Files in IOBR/IOBR
Immune Oncology Biological Research
.Rbuildignore
.gitignore
DESCRIPTION
IOBR.Rproj
LICENSE
NAMESPACE
R/BinomialModel.R
R/CIBERSORT.R
R/EPIC_helper.R
R/IPS_calculation.R
R/IPS_helper.R
R/LR_cal.R
R/PrognosticModel.R
R/anno_eset.R
R/assimilate_data.R
R/batch_cor.R
R/batch_kruskal.R
R/batch_pcc.R
R/batch_sig_surv_plot.R
R/batch_surv.R
R/batch_wilcoxon.R
R/best_cutoff.R
R/best_cutoff2.R
R/calculate_sig_score.R
R/cell_bar_plot.R
R/check_eset.R
R/combine_pd_eset.R
R/count2tpm.R
R/creat_folder.R
R/deconvo_tme.R
R/design_mytheme.R
R/enrichment_barplot.R
R/eset_distribution.R
R/estimate_helper.R
R/extract_sc_data.R
R/feature_manipulation.R
R/feature_selection.R
R/find_markers_in_bulk.R
R/find_mutations.R
R/find_outlier_samples.R
R/find_variable_genes2.R
R/format_msigdb.R
R/format_signatures.R
R/generateRef.R
R/generateRef_DEseq2.R
R/generateRef_limma.R
R/generateRef_rnaseq.R
R/generateRef_seurat.R
R/getHRandCIfromCoxph.R
R/get_cols.R
R/get_cor.R
R/get_cor_matrix.R
R/get_sig_sc.R
R/high_var_fea.R
R/iobr_cor_plot.R
R/iobr_deconvo_pieline.R
R/iobr_deg.R
R/iobr_pca.R
R/lasso_select.R
R/log2eset.R
R/make_mut_matrix.R
R/mcpcounter.R
R/merge_duplicate.R
R/merge_eset.R
R/mouse2human_eset.R
R/output_sig.R
R/palettes.R
R/percent_bar.R
R/quantiseq.R
R/quantiseq_helper.R
R/rbind_iobr.R
R/remove_batcheffect.R
R/remove_duplicate_genes.R
R/remove_names.R
R/roc_time.R
R/scale_matrix.R
R/select_method.R
R/sigScore.R
R/sig_box.R
R/sig_box_batch.R
R/sig_forest.R
R/sig_gsea.R
R/sig_heatmap.R
R/sig_pheatmap.R
R/sig_roc.R
R/sig_surv_plot.R
R/subgroup_survival.R
R/surv_group.R
R/tcga_rna_pres.R
R/timer.R
R/tme_cluster.R
R/transform_data.R
R/xCell.R
R/zzz.R
README.Rmd
README.md
data/BRef.rda
data/PurityDataAffy.rda
data/SI_geneset.rda
data/TRef.rda
data/anno_gc_vm32.rda
data/anno_grch38.rda
data/anno_hug133plus2.rda
data/anno_illumina.rda
data/anno_rnaseq.rda
data/cancer_type_genes.rda
data/cellmarkers.rda
data/common_genes.rda
data/deg.rda
data/eset_blca.rda
data/eset_gse62254.rda
data/eset_stad.rda
data/eset_tme_stad.rda
data/go_bp.rda
data/go_cc.rda
data/go_mf.rda
data/hallmark.rda
data/immuneCuratedData.rda
data/imvigor210_eset.rda
data/imvigor210_pdata.rda
data/imvigor210_sig.rda
data/ips_gene_set.rda
data/kegg.rda
data/length_ensembl.rda
data/lm22.rda
data/mRNA_cell_default.rda
data/mcp_genes.rda
data/mcp_probesets.rda
data/melanoma_data.rda
data/msig_immune.rda
data/msig_sc.rda
data/mus_human_gene_symbol.rda
data/onco_sig.rda
data/palette1.rda
data/palette2.rda
data/palette3.rda
data/palette4.rda
data/panel_for_gene.rda
data/panel_for_signature.rda
data/patterns_to_na.rda
data/pdata_GSE63557.rda
data/pdata_acrg.rda
data/pdata_sig_tme.rda
data/pdata_sig_tme_binary.rda
data/pdata_stad.rda
data/pdata_tme_binary.rda
data/quantiseq_data.rda
data/reactome.rda
data/sig_excel.rda
data/sig_group.rda
data/sig_stad.rda
data/signature_collection.rda
data/signature_collection_citation.rda
data/signature_metabolism.rda
data/signature_sc.rda
data/signature_tme.rda
data/signature_tumor.rda
data/stad_group.rda
data/subgroup_data.rda
data/tcga_stad_pdata.rda
data/tcga_stad_sig.rda
data/tcga_stad_var.rda
data/xCell.data.rda
man/BinomialAUC.Rd
