Rummel, Teresa and Sakellaridi, Lygeri and Erhard, Florian (2023) grandR: a comprehensive package for nucleotide conversion RNA-seq data analysis. NATURE COMMUNICATIONS, 14 (1): 3559. ISSN , 2041-1723
Full text not available from this repository. (Request a copy)Abstract
Metabolic labeling of RNA is a powerful technique for studying the temporal dynamics of gene expression. Nucleotide conversion approaches greatly facilitate the generation of data but introduce challenges for their analysis. Here we present grandR, a comprehensive package for quality control, differential gene expression analysis, kinetic modeling, and visualization of such data. We compare several existing methods for inference of RNA synthesis rates and half-lives using progressive labeling time courses. We demonstrate the need for recalibration of effective labeling times and introduce a Bayesian approach to study the temporal dynamics of RNA using snapshot experiments.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | DYNAMICS; REVEALS; KEY; |
| Subjects: | 000 Computer science, information & general works > 004 Computer science |
| Divisions: | Languages and Literatures > Institut für Information und Medien, Sprache und Kultur (I:IMSK) > Lehrstuhl für Medieninformatik (Prof. Dr. Christian Wolff) Informatics and Data Science > Lehrstuhl für Medieninformatik (Prof. Dr. Christian Wolff) |
| Depositing User: | Dr. Gernot Deinzer |
| Date Deposited: | 12 Mar 2024 11:08 |
| Last Modified: | 12 Mar 2024 11:08 |
| URI: | https://pred.uni-regensburg.de/id/eprint/59737 |
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