Package: omada
Type: Package
Title: Machine learning tools for automated transcriptome clustering
        analysis
Version: 1.12.0
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
git_url: https://git.bioconductor.org/packages/omada
git_branch: RELEASE_3_22
git_last_commit: 53ba5ea
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-29
NeedsCompilation: no
Packaged: 2025-10-30 05:29:55 UTC; biocbuild
Author: Sokratis Kariotis [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-9993-6017>)
Maintainer: Sokratis Kariotis <sokratiskariotis@gmail.com>
