Package: OmicFlow
Title: Fast and Efficient (Automated) Analysis of Sparse Omics Data
Version: 1.7.0
Date: 2026-10-11
Authors@R: c(
    person(
        "Alem", "Gusinac",
        email = "alem.gusinac@gmail.com", 
        role = c("aut", "cre"),
        comment = c(ORCID = "0009-0006-1896-4176")),
    person(
        "Thomas", "Ederveen", 
        role = "aut",
        comment = c(ORCID = "0000-0003-0068-1275")),
    person(
        "Annemarie", "Boleij", 
        role = c("aut", "fnd"),
        comment = c(ORCID = "0000-0003-4495-5880"))
  )
Description: A generalised data structure for fast and efficient
        loading and data munching of sparse omics data. The 'OmicFlow'
        requires an up-front validated metadata template from the user,
        which serves as a guide to connect all the pieces together by
        aligning them into a single object that is defined as an
        'omics' class. Once this unified structure is established,
        users can perform manual subsetting, visualisation, and
        statistical analysis, or leverage the automated 'autoFlow'
        method to generate a comprehensive report.
License: MIT + file LICENSE
URL: https://agusinac.github.io/OmicFlow/
BugReports: https://github.com/agusinac/OmicFlow/issues
Config/testthat/edition: 3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
Depends: R (>= 4.3.0)
Imports: ape, cli, data.table, ggrepel, ggplot2, grDevices,
        jsonvalidate, lifecycle, methods, Matrix, matrixTests,
        matrixStats, patchwork, R6, RColorBrewer, rhdf5, Rcpp (>=
        0.12.6), RcppParallel (>= 4.3.20), stats, utils, vegan, yyjsonr
Suggests: DT, downloadthis, rmarkdown, parallel, testthat (>= 3.0.0)
LinkingTo: Rcpp, RcppParallel, RcppArmadillo
Config/roxygen2/version: 8.1.0
Config/Needs/website: rmarkdown
Config/pak/sysreqs: cmake libssl-dev libnode-dev
Repository: https://agusinac.r-universe.dev
Date/Publication: 2026-10-15 12:09:58 UTC
RemoteUrl: https://github.com/agusinac/omicflow
RemoteRef: HEAD
RemoteSha: 04bb6943a237475aca384611b0cf104e9024a4c9
NeedsCompilation: yes
Packaged: 2026-10-15 17:30:50 UTC; root
Author: Alem Gusinac [aut, cre] (ORCID:
    <https://orcid.org/0009-0006-1896-4176>),
  Thomas Ederveen [aut] (ORCID: <https://orcid.org/0000-0003-0068-1275>),
  Annemarie Boleij [aut, fnd] (ORCID:
    <https://orcid.org/0000-0003-4495-5880>)
Maintainer: Alem Gusinac <alem.gusinac@gmail.com>