{ "_id": "6a1c56131d7bb097a0a30e0d", "Package": "IOBR", "Title": "Immune Oncology Biological Research", "Version": "2.2.3.9000", "Authors@R": "c(\nperson(\"Dongqiang\", \"Zeng\", , \"interlaken@smu.edu.cn\", role = \"aut\"),\nperson(\"Yiran\", \"Fang\", , \"fyr_nate@163.com\", role = \"aut\"),\nperson(\"Shixiang\", \"Wang\", , \"w_shixiang@163.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-9855-7357\")),\nperson(\"Qingcong\", \"Luo\", , \"qingcongl@163.com\", role = \"aut\"),\nperson(\"Hongqian\", \"Qian\", , \"536769786@qq.com\", role = \"aut\")\n)", "Description": "Provides six modules for tumor microenvironment (TME)\nanalysis based on multi-omics data. These modules cover data\npreprocessing, TME estimation, TME infiltrating patterns,\ncellular interactions, genome and TME interaction, and\nvisualization for TME relevant features, as well as modelling\nbased on key features. It integrates multiple\nmicroenvironmental analysis algorithms and signature estimation\nmethods, simplifying the analysis and downstream visualization\nof the TME. In addition to providing a quick and easy way to\nconstruct gene signatures from single-cell RNA-seq data, it\nalso provides a way to construct a reference matrix for TME\ndeconvolution from single-cell RNA-seq data. The analysis\npipeline and feature visualization are user-friendly and\nprovide a comprehensive description of the complex TME,\noffering insights into tumour-immune interactions (Zeng D, et\nal. (2024) . Fang Y, et al.\n(2025) ).", "License": "GPL-3", "URL": "https://doi.org/10.3389/fimmu.2021.687975 (paper),\nhttps://iobr.github.io/book/ (docs),\nhttps://iobr.github.io/IOBR/", "BugReports": "https://github.com/IOBR/IOBR/issues", "VignetteBuilder": "knitr", "Additional_repositories": "https://bioconductor.org/packages/3.22/bioc,\nhttps://bioconductor.org/packages/3.22/data/annotation,\nhttps://bioconductor.org/packages/3.22/data/experiment,\nhttps://bioconductor.org/packages/3.23/bioc,\nhttps://bioconductor.org/packages/3.23/data/annotation,\nhttps://bioconductor.org/packages/3.23/data/experiment", "biocViews": "GeneExpression, DifferentialExpression, ImmunoOncology,\nTranscriptomics, Clustering, Survival, Visualization", "Config/testthat/edition": "3", "Encoding": "UTF-8", "LazyData": "FALSE", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "cmake make libmagick++-dev gsfonts libicu-dev\nlibjpeg-dev libpng-dev libxml2-dev libssl-dev zlib1g-dev", "Repository": 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