Usage

Jupyter Notebook interface

The first step is to use the buttons to upload the files into the notebook (or generate the template).

  1. Upload datafile. This is always the first thing to do when you first launch the notebook. Use the “Upload datafile” button to select the data file. This will enable the other upload buttons.

  2. Uplaod Database. Use this button to upload the database file into the notebook.

  3. Generate Template Next, if needed, click the “Generate Template” button to create the Template in the folder containing the notebook file. Fill out the file with the experiment’s metadata

  4. Uplaod Template Use this button to upload the template into the notebook.

Now that the different input files are loaded, you can choose if the means should be calculated for the run by clicking or not on the mean export checkbox. Once this is done, fill out the run name (to name the end folder), the dilution factor and the concentration in standard molecule (if calibration is external). Once this is done, press the “Calculate” button to generate the results file. To visualize the data using the plotting module, finish by choosing the plots you want from the multiple selection list, and click the “Make plots” button.

Command Line Interface

To process your data, type in a terminal:

nmrquant [command line options]

Here after the available options with their full names are enumerated and detailed.

usage: nmrquant [-h] [-d DATABASE] [-F DILUTION_FACTOR] [-t TEMPLATE]
                [-k MAKE_TEMPLATE] [-f FORMAT] [-b {individual,meaned}]
                [-l {individual,meaned}] [-m] [-c TSP_CONCENTRATION]
                [-e EXPORT] [-v]
                datafile

Positional Arguments

datafile

Path to data file to process

Named Arguments

-d, --database

Path to proton database

-F, --dilution_factor

Dilution factor used to calculate concentrations

Default: 1.11

-t, --template

Path to template file.

-k, --make_template

Input path to export template to

-f, --format

Choose a format for the plots. Choices: svg, png, jpeg

Default: “svg”

-b, --barplot

Possible choices: individual, meaned

Choose histogram to build. Enter “individual” or “meaned”

-l, --lineplot

Possible choices: individual, meaned

Choose lineplot to build. Enter “individual” or “meaned”

-m, --mean

Add if means and stds should be calculated on replicates

Default: False

-c, --tsp_concentration

Add tsp concentration if calibration is external

-e, --export

Name for exported file

-v, --verbose

Add option for debug mode

Default: False

NmrQuant proceeds automatically to the data processing and displays progress and important messages in the standard output.