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-any)IOBR_2.2.3.9000.zip(r-4.6-any)IOBR_2.2.3.9000.zip(r-4.5-any)
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✨
DESCRIPTION |NEWS
card.svg |card.png
IOBR/json (API)

# 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:

imvigor210_pdata - IMvigor210 Bladder Cancer Immunotherapy Cohort Data
null_models - NULL Model Coefficients for MCPcounter
pdata_stad - Toy STAD Phenotype Data
sig_group - Grouped gene signatures for IOBR analysis
signature_collection - Gene signature collection for pathway and immune analysis
stad_group - Example Clinical Data for TCGA-STAD Gastric Cancer Analysis
subgroup_data - Example Dataset for Subgroup Survival Analysis
tcga_stad_pdata - TCGA-STAD Clinical and Molecular Annotation Data

On CRAN:

geneexpression differentialexpression immunooncology transcriptomics clustering survival visualization immuno-oncology signature-collection tumor-microenvironment

9.72 score 293 stars 215 scripts 1.5k downloads 148 exports 158 dependencies

Last updated from:635effe4d0. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	510
source / vignettes	OK	555
linux-release	OK	429
macos-release	OK	259
macos-oldrel	OK	282
windows-devel	OK	366
windows-release	OK	293
windows-oldrel	OK	319
wasm-release	OK	364

Exports:add_iobr_mirror add_riskscore anno_eset assimilate_data batch_cor batch_kruskal batch_pcc batch_sig_surv_plot batch_surv batch_wilcoxon best_cutoff best_cutoff2 BinomialAUC BinomialModel calculate_break_month calculate_sig_score calculate_sig_score_integration calculate_sig_score_pca calculate_sig_score_ssgsea calculate_sig_score_zscore CalculatePref CalculateTimeROC cell_bar_plot check_cancer_types check_eset CIBERSORT clear_iobr_cache combine_pd_eset Construct_con ConvertRownameToLoci CoreAlg count2tpm creat_folder deconvo_cibersort deconvo_epic deconvo_estimate deconvo_ips deconvo_mcpcounter deconvo_quantiseq deconvo_ref deconvo_timer deconvo_tme deconvo_xcell deconvolute_quantiseq.default deconvolute_timer.default design_mytheme doPerm download_iobr_data DrawQQPlot Enet enrichment_barplot EPIC eset_distribution estimateScore exact_pvalue extract_sc_data feature_manipulation feature_select filterCommonGenes find_markers_in_bulk find_mutations find_outlier_samples find_variable_genes format_msigdb format_signatures generateRef generateRef_DEseq2 generateRef_limma generateRef_rnaseq generateRef_seurat get_cols get_cor get_cor_matrix get_iobr_cache_dir get_sig_sc GetFractions.Abbas getHRandCIfromCoxph GetOutlierGenes high_var_fea iobr_cor_plot iobr_deconvo_pipeline iobr_deg iobr_pca IPS_calculation ipsmap lasso_select limma.dif list_github_datasets list_iobr_mirrors load_data log2eset LR_cal make_mut_matrix mapbw mapcolors MCPcounter.estimate merge_duplicate merge_eset mouse2human_eset output_sig outputGCT palettes parallel_doperm ParseInputExpression patterns_to_na percent_bar_plot pie_chart PlotAUC plotPurity PlotTimeROC ProcessingData PrognosticAUC PrognosticModel PrognosticResult random_strata_cells rbind_iobr RegressionResult remove_batcheffect remove_duplicate_genes remove_names RemoveBatchEffect reset_iobr_cache_dir reset_iobr_mirrors roc_time scale_matrix select_method set_iobr_cache_dir sig_box sig_box_batch sig_forest sig_gsea sig_heatmap sig_pheatmap sig_roc sig_surv_plot signature_score_calculation_methods sigScore SplitTrainTest subgroup_survival surv_group tcga_rna_preps test_for_infiltration timer_available_cancers timer_info tme_cluster tme_deconvolution_methods Top_probe transform_data

