Package: IOBR
Title: Immune Oncology Biological Research
Version: 2.2.3
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
NeedsCompilation: no
Packaged: 2026-05-30 14:20:59 UTC; wsx
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>
Repository: CRAN
Date/Publication: 2026-05-30 15:30:02 UTC
