Package: omada
Type: Package
Title: Machine learning tools for automated transcriptome clustering
        analysis
Version: 1.15.0
Authors@R: person("Sokratis", "Kariotis", role = c("aut", "cre"),
                        email = "sokratiskariotis@gmail.com",
                        comment = c(ORCID = "0000-0001-9993-6017"))
Description: Symptomatic heterogeneity in complex diseases reveals
        differences in molecular states that need to be investigated.
        However, selecting the numerous parameters of an exploratory
        clustering analysis in RNA profiling studies requires deep
        understanding of machine learning and extensive computational
        experimentation. Tools that assist with such decisions without
        prior field knowledge are nonexistent and further gene
        association analyses need to be performed independently. We
        have developed a suite of tools to automate these processes and
        make robust unsupervised clustering of transcriptomic data more
        accessible through automated machine learning based functions.
        The efficiency of each tool was tested with four datasets
        characterised by different expression signal strengths. Our
        toolkit’s decisions reflected the real number of stable
        partitions in datasets where the subgroups are discernible.
        Even in datasets with less clear biological distinctions,
        stable subgroups with different expression profiles and
        clinical associations were found.
Depends: pdfCluster (>= 1.0-3), kernlab (>= 0.9-29), R (>= 4.2), fpc
        (>= 2.2-9), Rcpp (>= 1.0.7), diceR (>= 0.6.0), ggplot2 (>=
        3.3.5), reshape (>= 0.8.8), genieclust (>= 1.1.3), clValid (>=
        0.7), glmnet (>= 4.1.3), dplyr(>= 1.0.7), stats (>= 4.1.2),
        clValid(>= 0.7)
Suggests: rmarkdown, knitr, testthat
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.3.1
VignetteBuilder: knitr
biocViews: Software, Clustering, RNASeq, GeneExpression
LazyData: true
Config/pak/sysreqs: cmake make libicu-dev libuv1-dev libx11-dev
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:58:54 UTC
RemoteUrl: https://github.com/bioc/omada
RemoteRef: HEAD
RemoteSha: 29dae47fa8299e9c57e0b1129fade4d67d41e7b5
NeedsCompilation: no
Packaged: 2026-07-04 23:24:54 UTC; root
Author: Sokratis Kariotis [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-9993-6017>)
Maintainer: Sokratis Kariotis <sokratiskariotis@gmail.com>