------------- /4.Figure4/crispr.Rdata: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Yelab1994/iMLGAM/HEAD/4.Figure4/crispr.Rdata 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