DEGGs: an R package with shiny app for the identification of differentially expressed gene–gene interactions in high-throughput sequencing data

SUMMARY: The discovery of differential gene–gene correlations across phenotypical groups can help identify the activation/deactivation of critical biological processes underlying specific conditions. The presented R package, provided with a count and design matrix, extract networks of group-specific...

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Autores principales: Sciacca, Elisabetta, Alaimo, Salvatore, Silluzio, Gianmarco, Ferro, Alfredo, Latora, Vito, Pitzalis, Costantino, Pulvirenti, Alfredo, Lewis, Myles J
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10133399/
https://www.ncbi.nlm.nih.gov/pubmed/37084249
http://dx.doi.org/10.1093/bioinformatics/btad192
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author Sciacca, Elisabetta
Alaimo, Salvatore
Silluzio, Gianmarco
Ferro, Alfredo
Latora, Vito
Pitzalis, Costantino
Pulvirenti, Alfredo
Lewis, Myles J
author_facet Sciacca, Elisabetta
Alaimo, Salvatore
Silluzio, Gianmarco
Ferro, Alfredo
Latora, Vito
Pitzalis, Costantino
Pulvirenti, Alfredo
Lewis, Myles J
author_sort Sciacca, Elisabetta
collection PubMed
description SUMMARY: The discovery of differential gene–gene correlations across phenotypical groups can help identify the activation/deactivation of critical biological processes underlying specific conditions. The presented R package, provided with a count and design matrix, extract networks of group-specific interactions that can be interactively explored through a shiny user-friendly interface. For each gene–gene link, differential statistical significance is provided through robust linear regression with an interaction term. AVAILABILITY AND IMPLEMENTATION: DEGGs is implemented in R and available on GitHub at https://github.com/elisabettasciacca/DEGGs. The package is also under submission on Bioconductor.
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spelling pubmed-101333992023-04-28 DEGGs: an R package with shiny app for the identification of differentially expressed gene–gene interactions in high-throughput sequencing data Sciacca, Elisabetta Alaimo, Salvatore Silluzio, Gianmarco Ferro, Alfredo Latora, Vito Pitzalis, Costantino Pulvirenti, Alfredo Lewis, Myles J Bioinformatics Applications Note SUMMARY: The discovery of differential gene–gene correlations across phenotypical groups can help identify the activation/deactivation of critical biological processes underlying specific conditions. The presented R package, provided with a count and design matrix, extract networks of group-specific interactions that can be interactively explored through a shiny user-friendly interface. For each gene–gene link, differential statistical significance is provided through robust linear regression with an interaction term. AVAILABILITY AND IMPLEMENTATION: DEGGs is implemented in R and available on GitHub at https://github.com/elisabettasciacca/DEGGs. The package is also under submission on Bioconductor. Oxford University Press 2023-04-21 /pmc/articles/PMC10133399/ /pubmed/37084249 http://dx.doi.org/10.1093/bioinformatics/btad192 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Sciacca, Elisabetta
Alaimo, Salvatore
Silluzio, Gianmarco
Ferro, Alfredo
Latora, Vito
Pitzalis, Costantino
Pulvirenti, Alfredo
Lewis, Myles J
DEGGs: an R package with shiny app for the identification of differentially expressed gene–gene interactions in high-throughput sequencing data
title DEGGs: an R package with shiny app for the identification of differentially expressed gene–gene interactions in high-throughput sequencing data
title_full DEGGs: an R package with shiny app for the identification of differentially expressed gene–gene interactions in high-throughput sequencing data
title_fullStr DEGGs: an R package with shiny app for the identification of differentially expressed gene–gene interactions in high-throughput sequencing data
title_full_unstemmed DEGGs: an R package with shiny app for the identification of differentially expressed gene–gene interactions in high-throughput sequencing data
title_short DEGGs: an R package with shiny app for the identification of differentially expressed gene–gene interactions in high-throughput sequencing data
title_sort deggs: an r package with shiny app for the identification of differentially expressed gene–gene interactions in high-throughput sequencing data
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10133399/
https://www.ncbi.nlm.nih.gov/pubmed/37084249
http://dx.doi.org/10.1093/bioinformatics/btad192
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