Dependencies:abind annotate AnnotationDbi askpass backports BH Biobase BiocBaseUtils BiocFileCache BiocGenerics biocmake BiocParallel Biostrings bit bit64 blob boot broom cachem car carData cli codetools colorspace commonmark corrplot cowplot cpp11 crayon curl DBI dbplyr DelayedArray DelayedMatrixStats Deriv dir.expiry doBy dplyr exactRankTests farver fastmap filelock foreach forecast formatR Formula fracdiff futile.logger futile.options generics GenomicRanges ggplot2 ggpubr ggrepel ggsci ggsignif ggtext glmnet glue graph gridExtra gridtext GSEABase GSVA gtable h5mread HDF5Array httr httr2 IRanges isoband iterators jpeg jsonlite KEGGREST labeling lambda.r lattice lifecycle litedown lme4 lmtest magick magrittr markdown MASS Matrix MatrixGenerics MatrixModels matrixStats maxstat memoise memuse mgcv mime minqa modelr mvtnorm nlme nloptr nnet numDeriv openssl pbkrtest pillar pkgconfig png polynom purrr quantreg R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas rhdf5 rhdf5filters Rhdf5lib rjson rlang RSQLite rstatix S4Arrays S4Vectors S7 scales Seqinfo shape SingleCellExperiment snow SparseArray SparseM sparseMatrixStats SpatialExperiment stringi stringr SummarizedExperiment survival survminer sys tibble tidyr tidyselect timeDate urca utf8 vctrs viridisLite withr xfun XML xml2 xtable XVector zoo

