├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── Data.R ├── Dataloader.R ├── Feature_Engineering.R ├── LogitBoost.R ├── Score_biomk.R ├── TIMER_SE.R ├── biomk_utilities.R ├── browse_BE.R ├── browse_biomk.R ├── build_CellType_Ref.R ├── build_Model.R ├── cell_name_filter.R ├── cell_name_standardization.R ├── compare_biomk.R ├── compare_roc.R ├── count2tpm.R ├── dataPreprocess_SE.R ├── dataProcess_SE.R ├── data_standardization.R ├── deconv_TME.R ├── diff_TME.R ├── diff_biomk.R ├── draw_bar.R ├── fraction_pie.R ├── integrate_analysis.R ├── remove_BE.R ├── response_prediction.R ├── roc_biomk.R ├── score_biomk_SE.R ├── surv_biomk.R ├── test_Model.R └── utilities.R ├── README.md ├── data ├── .DS_Store ├── ABIS_RNA_seq.rda ├── Average_mean_Sigs.rda ├── Dataset_info.rda ├── GBM_PRJNA482620.rda ├── LM22.rda ├── MEL_GSE78220.rda ├── MEL_GSE93157.rda ├── NSCLC_GSE135222.rda ├── Stem.Sig.rda ├── Stem.Sig.version.rda ├── Weighted_mean_Sigs.rda ├── ZScore_PCA_Sigs.rda ├── bayesmodel.rda ├── ipt.rda └── nonsqNSCLC_GSE93157.rda ├── dev.Rproj ├── inst └── extdata │ ├── Common_genes.rds │ ├── IPSG.rds │ ├── Signature_genesets.rds │ ├── TIMER.Immune.rds │ ├── TIMER.Markers.rds │ ├── gene_length.rds │ ├── genes.txt │ ├── pbmc.rds │ └── probesets.txt ├── man ├── ABIS_RNA_seq.Rd ├── Average_mean_Sigs.Rd ├── CIBERSORT.Rd ├── Ciber.Rd ├── Common_genes.Rd ├── ConsensusTME.Rd ├── Core.Rd ├── CoreAlg.Rd ├── DEA_Response.Rd ├── DEA_Treatment.Rd ├── Dataloader.Rd ├── Dataset_info.Rd ├── ESTIMATE.Rd ├── GBM_PRJNA482620.Rd ├── Gini.Rd ├── Gini_gene.Rd ├── IPS.Rd ├── IRS_grading.Rd ├── Immunotherapy_Response_Batch.Rd ├── LM22.Rd ├── LogitBoost.Rd ├── MCPCounter.Rd ├── MCPcounter.estimate.Rd ├── MEL_GSE78220.Rd ├── MEL_GSE93157.Rd ├── NSCLC_GSE135222.Rd ├── PT_filter.Rd ├── Signature_genesets.Rd ├── Stem.Sig.Rd ├── Stem.Sig.version.Rd ├── TIMER.Rd ├── TIMER_SE.Rd ├── Weighted_mean_Sigs.Rd ├── ZScore_PCA_Sigs.Rd ├── ZScore_PCA_signature.Rd ├── abis.Rd ├── average_mean_signature.Rd ├── bayesmodel.Rd ├── bind_meta.Rd ├── bind_mtr.Rd ├── browse_BE.Rd ├── browse_biomk.Rd ├── build_Adaboost_model.Rd ├── build_CC_model.Rd ├── build_CellType_Ref.Rd ├── build_Logistics_model.Rd ├── build_Logitboost_model.Rd ├── build_Model-build_Model.matrix-build_Model.default.Rd ├── build_NB_model.Rd ├── build_RF_model.Rd ├── build_SURV_Model.Rd ├── build_SVM_model.Rd ├── cell_name_filter.Rd ├── cell_name_standardization.Rd ├── compare_biomk.Rd ├── compare_roc.Rd ├── count2tpm.Rd ├── dataPreprocess.Rd ├── dataPreprocess_SE.Rd ├── dataProcess.Rd ├── dataProcess_SE.Rd ├── data_standardization.Rd ├── deconv_TME.Rd ├── diff_TME.Rd ├── diff_biomk.Rd ├── diff_gene.Rd ├── doPerm.Rd ├── draw_bar.Rd ├── epic.Rd ├── extract_label.Rd ├── extract_mtr.Rd ├── fpkm2tpm.Rd ├── fraction_pie.Rd ├── generate_result.Rd ├── integrate_analysis.Rd ├── ipsmap.Rd ├── ipt.Rd ├── is.NA_vec.Rd ├── load_from_ExperimentHub.Rd ├── load_from_WebServer.Rd ├── log2SE.Rd ├── mapbw.Rd ├── mapcolors.Rd ├── matrix_cox.Rd ├── matrix_t.test.Rd ├── max_min_normalization.Rd ├── merge_SE.Rd ├── nonsqNSCLC_GSE93157.Rd ├── plt_Preprocess.Rd ├── plt_roc.Rd ├── plt_style.Rd ├── pred_response.Rd ├── quanTIseq.Rd ├── remove_BE.Rd ├── response_filter.Rd ├── response_prediction.Rd ├── response_standardize.Rd ├── rmBE.Rd ├── roc_biomk.Rd ├── score_biomk.Rd ├── score_biomk_SE.Rd ├── surv_biomk.Rd ├── surv_styling.Rd ├── survival_Score.Rd ├── tGE8_grading.Rd ├── test_Adaboost_model.Rd ├── test_CC_model.Rd ├── test_Logistics_model.Rd ├── test_Logitboost_model.Rd ├── test_Model.Rd ├── test_Model.default.Rd ├── test_Model.matrix.Rd ├── test_NB_model.Rd ├── test_RF_model.Rd ├── test_SURV_Model.Rd ├── test_SVM_model.Rd ├── tigeR_Combat.Rd ├── tigeR_Combat_seq.Rd ├── tigeR_DWD.Rd ├── to1.Rd ├── turNA.Rd ├── weight_mean_signature.Rd ├── xCell.Rd └── zero2na.Rd └── vignettes ├── .gitignore └── tigeR.Rmd /.Rbuildignore: 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