qpycr 1.2.0

qPCR Analysis with Recursive PCR Model for robust quantification

qPyCR

qPyCR is a notebook‑first qPCR analysis workflow that implements global data fitting using a recursive PCR model.
It accepts raw, unadjusted CSV data and produces Cq, Seed, Max, KD, and Max/KD outputs.

Example Outputs

Recommended Use

This project is designed to run as a Jupyter notebook. Choose one:

Option 1: Binder (no install)
Click the badge above to launch the notebook in your browser — no setup required.
Use ../examples/test_data.csv as the input path. Outputs are saved to notebooks/outputs/ — download before closing the session.

Option 2: Google Colab
Upload the notebook from notebooks/ to Google Colab.

Option 3: Local Jupyter
Clone the repo and run pip install -r requirements.txt, then open the notebook in notebooks/.

Running the Analysis

1. Run cells in order (Cell‑0 → Cell‑11).
2. Use -e for evaluation outputs or -d for full debug outputs.
3. In some environments, 'Run All' may hang after providing input selections; you can click 'Run' repeatedly to step through the remaining cells.

Inputs

CSV format with a Cycle column and one or more sample columns containing qPCR data for each cycle.

Outputs

Cell‑11 generates the final report:

• *_qPCR_Analysis_Outputs_*.csv

Evaluation/Debug modes add intermediate CSVs and plots in outputs/.

Folder Structure

qPyCR/
├── notebooks/      # Jupyter notebooks (run these)
├── cells/          # Individual cell scripts (for inspection/modification)
├── examples/       # Example datasets
├── images/         # Images for Readme
└── requirements.txt

Scientific Background

This software implements and extends the use of the recursive PCR model described in:

Carr AC, Moore SD (2012) Robust quantification of polymerase chain reactions using global fitting.
PLoS ONE 7(5): e37640. https://doi.org/10.1371/journal.pone.0037640

Is also generates the max/KD ratio for reaction performance evaluation described in:

Moore SD (2025) Thermal-bias PCR: generation of amplicon libraries without degenerate primer interference. Peer J. Oct 24:13:e20241. https://doi.org/10.7717/peerj.20241

Citation

Manuscript pending. If you use this software, please cite this repository for now:

• qPyCR (repository): https://github.com/sdmoore-labs/qpycr

We will update this section with the formal paper citation once available.

License

MIT (see LICENSE).