qDATA - an R application implementing a practical framework for analyzing quantitative real-time PCR data
Gene expression assays that are based on quantitative real-time PCR (qRT-PCR) method are still very popular, therefore, we developed qDATA, an open-source R-based bioinformatics application that offers a quick and intuitive analysis of raw cycle threshold (Ct) values. The application relies on a str...
Saved in:
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Taylor & Francis Group
2024-12-01
|
| Series: | BioTechniques |
| Subjects: | |
| Online Access: | https://www.tandfonline.com/doi/10.1080/07366205.2024.2442217 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832086431574523904 |
|---|---|
| author | Adrian Ionascu Alexandru Al. Ecovoiu Mariana Carmen Chifiriuc Attila Cristian Ratiu |
| author_facet | Adrian Ionascu Alexandru Al. Ecovoiu Mariana Carmen Chifiriuc Attila Cristian Ratiu |
| author_sort | Adrian Ionascu |
| collection | DOAJ |
| description | Gene expression assays that are based on quantitative real-time PCR (qRT-PCR) method are still very popular, therefore, we developed qDATA, an open-source R-based bioinformatics application that offers a quick and intuitive analysis of raw cycle threshold (Ct) values. The application relies on a straightforward data input consisting in Ct values and on other mandatory fields specifying the experimental and control groups. qDATA automatically performs descriptive statistics, normality and statistical testing on 2–ΔCt (or ΔCt) and 2–ΔΔCt terms calculated with Livak’s method. We also propose a qRT-PCR data analysis framework that depends on performing exhaustive ΔCt calculations within discrete biological replicates (BRs) and subsequently using the Livak formula for the complete sets of available data. These prerequisites arguably lead to an improved data analysis and statistical relevance. The efficiency of our computing approach was tested using input Ct values corresponding to immune related gene expression evaluated in experimental infection of Drosophila melanogaster and Apis mellifera workers. The presented results reveal that our working strategy is reliable and highlight the efficacy and performance of qDATA application. |
| format | Article |
| id | doaj-art-54ce3ffcaa5949fba4b0497f6accd0bf |
| institution | Kabale University |
| issn | 0736-6205 1940-9818 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | BioTechniques |
| spelling | doaj-art-54ce3ffcaa5949fba4b0497f6accd0bf2025-02-06T15:38:40ZengTaylor & Francis GroupBioTechniques0736-62051940-98182024-12-01761255957310.1080/07366205.2024.2442217qDATA - an R application implementing a practical framework for analyzing quantitative real-time PCR dataAdrian Ionascu0Alexandru Al. Ecovoiu1Mariana Carmen Chifiriuc2Attila Cristian Ratiu3Drosophila Laboratory, Faculty of Biology, University of Bucharest, 060101 Bucharest, RomaniaDrosophila Laboratory, Faculty of Biology, University of Bucharest, 060101 Bucharest, RomaniaDepartment of Botany and Microbiology, Faculty of Biology, University of Bucharest, 060101 BucharestDrosophila Laboratory, Faculty of Biology, University of Bucharest, 060101 Bucharest, RomaniaGene expression assays that are based on quantitative real-time PCR (qRT-PCR) method are still very popular, therefore, we developed qDATA, an open-source R-based bioinformatics application that offers a quick and intuitive analysis of raw cycle threshold (Ct) values. The application relies on a straightforward data input consisting in Ct values and on other mandatory fields specifying the experimental and control groups. qDATA automatically performs descriptive statistics, normality and statistical testing on 2–ΔCt (or ΔCt) and 2–ΔΔCt terms calculated with Livak’s method. We also propose a qRT-PCR data analysis framework that depends on performing exhaustive ΔCt calculations within discrete biological replicates (BRs) and subsequently using the Livak formula for the complete sets of available data. These prerequisites arguably lead to an improved data analysis and statistical relevance. The efficiency of our computing approach was tested using input Ct values corresponding to immune related gene expression evaluated in experimental infection of Drosophila melanogaster and Apis mellifera workers. The presented results reveal that our working strategy is reliable and highlight the efficacy and performance of qDATA application.https://www.tandfonline.com/doi/10.1080/07366205.2024.2442217Bioinformatics softwaredata analysisqRT-PCRR programmingstatistics |
| spellingShingle | Adrian Ionascu Alexandru Al. Ecovoiu Mariana Carmen Chifiriuc Attila Cristian Ratiu qDATA - an R application implementing a practical framework for analyzing quantitative real-time PCR data BioTechniques Bioinformatics software data analysis qRT-PCR R programming statistics |
| title | qDATA - an R application implementing a practical framework for analyzing quantitative real-time PCR data |
| title_full | qDATA - an R application implementing a practical framework for analyzing quantitative real-time PCR data |
| title_fullStr | qDATA - an R application implementing a practical framework for analyzing quantitative real-time PCR data |
| title_full_unstemmed | qDATA - an R application implementing a practical framework for analyzing quantitative real-time PCR data |
| title_short | qDATA - an R application implementing a practical framework for analyzing quantitative real-time PCR data |
| title_sort | qdata an r application implementing a practical framework for analyzing quantitative real time pcr data |
| topic | Bioinformatics software data analysis qRT-PCR R programming statistics |
| url | https://www.tandfonline.com/doi/10.1080/07366205.2024.2442217 |
| work_keys_str_mv | AT adrianionascu qdataanrapplicationimplementingapracticalframeworkforanalyzingquantitativerealtimepcrdata AT alexandrualecovoiu qdataanrapplicationimplementingapracticalframeworkforanalyzingquantitativerealtimepcrdata AT marianacarmenchifiriuc qdataanrapplicationimplementingapracticalframeworkforanalyzingquantitativerealtimepcrdata AT attilacristianratiu qdataanrapplicationimplementingapracticalframeworkforanalyzingquantitativerealtimepcrdata |