Package: IOBR 2.2.3.9000

Shixiang Wang

IOBR: Immune Oncology Biological Research

Provides six modules for tumor microenvironment (TME) analysis based on multi-omics data. These modules cover data preprocessing, TME estimation, TME infiltrating patterns, cellular interactions, genome and TME interaction, and visualization for TME relevant features, as well as modelling based on key features. It integrates multiple microenvironmental analysis algorithms and signature estimation methods, simplifying the analysis and downstream visualization of the TME. In addition to providing a quick and easy way to construct gene signatures from single-cell RNA-seq data, it also provides a way to construct a reference matrix for TME deconvolution from single-cell RNA-seq data. The analysis pipeline and feature visualization are user-friendly and provide a comprehensive description of the complex TME, offering insights into tumour-immune interactions (Zeng D, et al. (2024) <doi:10.1016/j.crmeth.2024.100910>. Fang Y, et al. (2025) <doi:10.1002/mdr2.70001>).

Authors:Dongqiang Zeng [aut], Yiran Fang [aut], Shixiang Wang [aut, cre], Qingcong Luo [aut], Hongqian Qian [aut]

IOBR_2.2.3.9000.tar.gz
IOBR_2.2.3.9000.zip(r-4.7)IOBR_2.2.3.9000.zip(r-4.6)IOBR_2.2.3.9000.zip(r-4.5)
IOBR_2.2.3.9000.tgz(r-4.6-any)IOBR_2.2.3.9000.tgz(r-4.5-any)
IOBR_2.2.3.9000.tar.gz(r-4.7-any)IOBR_2.2.3.9000.tar.gz(r-4.6-any)
IOBR_2.2.3.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
IOBR/json (API)
NEWS

# Install 'IOBR' in R:
install.packages('IOBR', repos = c('https://iobr.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/iobr/iobr/issues

Pkgdown/docs site:https://iobr.github.io

Datasets:

On CRAN:

Conda:

geneexpressiondifferentialexpressionimmunooncologytranscriptomicsclusteringsurvivalvisualizationimmuno-oncologysignature-collectiontumor-microenvironment

9.82 score 290 stars 216 scripts 1.9k downloads 148 exports 165 dependencies

Last updated from:dc49d902d7. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK474
source / vignettesOK560
linux-release-x86_64OK543
macos-release-arm64OK760
macos-oldrel-arm64OK875
windows-develOK943
windows-releaseOK915
windows-oldrelOK511
wasm-releaseOK414

Exports:add_iobr_mirroradd_riskscoreanno_esetassimilate_databatch_corbatch_kruskalbatch_pccbatch_sig_surv_plotbatch_survbatch_wilcoxonbest_cutoffbest_cutoff2BinomialAUCBinomialModelcalculate_break_monthcalculate_sig_scorecalculate_sig_score_integrationcalculate_sig_score_pcacalculate_sig_score_ssgseacalculate_sig_score_zscoreCalculatePrefCalculateTimeROCcell_bar_plotcheck_cancer_typescheck_esetCIBERSORTclear_iobr_cachecombine_pd_esetConstruct_conConvertRownameToLociCoreAlgcount2tpmcreat_folderdeconvo_cibersortdeconvo_epicdeconvo_estimatedeconvo_ipsdeconvo_mcpcounterdeconvo_quantiseqdeconvo_refdeconvo_timerdeconvo_tmedeconvo_xcelldeconvolute_quantiseq.defaultdeconvolute_timer.defaultdesign_mythemedoPermdownload_iobr_dataDrawQQPlotEnetenrichment_barplotEPICeset_distributionestimateScoreexact_pvalueextract_sc_datafeature_manipulationfeature_selectfilterCommonGenesfind_markers_in_bulkfind_mutationsfind_outlier_samplesfind_variable_genesformat_msigdbformat_signaturesgenerateRefgenerateRef_DEseq2generateRef_limmagenerateRef_rnaseqgenerateRef_seuratget_colsget_corget_cor_matrixget_iobr_cache_dirget_sig_scGetFractions.AbbasgetHRandCIfromCoxphGetOutlierGeneshigh_var_feaiobr_cor_plotiobr_deconvo_pipelineiobr_degiobr_pcaIPS_calculationipsmaplasso_selectlimma.diflist_github_datasetslist_iobr_mirrorsload_datalog2esetLR_calmake_mut_matrixmapbwmapcolorsMCPcounter.estimatemerge_duplicatemerge_esetmouse2human_esetoutput_sigoutputGCTpalettesparallel_dopermParseInputExpressionpatterns_to_napercent_bar_plotpie_chartPlotAUCplotPurityPlotTimeROCProcessingDataPrognosticAUCPrognosticModelPrognosticResultrandom_strata_cellsrbind_iobrRegressionResultremove_batcheffectremove_duplicate_genesremove_namesRemoveBatchEffectreset_iobr_cache_dirreset_iobr_mirrorsroc_timescale_matrixselect_methodset_iobr_cache_dirsig_boxsig_box_batchsig_forestsig_gseasig_heatmapsig_pheatmapsig_rocsig_surv_plotsignature_score_calculation_methodssigScoreSplitTrainTestsubgroup_survivalsurv_grouptcga_rna_prepstest_for_infiltrationtimer_available_cancerstimer_infotme_clustertme_deconvolution_methodsTop_probetransform_data

