---
title: "Multidimensional Decoding Tumor Microenvironment for Immuno-Oncology Research"
author: 
- name: Dongqiang Zeng, Yiran Fang
  email: interlaken@smu.edu.com, fyr_nate@163.com
  affiliation: Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P. R. China
date: "`r Sys.Date()`"
output:
  prettydoc::html_pretty:
    theme: cayman
    highlight: github
  pdf_document:
    toc: true
vignette: >
  %\VignetteIndexEntry{IOBR User Manual}
  %\VignetteEngine{knitr::rmarkdown}
  %\usepackage[utf8]{inputenc}
  %\VignetteEncoding{UTF-8}
---

```{r style, echo=FALSE, results="asis", message=FALSE}
knitr::opts_chunk$set(
  tidy = FALSE,
  warning = FALSE,
  message = FALSE
)
```

# Overview

IOBR is the acronym for [Immuno-Oncology Biological Research](https://github.com/IOBR/IOBR)  to perform multi-omics immuno-oncology biological research to decipher tumour microenvironment and signatures for clinical translation.

# Module Introduction

![](Figure_1.jpg)

IOBR encompasses six functional modules: 


+ __*Transcriptome data prepare module*__ : pre-procession of transcriptome data, as well as pertinent batch statistical analyses; 
+ __*TME deconvolution and signature estimation module*__ : estimation of signature scores and identification of phenotype relevant signatures, along with decoding immune contexture; 
+ __*TME interaction module*__ : clustering TME characteristics and analyzing receptor-ligand interactions; 
+ __*Genome and TME interaction module*__ : analysis of signature associated mutations; 
+ __*TME data visualization and Statistical analysis module*__ : visual representation and statistical examination of TME data; 
+ __*TME modeling module*__ : fast model construction and the assessment of model performance.


# Methodology

IOBR integrates eight open-source deconvolution methodologies: __*CIBERSORT*__ , __*ESTIMATE*__ , __*quanTIseq*__ , __*TIMER*__ , __*IPS*__ , __*MCPCounter*__ , __*xCell*__ and __*EPIC*__ . In addition, 323 published signature gene sets have been collected by IOBR covering __*tumour microenvironment*__ , __*tumour metabolism*__ , __*m6A*__ , __*exosomes*__ , __*microsatellite instability*__ and __*tertiary lymphoid structure*__. IOBR has used three computational methods to calculate the signature score, including __*PCA*__ , __*z-score*__ and __*ssGSEA*__.

# Visualization

IOBR integrates visualization function, including __*boxplots*__ , __*heatmaps*__ , __*percentage bar charts*__ , __*scatter plots*__ , __*KM plot*__ , __*PCA plot*__ etc.

# Tutorial

Please go to <https://iobr.github.io/book/> for the full tutorial.

# Citation

If you use [IOBR](https://github.com/IOBR/IOBR) in published research, please cite:


__*Zeng D*__, Fang Y, …, Liao W (2024) IOBR2: Multidimensional Decoding of Tumor Microenvironment for Immuno-Oncology Research. **_Cell Reports Methods_**_. 4(9):100910.
doi:[10.1016/j.crmeth.2024.100910](https://doi.org/10.1016/j.crmeth.2024.100910)


__*Zeng D*__, Ye Z, Shen R, Yu G, Wu J, Xiong Y,…, Liao W (2021) IOBR: Multi-Omics Immuno-Oncology Biological Research to Decode Tumor Microenvironment and Signatures. **_Frontiers in Immunology_**. 12:687975.
doi:[10.3389/fimmu.2021.687975](https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2021.687975/full)



# Feedback and helps

Should any queries or concerns arise, consider checking the [IOBR primary webpage](https://github.com/IOBR/IOBR) initially. The majority of your issues are likely already addressed there. Supposing you've detected a fault, adhere to the instructions, and offer a replicable instance to be showcased on the [github issue tracker](https://github.com/IOBR/IOBR/issues).