Table 1 Comparison of principal features among currently available web-based applications for qPCR data analysis
Software | Accepted input formats | qPCR data normalization | Languages for web-based use | Support for more than one housekeeping region | Number of replicates allowed per sample | Variables allowed to be compared per run | Online visualization and customized download of the results | Additional functions | References |
|---|---|---|---|---|---|---|---|---|---|
qRAT | .txt, .csv | Livak | back-end: R, front-end: HTML (free) | Yes. Arithmetic mean with no stability evaluation | Unlimited once identical for all samples | Only one variable | Yes | Filter by replicate variability and range of Ct, allow to download the normalized data and tabular results of analyses | [10] |
Auto-qPCR | .txt, .csv | Livak | back-end: Python, front-end: HTML (free) | Yes. Arithmetic mean with no stability evaluation | Unlimited once identical for all samples | Up to two variables | No | Filter by replicate variability, allow to set the order of targets and samples, allow to download the normalized data | [11] |
PIPE-T | .txt | Livak | back-end: R, front-end: HTML (inside Galaxy) | Yes. Arithmetic mean after stability evaluation (geNorm) | Unlimited, not required to be identical for all samples | Only one variable | No | Data imputation (cubic spline) | [12] |
Shinycurves | .xls, .xlsx, .csv | Not specified | back-end: R, front-end: HTML (free) | No | Unlimited once identical for all samples | No variables allowed | Yes | Classification of samples as positive or negative (COVID-19 diagnosis), allow to download the normalized data and tabular results of analyses | [13] |
ΔXpress | .xls, .xlsx, .txt, .csv | Livak | back-end: R, front-end: HTML (free) | Yes. Arithmetic mean after stability evaluation (Normfinder) or user-defined | Unlimited, not required to be identical for all samples | Unlimited variables (allowed for .xlsx or .xls files) | Yes | Generation of Volcano plots, analysis of differentially correlated genes,allow to download the normalized data and tabular results of analyses, annotate participating genes (Ensembl, NCBI) | This study |