Package: IOBR
Title: Immune Oncology Biological Research
Version: 2.2.3.9000
Authors@R: c(
    person("Dongqiang", "Zeng", , "interlaken@smu.edu.cn", role = "aut"),
    person("Yiran", "Fang", , "fyr_nate@163.com", role = "aut"),
    person("Shixiang", "Wang", , "w_shixiang@163.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0001-9855-7357")),
    person("Qingcong", "Luo", , "qingcongl@163.com", role = "aut"),
    person("Hongqian", "Qian", , "536769786@qq.com", role = "aut")
  )
Description: 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>).
License: GPL-3
URL: https://doi.org/10.3389/fimmu.2021.687975 (paper),
        https://iobr.github.io/book/ (docs),
        https://iobr.github.io/IOBR/
BugReports: https://github.com/IOBR/IOBR/issues
Depends: R (>= 3.6.0)
Imports: cli, dplyr, ggplot2, glmnet, GSVA, methods, purrr, rlang,
        stringr, survival, survminer, tibble, tidyr
Suggests: BiocManager, BiocParallel, biomaRt, circlize,
        clusterProfiler, ComplexHeatmap, corrplot, DESeq2, doParallel,
        DOSE, e1071, easier, enrichplot, factoextra, FactoMineR,
        foreach, ggdensity, ggpp, ggpubr, ggsci, gridExtra, Hmisc,
        knitr, limma, limSolve, maftools, MASS, Matrix, msigdbr,
        NbClust, org.Hs.eg.db, org.Mm.eg.db, patchwork, PMCMRplus,
        pracma, preprocessCore, prettydoc, pROC, psych, RColorBrewer,
        reshape2, rmarkdown, ROCR, sampling, scales, Seurat,
        SeuratObject, sva, testthat (>= 3.0.0), tidyHeatmap, timeROC,
        webr, WGCNA
VignetteBuilder: knitr
Additional_repositories: https://bioconductor.org/packages/3.22/bioc,
        https://bioconductor.org/packages/3.22/data/annotation,
        https://bioconductor.org/packages/3.22/data/experiment,
        https://bioconductor.org/packages/3.23/bioc,
        https://bioconductor.org/packages/3.23/data/annotation,
        https://bioconductor.org/packages/3.23/data/experiment
biocViews: GeneExpression, DifferentialExpression, ImmunoOncology,
        Transcriptomics, 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
        libjpeg-dev libpng-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://iobr.r-universe.dev
Date/Publication: 2026-07-23 15:21:37 UTC
RemoteUrl: https://github.com/iobr/iobr
RemoteRef: HEAD
RemoteSha: 635effe4d05f37a244c04f2d5cf2a5e73c38a798
NeedsCompilation: no
Packaged: 2026-09-26 07:47:22 UTC; root
Author: Dongqiang Zeng [aut],
  Yiran Fang [aut],
  Shixiang Wang [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-9855-7357>),
  Qingcong Luo [aut],
  Hongqian Qian [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>