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DrGA: cancer driver gene analysis in a simpler manner

BACKGROUND: To date, cancer still is one of the leading causes of death worldwide, in which the cumulative of genes carrying mutations was said to be held accountable for the establishment and development of this disease mainly. From that, identification and analysis of driver genes were vital. Our...

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Detalles Bibliográficos
Autores principales: Nguyen, Quang-Huy, Nguyen, Tin, Le, Duc-Hau
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8897886/
https://www.ncbi.nlm.nih.gov/pubmed/35247965
http://dx.doi.org/10.1186/s12859-022-04606-0
Descripción
Sumario:BACKGROUND: To date, cancer still is one of the leading causes of death worldwide, in which the cumulative of genes carrying mutations was said to be held accountable for the establishment and development of this disease mainly. From that, identification and analysis of driver genes were vital. Our previous study indicated disagreement on a unifying pipeline for these tasks and then introduced a complete one. However, this pipeline gradually manifested its weaknesses as being unfamiliar to non-technical users, time-consuming, and inconvenient. RESULTS: This study presented an R package named DrGA, developed based on our previous pipeline, to tackle the mentioned problems above. It wholly automated four widely used downstream analyses for predicted driver genes and offered additional improvements. We described the usage of the DrGA on driver genes of human breast cancer. Besides, we also gave the users another potential application of DrGA in analyzing genomic biomarkers of a complex disease in another organism. CONCLUSIONS: DrGA facilitated the users with limited IT backgrounds and rapidly created consistent and reproducible results. DrGA and its applications, along with example data, were freely provided at https://github.com/huynguyen250896/DrGA. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-022-04606-0.