# -------------------------------------------- # CITATION file created with {cffr} R package # See also: https://docs.ropensci.org/cffr/ # -------------------------------------------- cff-version: 1.2.0 message: 'To cite package "IOBR" in publications use:' type: software license: GPL-3.0-only title: 'IOBR: Immune Oncology Biological Research' version: 2.2.3.9000 doi: 10.1016/j.crmeth.2024.100910 identifiers: - type: doi value: 10.32614/CRAN.package.IOBR - type: url value: https://iobr.github.io/book/ - type: url value: https://iobr.github.io/IOBR/ abstract: 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) . Fang Y, et al. (2025) ). authors: - family-names: Zeng given-names: Dongqiang email: interlaken@smu.edu.cn - family-names: Fang given-names: Yiran email: fyr_nate@163.com - family-names: Wang given-names: Shixiang email: w_shixiang@163.com orcid: https://orcid.org/0000-0001-9855-7357 - family-names: Luo given-names: Qingcong email: qingcongl@163.com - family-names: Qian given-names: Hongqian email: 536769786@qq.com preferred-citation: type: article title: Enhancing Immuno-Oncology Investigations Through Multidimensional Decoding of Tumour Microenvironment with IOBR 2.0 authors: - family-names: Zeng given-names: Dongqiang email: interlaken@smu.edu.cn - family-names: Fang given-names: Yiran email: fyr_nate@163.com - family-names: Luo given-names: Peng - family-names: Qiu given-names: Wenjun - family-names: Wang given-names: Shixiang email: w_shixiang@163.com orcid: https://orcid.org/0000-0001-9855-7357 - family-names: Shen given-names: Rongfang - family-names: Gu given-names: Wenchao - family-names: Huang given-names: Xiatong - family-names: Mao given-names: Qianqian - family-names: Lai given-names: Yonghong - family-names: Xu given-names: Xi - family-names: Shi given-names: Min - family-names: Yu given-names: Guangchuang - family-names: Liao given-names: Wangjun journal: Cell Reports Methods year: '2024' volume: '4' issue: '9' doi: 10.1016/j.crmeth.2024.100910 start: '100910' repository: https://iobr.r-universe.dev repository-code: https://github.com/IOBR/IOBR commit: de5dc72d0145551dd9cf7a421b18d679934b052e url: https://doi.org/10.3389/fimmu.2021.687975 date-released: '2026-05-31' contact: - family-names: Wang given-names: Shixiang email: w_shixiang@163.com orcid: https://orcid.org/0000-0001-9855-7357 references: - type: article title: 'IOBR: Multi-Omics Immuno-Oncology Biological Research to Decode Tumor Microenvironment and Signatures' authors: - family-names: Zeng given-names: Dongqiang - family-names: Ye given-names: Zilan - family-names: Shen given-names: Rongfang - family-names: Yu given-names: Guangchuang - family-names: Wu given-names: Jiani - family-names: Xiong given-names: Yi - family-names: Zhou given-names: Rui - family-names: Qiu given-names: Wenjun - family-names: Huang given-names: Na - family-names: Sun given-names: Li - family-names: Li given-names: Xuejun - family-names: Bin given-names: Jianping - family-names: Liao given-names: Yulin - family-names: Shi given-names: Min - family-names: Liao given-names: Wangjun journal: Frontiers in Immunology year: '2021' volume: '12' doi: 10.3389/fimmu.2021.687975 start: '687975'