Package: sciNOME
Title: Region-Centric Integration for Single-Cell Multi-Omics
Version: 0.99.4
Authors@R: 
    c(person(given = "Shitao",
             family = "Zhou",
             role = c("aut", "cre"),
             email = "m18231838586@163.com",
             comment = c(ORCID = "0009-0005-0386-8870")),
      person(given = "Medinfo",
             family = "Lab",
             role = "fnd"))
Description: Provides an end-to-end pipeline for processing RNA, DNA
        methylation, and chromatin accessibility data at the
        single-cell level. It features ultra-fast data aggregation,
        quality control, dimensionality reduction, and multi-omics
        integration based on genomic regions. Additionally, it offers
        extensive publication-ready visualization tools for downstream
        analysis.
License: GPL-3
URL: https://github.com/Medinfo-Lab/sciNOME
BugReports: https://github.com/Medinfo-Lab/sciNOME/issues
biocViews: Software, SingleCell, Epigenetics, Transcriptomics,
        DNAMethylation, DifferentialExpression, DimensionReduction,
        Clustering, QualityControl
Depends: R (>= 4.2.0)
Imports: data.table, dplyr, FNN, GenomicRanges, ggplot2, grDevices,
        ggpubr, ggrepel, ggridges, igraph, impute, IRanges, irlba,
        magrittr, Matrix, methods, NMF, parallel, patchwork, pbapply,
        princurve, Rtsne, S4Vectors, stats, tidyr, tidyselect, tools,
        utils, uwot
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle
VignetteBuilder: knitr
Encoding: UTF-8
RoxygenNote: 7.3.2
Config/testthat/edition: 3
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libxml2-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-08-26 08:17:39 UTC
RemoteUrl: https://github.com/BiocStaging/sciNOME
RemoteRef: HEAD
RemoteSha: af1b85c1eecc5789cc11d8a03c2d36340f5bf670
NeedsCompilation: no
Packaged: 2026-10-14 09:25:36 UTC; root
Author: Shitao Zhou [aut, cre] (ORCID: <https://orcid.org/0009-0005-0386-8870>),
  Medinfo Lab [fnd]
Maintainer: Shitao Zhou <m18231838586@163.com>