Multidimensional Decoding Tumor Microenvironment for Immuno-Oncology Research

Rendered fromIOBR-user-manual.Rmdusingknitr::rmarkdown

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

Help page	Topics
Add Custom Download Mirror	add_iobr_mirror
Add Risk Score to Dataset	add_riskscore
Annotate Gene Expression Matrix and Remove Duplicated Genes	anno_eset
Harmonize Two Data Frames by Column Structure	assimilate_data
Batch Correlation Analysis	batch_cor
Batch Kruskal-Wallis Test	batch_kruskal
Batch Calculation of Partial Correlation Coefficients	batch_pcc
Batch Signature Survival Plot	batch_sig_surv_plot
Batch Survival Analysis	batch_surv
Batch Wilcoxon Rank-Sum Test Between Two Groups	batch_wilcoxon
Extract Best Cutoff and Add Binary Variable to Data Frame	best_cutoff
Extract Best Cutoff and Add Binary Variable to Data Frame	best_cutoff2
Calculate AUC for Binomial Model	BinomialAUC
Binomial Model Construction	BinomialModel
Break Time Into Blocks	calculate_break_month
Calculate Signature Score	calculate_sig_score
Calculate Signature Score Using Integration Method	calculate_sig_score_integration
Calculate Signature Score Using PCA Method	calculate_sig_score_pca
Calculate Signature Score Using ssGSEA Method	calculate_sig_score_ssgsea
Calculate Signature Score Using Z-Score Method	calculate_sig_score_zscore
Calculate Performance Metrics	CalculatePref
Calculate Time-Dependent ROC Curve	CalculateTimeROC
Visualize Cell Fractions as Stacked Bar Chart	cell_bar_plot
Process Batch Table and Validate Cancer Types	check_cancer_types
Check Integrity and Outliers of Expression Set	check_eset
CIBERSORT Deconvolution Algorithm	CIBERSORT
Clear IOBR Data Cache	clear_iobr_cache
Combine Phenotype Data and Expression Set	combine_pd_eset
Construct Contrast Matrix	Construct_con
Convert Rowname To Loci	ConvertRownameToLoci
Core Algorithm for CIBERSORT Deconvolution	CoreAlg
Convert Read Counts to Transcripts Per Million (TPM)	count2tpm
Create Nested Output Folders	creat_folder
Deconvolve Using CIBERSORT	deconvo_cibersort
Deconvolve Immune Microenvironment Using EPIC	deconvo_epic
Calculate ESTIMATE Scores	deconvo_estimate
Calculate Immunophenoscore (IPS)	deconvo_ips
Deconvolve Immune Microenvironment Using MCP-Counter	deconvo_mcpcounter
Deconvolve Using quanTIseq	deconvo_quantiseq
Deconvolve Using Custom Reference	deconvo_ref
Deconvolve Using TIMER	deconvo_timer
Main TME Deconvolution Function	deconvo_tme
Deconvolve Immune Microenvironment Using xCell	deconvo_xcell
Use quanTIseq to Deconvolute a Gene Expression Matrix	deconvolute_quantiseq.default
Deconvolute Tumor Microenvironment Using TIMER	deconvolute_timer.default
Design Custom Theme for ggplot2 Plots	design_mytheme
Permutation Test for CIBERSORT	doPerm
Download IOBR Data from GitHub with Mirror Support	download_iobr_data
Draw QQ Plot Comparing Cancer and Immune Expression	DrawQQPlot
Elastic Net Model Fitting	Enet
Enrichment Bar Plot with Two Directions	enrichment_barplot
Estimate the proportion of immune and cancer cells.	EPIC
Visualize Expression Set Distribution	eset_distribution
estimateScore	estimateScore
Calculate Exact P-Value for Correlation	exact_pvalue
Extract Data Frame from Seurat Object	extract_sc_data
Feature Quality Control and Filtering	feature_manipulation
Feature Selection via Correlation or Differential Expression	feature_select
filterCommonGenes	filterCommonGenes
Identify Marker Features in Bulk Expression Data	find_markers_in_bulk
Analyze Mutations Related to Signature Scores	find_mutations
Identify Outlier Samples in Gene Expression Data	find_outlier_samples
Identify Variable Genes in Expression Data	find_variable_genes
Format Input Signatures from MSigDB	format_msigdb
Transform Signature Data into List Format	format_signatures
Generate Reference Signature Matrix	generateRef
Generate Reference Signature Matrix Using DESeq2	generateRef_DEseq2
Generate Reference Signature Matrix Using Limma	generateRef_limma
Generate Reference Gene Matrix from RNA-seq DEGs	generateRef_rnaseq
Generate Reference Matrix from Seurat Object	generateRef_seurat
Set and View Color Palettes	get_cols
Calculate and Visualize Correlation Between Two Variables	get_cor
Calculate and Visualize Correlation Matrix Between Two Variable Sets	get_cor_matrix
Get IOBR Cache Directory	get_iobr_cache_dir
Extract Top Marker Genes from Single-Cell Differential Results	get_sig_sc
Constrained Regression Method (Abbas et al., 2009)	GetFractions.Abbas