Dependencies:abindannotateAnnotationDbiaskpassassortheadbackportsbeachmatBHBiobaseBiocFileCacheBiocGenericsbiocmakeBiocParallelBiocSingularBiostringsbitbit64blobbootbroomcachemcarcarDataclicodetoolscolorspacecommonmarkcorrplotcowplotcpp11crayoncurlDBIdbplyrDelayedArrayDelayedMatrixStatsDerivdir.expirydoBydplyrexactRankTestsfarverfastmapfilelockforeachforecastformatRFormulafracdifffutile.loggerfutile.optionsgenericsGenomicRangesggplot2ggpubrggrepelggsciggsignifggtextglmnetgluegraphgridExtragridtextGSEABaseGSVAgtableh5mreadHDF5Arrayhttrhttr2IRangesirlbaisobanditeratorsjpegjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelitedownlme4lmtestmagickmagrittrmarkdownMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmaxstatmemoisememusemgcvmicrobenchmarkmimeminqamodelrmvtnormnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigpngpolynompurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrhdf5rhdf5filtersRhdf5librjsonrlangRSQLiterstatixrsvdS4ArraysS4VectorsS7ScaledMatrixscalesSeqinfoshapeSingleCellExperimentsnowSparseArraySparseMsparseMatrixStatsSpatialExperimentstringistringrSummarizedExperimentsurvivalsurvminersystibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithrxfunXMLxml2xtableXVectorzoo

Multidimensional Decoding Tumor Microenvironment for Immuno-Oncology Research

Dongqiang Zeng, Yiran Fang

Rendered fromIOBR-user-manual.Rmdusingknitr::rmarkdownon Jun 17 2026.

