Install all dependencies with Anaconda or Miniconda
conda env create -f htqpcr_env.yml
Activate environment
conda activate htqpcr_env
Start Jupyter Notebook
jupyter-notebook
Open and Run the notebooks
- htqpcr_validation_figures.ipynb
- bm_rawdata_annotation.ipynb
Usage examples for the biomarkdataparser.py script can be found in the notebooks, you can use the biomarkdataparser.py script in the terminal or in the notebooks.
Command line options
| Command line option [Input] | Abbreviation | Description | Default |
|---|---|---|---|
| --help | -h | Display help message | - |
| --inputfile [str] | -i | Path to csv file (BM qPCR data export) | - |
| --outdir [str] | -o | Path/Name of the output directory | current directory |
| --validation | -v | Create labels for the annotation of raw Cq data image (examples in bm_rawdata_annotation.ipynb) | - |
| --replicates [assay, sample, None] | -r | Technical replicates were made with assays (primer) or samples | assay |
| --number [int] | -n | Number of technical replicates measured | - |
| --typefilter [str ...] | -t | Filter sample types, e.g. NTC, Unknown, Standard | - |
| --samplefilter [str ...] | -s | Filter sample names* | - |
| --removesamples [str ...] | -x | Remove samples that have the input string(s) in the sample name | - |
| --standardcurve | -c | Draw plot with standard curves | - |
| --gformat [eps, png, jpg] | -f | Choose an output format for the figures | png |
| --assay_species [str] | -a | Path to csv file (no header) with first column: assay name* and the second column: the annotation (species) to display in the results (example: labelfiles/assay_species.csv) | - |
| --labelfile [str] | -l | Path to csv file (with header) with figure labels as columns (x, y) example: labelsfiles/cheese_labels.csv | - |
| --title [str] | Optional plot title | - | |
| --transpose | Flip x and y axes in heatmap (does not affect labelfiles) | - | |
| --italic [x, y ...] | Select axis with species names (italic label), (example with partial italic labels: labelfiles/inoculated_cheese_labels.csv | - | |
| --figsize [str ...] | Figure size in inches, format: width height | - | |
| --legendposition [str ...] | Adjust legend position, format: x y or x y width height | - | |
| --deltact [str ...] | Delta Cq of samples measured with and without pre-amplification, give sample name strings that identifies the two groups, format: preamp id no preamp id (e.g. "nopreamp" "preamp" ) | - | |
| --preamp [str ...] | Include qualitative pre-amplification data in results. First element preamp id, second element no preamp id | - | |
| --datatoplot [cq, copy, None] | Select data to display in the plots | - | |
| --color | Use color in plots | - | |
| --rawdata | Create plots with raw data (show replicates separately) | - | |
| --reverse | Sort sample names in reverse order | - | |
| --outfile [str] | filename for the output figure | - | |
| --axeslabels | Display axes labels in heatmaps | - |
*Make sure you use the exact same sample names and assay names as in the input csv file (Fluidigm Real-Time PCR Analysis software export file)