Extract Hazard Ratio and Confidence Intervals from Cox Model	getHRandCIfromCoxph
Get Outlier Genes	GetOutlierGenes
Identify High-Variance Features from Statistical Results	high_var_fea
IMvigor210 Bladder Cancer Immunotherapy Cohort Data	imvigor210_pdata
Integrative Correlation Analysis Between Phenotype and Features	iobr_cor_plot
Tumor Microenvironment (TME) Deconvolution Pipeline	iobr_deconvo_pipeline
Differential Expression Analysis	iobr_deg
Principal Component Analysis (PCA) Visualization	iobr_pca
Calculate Immunophenoscore (IPS)	IPS_calculation
Map Score to Immunophenoscore	ipsmap
Feature Selection for Predictive or Prognostic Models Using LASSO Regression	lasso_select
Differential Expression Analysis Using Limma	limma.dif
List Available GitHub Datasets	list_github_datasets
List Current Download Mirrors	list_iobr_mirrors
Load IOBR Datasets	load_data
Log2 Transformation of Gene Expression Matrix	log2eset
Calculate Ligand-Receptor Interaction Scores	LR_cal
Construct Mutation Matrices from MAF Data	make_mut_matrix
Map Score to Black and White Color	mapbw
Map Score to Color	mapcolors
MCP-counter Cell Population Abundance Estimation	MCPcounter.estimate
Merge Data Frames with Duplicated Column Names	merge_duplicate
Merge Expression Sets by Row Names	merge_eset
Convert Mouse Gene Symbols to Human Gene Symbols	mouse2human_eset
NULL Model Coefficients for MCPcounter	null_models
Save Signature Data to File	output_sig
outputGCT	outputGCT
Select Color Palettes for Visualization	palettes
Parallel Permutation Test for CIBERSORT	parallel_doperm
Parse Input Gene Expression Data	ParseInputExpression
Default Pattern List for Name Cleaning	patterns_to_na
Toy STAD Phenotype Data	pdata_stad
Create a Percent Bar Plot	percent_bar_plot
Create Pie or Donut Charts	pie_chart
Plot AUC ROC Curves	PlotAUC
plotPurity	plotPurity
Plot Time-Dependent ROC Curves	PlotTimeROC
Process Data for Model Construction	ProcessingData
Calculate Time-Dependent AUC for Survival Models	PrognosticAUC
Build Prognostic Models Using LASSO and Ridge Regression	PrognosticModel
Compute Prognostic Results for Survival Models	PrognosticResult
Stratified Random Sampling of Cells	random_strata_cells
Row Bind Multiple Data Sets	rbind_iobr
Regression Result Computation	RegressionResult
Removing Batch Effect from Expression Sets	remove_batcheffect
Remove Duplicate Gene Symbols in Gene Expression Data	remove_duplicate_genes
Remove Patterns from Column Names or Variables	remove_names
Remove Batch Effect of Expression Set	RemoveBatchEffect
Reset IOBR Cache Directory to Default	reset_iobr_cache_dir
Reset Download Mirrors to Default	reset_iobr_mirrors
Time-dependent ROC Curve for Survival Analysis	roc_time
Scale and Manipulate a Matrix	scale_matrix
Select a Signature Scoring Method Subset	select_method
Set IOBR Cache Directory	set_iobr_cache_dir
Signature Box Plot with Statistical Comparisons	sig_box
Batch Signature Box Plots for Group Comparisons	sig_box_batch
Forest Plot for Survival Analysis Results	sig_forest
Grouped gene signatures for IOBR analysis	sig_group
Perform Gene Set Enrichment Analysis (GSEA)	sig_gsea
Signature Heatmap with Optional Annotations	sig_heatmap
Generate Heatmap for Signature Data	sig_pheatmap
Plot ROC Curves and Compare Them	sig_roc
Generate Kaplan-Meier Survival Plot for Signature	sig_surv_plot
Gene signature collection for pathway and immune analysis	signature_collection
Signature Score Calculation Methods	signature_score_calculation_methods
Calculate Signature Score Using PCA, Mean, or Z-score Methods	sigScore
Split Data into Training and Testing Sets	SplitTrainTest
Example Clinical Data for TCGA-STAD Gastric Cancer Analysis	stad_group
Example Dataset for Subgroup Survival Analysis	subgroup_data
Subgroup Survival Analysis Using Cox Proportional Hazards Models	subgroup_survival
Generate Kaplan-Meier Survival Plots for Categorical Groups	surv_group
Preprocess TCGA RNA-seq Data	tcga_rna_preps
TCGA-STAD Clinical and Molecular Annotation Data	tcga_stad_pdata
Test for Cell Population Infiltration	test_for_infiltration
TIMER Available Cancer Types	timer_available_cancers
Source code for the TIMER deconvolution method.	timer_info
Identification of TME Cluster	tme_cluster
TME Deconvolution Methods	tme_deconvolution_methods
Top Probe Selector	Top_probe
Transform NA, Inf, or Zero Values in Data	transform_data

Package: IOBR 2.2.3.9000

IOBR: Immune Oncology Biological Research

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