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)