Multidimensional Decoding Tumor Microenvironment for Immuno-Oncology Research
In IOBR: Immune Oncology Biological Research

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Overview

IOBR is the acronym for Immuno-Oncology Biological Research to perform multi-omics immuno-oncology biological research to decipher tumour microenvironment and signatures for clinical translation.

Module Introduction

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 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

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

Feedback and helps

Should any queries or concerns arise, consider checking the IOBR primary webpage 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.