GeneSelectR: 'GeneSelectR' - Comprehensive Feature Selection Workflow for Bulk RNAseq Datasets

The workflow is a versatile R package designed for comprehensive feature selection in bulk RNAseq datasets. Its key innovation lies in the seamless integration of the 'Python' 'scikit-learn' (<https://scikit-learn.org/stable/index.html>) machine learning framework with R-based bioinformatics tools. 'GeneSelectR' performs robust Machine Learning-driven (ML) feature selection while leveraging 'Gene Ontology' (GO) enrichment analysis as described by Thomas PD et al. (2022) <doi:10.1002/pro.4218>, using 'clusterProfiler' (Wu et al., 2021) <doi:10.1016/j.xinn.2021.100141> and semantic similarity analysis powered by 'simplifyEnrichment' (Gu, Huebschmann, 2021) <doi:10.1016/j.gpb.2022.04.008>. This combination of methodologies optimizes computational and biological insights for analyzing complex RNAseq datasets.

Version: 1.0.1
Depends: R (≥ 3.5.0)
Imports: cowplot (≥ 1.1.1), dplyr (≥ 1.1.0), ggplot2 (≥ 3.4.2), glue (≥ 1.6.2), magrittr (≥ 2.0.3), methods (≥ 4.2.2), RColorBrewer (≥ 1.1.3), reshape2 (≥ 1.4.4), reticulate (≥ 1.28), rlang (≥ 1.1.1), testthat (≥ 3.0.0), tibble (≥ 3.2.1), tidyr (≥ 1.3.0), tmod (≥ 0.50.13)
Suggests: clusterProfiler (≥ 4.6.2), GO.db (≥ 3.17.0), knitr, rmarkdown, BiocManager (≥ 1.30.21), UpSetR (≥ 1.4.0), AnnotationHub (≥ 3.8.0), ensembldb (≥ 2.24.0), org.Hs.eg.db (≥ 3.17.0)
Enhances: simplifyEnrichment (≥ 1.8.0)
Published: 2024-02-03
Author: Damir Zhakparov ORCID iD [aut, cre]
Maintainer: Damir Zhakparov <dzhakparov at gmail.com>
BugReports: https://github.com/dzhakparov/GeneSelectR/issues
License: MIT + file LICENSE
URL: https://github.com/dzhakparov/GeneSelectR
NeedsCompilation: no
Materials: README
CRAN checks: GeneSelectR results

Documentation:

Reference manual: GeneSelectR.pdf
Vignettes: example

Downloads:

Package source: GeneSelectR_1.0.1.tar.gz
Windows binaries: r-devel: GeneSelectR_1.0.1.zip, r-release: GeneSelectR_1.0.1.zip, r-oldrel: GeneSelectR_1.0.1.zip
macOS binaries: r-release (arm64): GeneSelectR_1.0.1.tgz, r-oldrel (arm64): GeneSelectR_1.0.1.tgz, r-release (x86_64): GeneSelectR_1.0.1.tgz
Old sources: GeneSelectR archive

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