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omada

Machine learning tools for automated transcriptome clustering analysis


Bioconductor version: Release (3.18)

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.

Author: Sokratis Kariotis [aut, cre]

Maintainer: Sokratis Kariotis <sokratiskariotis at gmail.com>

Citation (from within R, enter citation("omada")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("omada")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("omada")
my-vignette HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Clustering, GeneExpression, RNASeq, Software
Version 1.4.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License GPL-3
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)
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package omada_1.4.0.tar.gz
Windows Binary omada_1.4.0.zip
macOS Binary (x86_64) omada_1.4.0.tgz
macOS Binary (arm64) omada_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/omada
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/omada
Bioc Package Browser https://code.bioconductor.org/browse/omada/
Package Short Url https://bioconductor.org/packages/omada/
Package Downloads Report Download Stats