qLOOK: A Minimal Information System for Digital Storage and Reproducible Analysis of qPCR experiments
Fuente:
arXiv
Salvato in:
| Autore principale: | |
|---|---|
| Natura: | Preprint |
| Pubblicazione: |
2025
|
| Soggetti: | |
| Accesso online: | |
| Tags: |
Aggiungi Tag
Nessun Tag, puoi essere il primo ad aggiungerne!!
|
| _version_ | 1866917016506466304 |
|---|---|
| author | Castoldi, Mirco |
| author_facet | Castoldi, Mirco |
| contents | Objective: Quantitative real-time PCR is widely used for gene expression analysis, yet inconsistencies in data storage and reporting limit reproducibility. While MIQE guidelines define the minimal information required for publication, they do not specify structured digital storage formats compatible with long-term reanalysis. This work presents qLOOK (qPCR-LOg-boOK), a tool for standardized digital storage and reproducible analysis of qPCR experiments. Results: qLOOK is a modular R-based system that extracts data from Thermo Fisher/ABI .EDS files, formats it into a structured table (qLOOK_Data.xlsx), performs normalization and statistical analysis, and generates a log file (qLOOK_Summary.txt) recording reference genes, calibrators, and analytical parameters. All required R libraries are automatically installed and loaded, allowing researchers without coding experience to use the scripts. By preserving the qLOOK_Data table and the qLOOK_Summary log, users can reproduce or extend analyses without reprocessing raw files. While currently limited to .EDS files, the modular design allows adaptation to additional qPCR formats in the future. Besides providing an easy and transparent approach to analyze qPCR experiments, qLOOK also provides a minimal, standardized, and transparent solution for digital documentation, enhancing reproducibility, supporting long-term data stewardship, and facilitating integration into electronic laboratory notebooks or publication supplementary material. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2510_13520 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | qLOOK: A Minimal Information System for Digital Storage and Reproducible Analysis of qPCR experiments Castoldi, Mirco Quantitative Methods Objective: Quantitative real-time PCR is widely used for gene expression analysis, yet inconsistencies in data storage and reporting limit reproducibility. While MIQE guidelines define the minimal information required for publication, they do not specify structured digital storage formats compatible with long-term reanalysis. This work presents qLOOK (qPCR-LOg-boOK), a tool for standardized digital storage and reproducible analysis of qPCR experiments. Results: qLOOK is a modular R-based system that extracts data from Thermo Fisher/ABI .EDS files, formats it into a structured table (qLOOK_Data.xlsx), performs normalization and statistical analysis, and generates a log file (qLOOK_Summary.txt) recording reference genes, calibrators, and analytical parameters. All required R libraries are automatically installed and loaded, allowing researchers without coding experience to use the scripts. By preserving the qLOOK_Data table and the qLOOK_Summary log, users can reproduce or extend analyses without reprocessing raw files. While currently limited to .EDS files, the modular design allows adaptation to additional qPCR formats in the future. Besides providing an easy and transparent approach to analyze qPCR experiments, qLOOK also provides a minimal, standardized, and transparent solution for digital documentation, enhancing reproducibility, supporting long-term data stewardship, and facilitating integration into electronic laboratory notebooks or publication supplementary material. |
| title | qLOOK: A Minimal Information System for Digital Storage and Reproducible Analysis of qPCR experiments |
| topic | Quantitative Methods |
| url | https://arxiv.org/abs/2510.13520 |