Data Analysis Hands-On for PXD04621

Data Analysis Hands-On for PXD04621#

In the GitHub workspace, we will use the base conda environment which you can activate with the following command:

conda activate base

Results data from QuantMS#

Are stored in this repository in the data/PXD04621/processed/ folder.

Required packages#

are mainly:

  • acore for some analytical functions (developed by DSP and MoNA at DTU)

  • vuegen for the report generation (developed by DSP and MoNA at DTU)

  • vuecore for the visualization (developed by DSP and MoNA at DTU)

The packages should have been installed automatically in the GitHub codespace. In case you need to manually install them, you can use the following command:

pip install acore 'numpy<2.1.0' nbformat vuecore vuegen

Open and run the notebook#

2_data_analysis.ipynb is a Jupyter notebook that will guide you through the analysis of the data.

We will go through it an discuss it together in the class.

VueGen Report#

We wrote some files in the notebook to data/PXD04621/report folder.

You can use the following command to generate a VueGen report from them:

vuegen -dir data/PXD040621/report

This will create a streamlit app in the streamlit_report folder. Check the options availble for the command line tool vuegen with the following command:

vuegen -h

Create and start the streamlit app with the following command:

vuegen -dir data/PXD040621/report -st_autorun

VueGen GUI (app)#

We also ship a GUI for VueGen. Check out our tutorials on youtube.

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