Last update: 2026-04-03
Started: 2024-08-14

Readme and manuals

Help Manual

Help pageTopics
Add Custom Download Mirroradd_iobr_mirror
Add Risk Score to Datasetadd_riskscore
Annotate Gene Expression Matrix and Remove Duplicated Genesanno_eset
Harmonize Two Data Frames by Column Structureassimilate_data
Batch Correlation Analysisbatch_cor
Batch Kruskal-Wallis Testbatch_kruskal
Batch Calculation of Partial Correlation Coefficientsbatch_pcc
Batch Signature Survival Plotbatch_sig_surv_plot
Batch Survival Analysisbatch_surv
Batch Wilcoxon Rank-Sum Test Between Two Groupsbatch_wilcoxon
Extract Best Cutoff and Add Binary Variable to Data Framebest_cutoff
Extract Best Cutoff and Add Binary Variable to Data Framebest_cutoff2
Calculate AUC for Binomial ModelBinomialAUC
Binomial Model ConstructionBinomialModel
Break Time Into Blockscalculate_break_month
Calculate Signature Scorecalculate_sig_score
Calculate Signature Score Using Integration Methodcalculate_sig_score_integration
Calculate Signature Score Using PCA Methodcalculate_sig_score_pca
Calculate Signature Score Using ssGSEA Methodcalculate_sig_score_ssgsea
Calculate Signature Score Using Z-Score Methodcalculate_sig_score_zscore
Calculate Performance MetricsCalculatePref
Calculate Time-Dependent ROC CurveCalculateTimeROC
Visualize Cell Fractions as Stacked Bar Chartcell_bar_plot
Process Batch Table and Validate Cancer Typescheck_cancer_types
Check Integrity and Outliers of Expression Setcheck_eset
CIBERSORT Deconvolution AlgorithmCIBERSORT
Clear IOBR Data Cacheclear_iobr_cache
Combine Phenotype Data and Expression Setcombine_pd_eset
Construct Contrast MatrixConstruct_con
Convert Rowname To LociConvertRownameToLoci
Core Algorithm for CIBERSORT DeconvolutionCoreAlg
Convert Read Counts to Transcripts Per Million (TPM)count2tpm
Create Nested Output Folderscreat_folder
Deconvolve Using CIBERSORTdeconvo_cibersort
Deconvolve Immune Microenvironment Using EPICdeconvo_epic
Calculate ESTIMATE Scoresdeconvo_estimate
Calculate Immunophenoscore (IPS)deconvo_ips
Deconvolve Immune Microenvironment Using MCP-Counterdeconvo_mcpcounter
Deconvolve Using quanTIseqdeconvo_quantiseq
Deconvolve Using Custom Referencedeconvo_ref
Deconvolve Using TIMERdeconvo_timer
Main TME Deconvolution Functiondeconvo_tme
Deconvolve Immune Microenvironment Using xCelldeconvo_xcell
Use quanTIseq to Deconvolute a Gene Expression Matrixdeconvolute_quantiseq.default
Deconvolute Tumor Microenvironment Using TIMERdeconvolute_timer.default
Design Custom Theme for ggplot2 Plotsdesign_mytheme
Permutation Test for CIBERSORTdoPerm
Download IOBR Data from GitHub with Mirror Supportdownload_iobr_data
Draw QQ Plot Comparing Cancer and Immune ExpressionDrawQQPlot
Elastic Net Model FittingEnet
Enrichment Bar Plot with Two Directionsenrichment_barplot
Estimate the proportion of immune and cancer cells.EPIC
Visualize Expression Set Distributioneset_distribution
estimateScoreestimateScore
Calculate Exact P-Value for Correlationexact_pvalue
Extract Data Frame from Seurat Objectextract_sc_data
Feature Quality Control and Filteringfeature_manipulation
Feature Selection via Correlation or Differential Expressionfeature_select
filterCommonGenesfilterCommonGenes
Identify Marker Features in Bulk Expression Datafind_markers_in_bulk
Analyze Mutations Related to Signature Scoresfind_mutations
Identify Outlier Samples in Gene Expression Datafind_outlier_samples
Identify Variable Genes in Expression Datafind_variable_genes
Format Input Signatures from MSigDBformat_msigdb
Transform Signature Data into List Formatformat_signatures
Generate Reference Signature MatrixgenerateRef
Generate Reference Signature Matrix Using DESeq2generateRef_DEseq2
Generate Reference Signature Matrix Using LimmagenerateRef_limma
Generate Reference Gene Matrix from RNA-seq DEGsgenerateRef_rnaseq
Generate Reference Matrix from Seurat ObjectgenerateRef_seurat
Set and View Color Palettesget_cols
Calculate and Visualize Correlation Between Two Variablesget_cor
Calculate and Visualize Correlation Matrix Between Two Variable Setsget_cor_matrix
Get IOBR Cache Directoryget_iobr_cache_dir
Extract Top Marker Genes from Single-Cell Differential Resultsget_sig_sc
Constrained Regression Method (Abbas et al., 2009)GetFractions.Abbas