man/BinomialModel.Rd
man/CIBERSORT.Rd
man/CalculatePref.Rd
man/CalculateTimeROC.Rd
man/Construct_con.Rd
man/ConvertRownameToLoci.Rd
man/CoreAlg.Rd
man/DrawQQPlot.Rd
man/EPIC.Rd
man/Enet.Rd
man/GetFractions.Abbas.Rd
man/GetOutlierGenes.Rd
man/IPS_calculation.Rd
man/LR_cal.Rd
man/ParseInputExpression.Rd
man/PlotAUC.Rd
man/PlotTimeROC.Rd
man/ProcessingData.Rd
man/PrognosticAUC.Rd
man/PrognosticModel.Rd
man/PrognosticResult.Rd
man/RegressionResult.Rd
man/RemoveBatchEffect.Rd
man/SplitTrainTest.Rd
man/TimerINFO.Rd
man/Top_probe.Rd
man/anno_eset.Rd
man/assimilate_data.Rd
man/batch_cor.Rd
man/batch_kruskal.Rd
man/batch_pcc.Rd
man/batch_sig_surv_plot.Rd
man/batch_surv.Rd
man/batch_wilcoxon.Rd
man/best_cutoff.Rd
man/best_cutoff2.Rd
man/break_month.Rd
man/calculate_sig_score.Rd
man/calculate_sig_score_integration.Rd
man/calculate_sig_score_pca.Rd
man/calculate_sig_score_ssgsea.Rd
man/calculate_sig_score_zscore.Rd
man/cell_bar_plot.Rd
man/check_cancer_types.Rd
man/check_eset.Rd
man/combine_pd_eset.Rd
man/count2tpm.Rd
man/creat_folder.Rd
man/deconvo_cibersort.Rd
man/deconvo_epic.Rd
man/deconvo_estimate.Rd
man/deconvo_ips.Rd
man/deconvo_mcpcounter.Rd
man/deconvo_quantiseq.Rd
man/deconvo_ref.Rd
man/deconvo_timer.Rd
man/deconvo_tme.Rd
man/deconvo_xcell.Rd
man/deconvolute_quantiseq.default.Rd
man/deconvolute_timer.default.Rd
man/design_mytheme.Rd
man/doPerm.Rd
man/enrichment_barplot.Rd
man/eset_distribution.Rd
man/estimateScore.Rd
man/exact_pvalue.Rd
man/extract_sc_data.Rd
man/feature_manipulation.Rd
man/feature_select.Rd
man/figures/IOBR-Package.png
man/figures/IOBR-Workflow.png
man/filterCommonGenes.Rd
man/find_markers_in_bulk.Rd
man/find_mutations.Rd
man/find_outlier_samples.Rd
man/find_variable_genes.Rd
man/format_msigdb.Rd
man/format_signatures.Rd
man/generateRef.Rd
man/generateRef_DEseq2.Rd
man/generateRef_limma.Rd
man/generateRef_rnaseq.Rd
man/generateRef_seurat.Rd
man/getHRandCIfromCoxph.Rd
man/get_cols.Rd
man/get_cor.Rd
man/get_cor_matrix.Rd
man/get_sig_sc.Rd
man/high_var_fea.Rd
man/iobr_cor_plot.Rd
man/iobr_deconvo_pieline.Rd
man/iobr_deg.Rd
man/iobr_pca.Rd
man/ipsmap.Rd
man/lasso_select.Rd
man/limma.dif.Rd
man/log2eset.Rd
man/make_mut_matrix.Rd
man/mapbw.Rd
man/mapcolors.Rd
man/merge_duplicate.Rd
man/merge_duplicates.Rd
man/merge_eset.Rd
man/microenvironmentScores.Rd
man/mouse2human_eset.Rd
man/outputGCT.Rd
man/output_sig.Rd
man/palettes.Rd
man/percent_bar_plot.Rd
man/pie_chart.Rd
man/plotPurity.Rd
man/quantiseq_helper.Rd
man/rawEnrichmentAnalysis.Rd
man/rbind_iobr.Rd
man/remove_batcheffect.Rd
man/remove_duplicate_genes.Rd
man/remove_names.Rd
man/roc_time.Rd
man/scaleCounts.Rd
man/scale_matrix.Rd
man/select_method.Rd
man/sigScore.Rd
man/sig_box.Rd
man/sig_box_batch.Rd
man/sig_forest.Rd
man/sig_gsea.Rd
man/sig_heatmap.Rd
man/sig_pheatmap.Rd
man/sig_roc.Rd
man/sig_surv_plot.Rd
man/signature_score_calculation_methods.Rd
man/spillOver.Rd
man/subgroup_survival.Rd
man/surv_group.Rd
man/tcga_rna_preps.Rd
man/timer_available_cancers.Rd
man/tme_cluster.Rd
man/tme_deconvolution_methods.Rd
man/transformScores.Rd
man/transform_data.Rd
man/xCellAnalysis.Rd
man/xCellSignifcanceBetaDist.Rd
man/xCellSignifcanceRandomMatrix.Rd
