omicScope/DESCRIPTION at main · junjunlab/omicScope · GitHub

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Package: omicScope
Title: A Comprehensive and Integrated Framework for Transcriptomic Data Analysis
Version: 0.0.4
Authors@R:
    person("Jun", "Zhang", , "3219030654@stu.cpu.edu.cn", role = c("aut", "cre"))
Description: Provides a streamlined and user-friendly workflow for the end-to-end
    analysis of transcriptomic data. 'omicScope' leverages the SummarizedExperiment
    class for robust data management and offers a suite of tools for essential analysis
    steps, including data normalization, differential expression analysis (interfacing
    with popular methods like DESeq2, edgeR, and limma), and advanced functional
    interpretation. A key feature is the implementation of pathway and transcription
    factor (TF) activity inference using the 'decoupleR' framework, enabling users
    to move from gene expression changes to functional biological insights within a
    single, cohesive environment..
License: GPL (>= 3)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Depends: R (>= 4.1.0)
Imports:
    clusterProfiler,
    ComplexHeatmap,
    cowplot,
    DESeq2,
    dplyr,
    edgeR,
    GenomicRanges,
    ggplot2,
    IRanges,
    limma,
    Matrix,
    methods,
    Rsubread,
    rtracklayer,
    S4Vectors,
    SummarizedExperiment,
    tibble,
    tidyr,
    corrplot,
    scales,
    data.table,
    magrittr,
    Rsamtools,
    ggbio,
    Signac,
    Seurat,
    SeuratObject,
    GenomeInfoDb
Enhances:
    Rtsne,
    umap
Suggests:
    ggpubr,
    decoupleR,
    ggpp,
    ggrepel,
    knitr,
    OmnipathR,
    rmarkdown,
    ggsurvfit,
    survival,
    maxstat,
    ggpubr,
    ggh4x,
    ggarrow,
    ggnewscale
VignetteBuilder: knitr