TimiRGeN: R/Bioconductor package for time series microRNA–mRNA integration and analysis
| العنوان: | TimiRGeN: R/Bioconductor package for time series microRNA–mRNA integration and analysis |
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| المؤلفون: | David Young, Krutik Patel, Carole J. Proctor, Sharmilla Chandrasegaran, Daryl P. Shanley, Ian M. Clark |
| المصدر: | Bioinformatics |
| بيانات النشر: | Oxford University Press (OUP), 2021. |
| سنة النشر: | 2021 |
| مصطلحات موضوعية: | Statistics and Probability, Supplementary data, 0303 health sciences, AcademicSubjects/SCI01060, Computer science, In silico, Gene regulatory network, Computational biology, Original Papers, Biochemistry, Computer Science Applications, Bioconductor, 03 medical and health sciences, Computational Mathematics, R package, 0302 clinical medicine, Computational Theory and Mathematics, 030220 oncology & carcinogenesis, microRNA, Data and Text Mining, Differential expression, Molecular Biology, Signalling pathways, 030304 developmental biology |
| الوصف: | Motivation The analysis of longitudinal datasets and construction of gene regulatory networks (GRNs) provide a valuable means to disentangle the complexity of microRNA (miRNA)–mRNA interactions. However, there are no computational tools that can integrate, conduct functional analysis and generate detailed networks from longitudinal miRNA–mRNA datasets. Results We present TimiRGeN, an R package that uses time point-based differential expression results to identify miRNA–mRNA interactions influencing signaling pathways of interest. miRNA–mRNA interactions can be visualized in R or exported to PathVisio or Cytoscape. The output can be used for hypothesis generation and directing in vitro or further in silico work such as GRN construction. Availability and implementation TimiRGeN is available for download on Bioconductor (https://bioconductor.org/packages/TimiRGeN) and requires R v4.0.2 or newer and BiocManager v3.12 or newer. Supplementary information Supplementary data are available at Bioinformatics online. |
| وصف الملف: | application/pdf |
| تدمد: | 1367-4811 1367-4803 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b6434cd9eac68b3e2d7f37e8143b9a9b https://doi.org/10.1093/bioinformatics/btab377 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....b6434cd9eac68b3e2d7f37e8143b9a9b |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 13674811 13674803 |
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