Extract Hazard Ratio and Confidence Intervals from Cox ModelgetHRandCIfromCoxph
Get Outlier GenesGetOutlierGenes
Identify High-Variance Features from Statistical Resultshigh_var_fea
IMvigor210 Bladder Cancer Immunotherapy Cohort Dataimvigor210_pdata
Integrative Correlation Analysis Between Phenotype and Featuresiobr_cor_plot
Tumor Microenvironment (TME) Deconvolution Pipelineiobr_deconvo_pipeline
Differential Expression Analysisiobr_deg
Principal Component Analysis (PCA) Visualizationiobr_pca
Calculate Immunophenoscore (IPS)IPS_calculation
Map Score to Immunophenoscoreipsmap
Feature Selection for Predictive or Prognostic Models Using LASSO Regressionlasso_select
Differential Expression Analysis Using Limmalimma.dif
List Available GitHub Datasetslist_github_datasets
List Current Download Mirrorslist_iobr_mirrors
Load IOBR Datasetsload_data
Log2 Transformation of Gene Expression Matrixlog2eset
Calculate Ligand-Receptor Interaction ScoresLR_cal
Construct Mutation Matrices from MAF Datamake_mut_matrix
Map Score to Black and White Colormapbw
Map Score to Colormapcolors
MCP-counter Cell Population Abundance EstimationMCPcounter.estimate
Merge Data Frames with Duplicated Column Namesmerge_duplicate
Merge Expression Sets by Row Namesmerge_eset
Convert Mouse Gene Symbols to Human Gene Symbolsmouse2human_eset
NULL Model Coefficients for MCPcounternull_models
Save Signature Data to Fileoutput_sig
outputGCToutputGCT
Select Color Palettes for Visualizationpalettes
Parallel Permutation Test for CIBERSORTparallel_doperm
Parse Input Gene Expression DataParseInputExpression
Default Pattern List for Name Cleaningpatterns_to_na
Toy STAD Phenotype Datapdata_stad
Create a Percent Bar Plotpercent_bar_plot
Create Pie or Donut Chartspie_chart
Plot AUC ROC CurvesPlotAUC
plotPurityplotPurity
Plot Time-Dependent ROC CurvesPlotTimeROC
Process Data for Model ConstructionProcessingData
Calculate Time-Dependent AUC for Survival ModelsPrognosticAUC
Build Prognostic Models Using LASSO and Ridge RegressionPrognosticModel
Compute Prognostic Results for Survival ModelsPrognosticResult
Stratified Random Sampling of Cellsrandom_strata_cells
Row Bind Multiple Data Setsrbind_iobr
Regression Result ComputationRegressionResult
Removing Batch Effect from Expression Setsremove_batcheffect
Remove Duplicate Gene Symbols in Gene Expression Dataremove_duplicate_genes
Remove Patterns from Column Names or Variablesremove_names
Remove Batch Effect of Expression SetRemoveBatchEffect
Reset IOBR Cache Directory to Defaultreset_iobr_cache_dir
Reset Download Mirrors to Defaultreset_iobr_mirrors
Time-dependent ROC Curve for Survival Analysisroc_time
Scale and Manipulate a Matrixscale_matrix
Select a Signature Scoring Method Subsetselect_method
Set IOBR Cache Directoryset_iobr_cache_dir
Signature Box Plot with Statistical Comparisonssig_box
Batch Signature Box Plots for Group Comparisonssig_box_batch
Forest Plot for Survival Analysis Resultssig_forest
Grouped gene signatures for IOBR analysissig_group
Perform Gene Set Enrichment Analysis (GSEA)sig_gsea
Signature Heatmap with Optional Annotationssig_heatmap
Generate Heatmap for Signature Datasig_pheatmap
Plot ROC Curves and Compare Themsig_roc
Generate Kaplan-Meier Survival Plot for Signaturesig_surv_plot
Gene signature collection for pathway and immune analysissignature_collection
Signature Score Calculation Methodssignature_score_calculation_methods
Calculate Signature Score Using PCA, Mean, or Z-score MethodssigScore
Split Data into Training and Testing SetsSplitTrainTest
Example Clinical Data for TCGA-STAD Gastric Cancer Analysisstad_group
Example Dataset for Subgroup Survival Analysissubgroup_data
Subgroup Survival Analysis Using Cox Proportional Hazards Modelssubgroup_survival
Generate Kaplan-Meier Survival Plots for Categorical Groupssurv_group
Preprocess TCGA RNA-seq Datatcga_rna_preps
TCGA-STAD Clinical and Molecular Annotation Datatcga_stad_pdata
Test for Cell Population Infiltrationtest_for_infiltration
TIMER Available Cancer Typestimer_available_cancers
Source code for the TIMER deconvolution method.timer_info
Identification of TME Clustertme_cluster
TME Deconvolution Methodstme_deconvolution_methods
Top Probe SelectorTop_probe
Transform NA, Inf, or Zero Values in Datatransform_data