Additional file 1. Example datasets: A qPCR dataset containing two example files derived from both, a single plate (SP) and a multiple plate (MP1, MP2) experiment conducted in our laboratory. Datasets are semi-colon-separated csv files exported from qPCRsoft 4.1 software and can be used as input for qRAT.

Additional file 1. Example datasets: A qPCR dataset containing two example files derived from both, a single plate (SP) and a multiple plate (MP1, MP2) experiment conducted in our laboratory. Datasets are semi-colon-separated csv files exported from qPCRsoft 4.1 software and can be used as input for qRAT.

Additional file 2. Output of qRAT filtering using single plate dataset: Table of detected outliers in the single plate dataset after applying a Cq standard deviation threshold of 0.5 on values of all target genes (gene of interest (GOI 1–7), reference gene (ref G)) in the treatment sample (T) and control sample (C). Respective replicate number is given in the rp.num column. xlsx file exported directly from qRAT.

Additional file 2. Output of qRAT filtering using single plate dataset: Table of detected outliers in the single plate dataset after applying a Cq standard deviation threshold of 0.5 on values of all target genes (gene of interest (GOI 1–7), reference gene (ref G)) in the treatment sample (T) and control sample (C). Respective replicate number is given in the rp.num column. xlsx file exported directly from qRAT.

Additional file 5. Output of qRAT $$\Delta$$ Δ Cq and $$\Delta \Delta$$ Δ Δ Cq methods using multiple plate dataset: Table of mean $$\Delta$$ Δ Cq, $$-\Delta$$ - Δ Cq and relative quantity (RQ) values, where values of the mutant samples (M) and wildtype samples (WT) are normalized to the reference gene and mean $$\Delta \Delta$$ Δ Δ Cq and fold change (FC) values, where M and WT samples are normalized to the reference gene and made relative to the calibrator WT C.

Additional file 5. Output of qRAT $$\Delta$$ Δ Cq and $$\Delta \Delta$$ Δ Δ Cq methods using multiple plate dataset: Table of mean $$\Delta$$ Δ Cq, $$-\Delta$$ - Δ Cq and relative quantity (RQ) values, where values of the mutant samples (M) and wildtype samples (WT) are normalized to the reference gene and mean $$\Delta \Delta$$ Δ Δ Cq and fold change (FC) values, where M and WT samples are normalized to the reference gene and made relative to the calibrator WT C.

Additional file 6. Output of qRAT $$\Delta$$ Δ Cq and $$\Delta \Delta$$ Δ Δ Cq methods using the SP dataset: Table of mean $$\Delta$$ Δ Cq, $$-\Delta$$ - Δ Cq and relative quantity (RQ) values, where values of the treatment sample (T) and control sample (C) are normalized to the reference gene and mean $$\Delta \Delta$$ Δ Δ Cq and fold change (FC) values, where T and C samples are normalized by both, the reference gene and the calibrator C.

Additional file 6. Output of qRAT $$\Delta$$ Δ Cq and $$\Delta \Delta$$ Δ Δ Cq methods using the SP dataset: Table of mean $$\Delta$$ Δ Cq, $$-\Delta$$ - Δ Cq and relative quantity (RQ) values, where values of the treatment sample (T) and control sample (C) are normalized to the reference gene and mean $$\Delta \Delta$$ Δ Δ Cq and fold change (FC) values, where T and C samples are normalized by both, the reference gene and the calibrator C.