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🎨 update enrichmentplot example (#24)
* 🎨 reoder example: from less to more functional enriched groups * 🎨 try rendering plotly figure in docs correctly using figurewidget see: https://plotly.com/python/figurewidget/ * 🐛 update nb metadata * 🐛 increase global execution timeout to 2mins * 🐛 exclude latest version * 🐛 check lower version * 🐛 FeatureWidget not available per default? * 🎨 improve layout and one plot * ⏪ only exclude latest gseapy version * 🎨 typos * 🐛 FigureWidget did not work, try Figure * 🐛 try show method, and use basic example from plotly Also started failing on mystnb docs: https://myst-nb.readthedocs.io/en/latest/render/interactive.html#plotly * 🐛 try to downgrad plotly * 🐛 fix installation * 🎨 cleanup notebook * 🎨 remove dependency again * 🎨 more explanations, less * 🎨 add explicit target and link to processing notebook reference: https://docs.readthedocs.com/platform/stable/guides/cross-referencing-with-sphinx.html * 🎨 update link * 🚧 create processing function for uniprot results - needs to be further tested and evaluated * 🎨 remove unused variable * 🎨 better plots (and one typo fix)
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docs/api_examples/Download_PRIDE_data.py

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# This notebook shows how `acore` can be used to download data from
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# the Proteomics Identifications Database - PRIDE -
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# ([ebi.ac.uk/pride/](https://www.ebi.ac.uk/pride/))
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# and parse the data to be used in the analytics core.
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# and parse the data to be used in the analytics core
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# and quickly formated to start analyzing them with the functionality in the analytics core.
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#
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# > based on CKG recipe: [Download PRIDE Data](https://ckg.readthedocs.io/en/latest/notebooks/recipes/Download_PRIDE_data.html)
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# %% [markdown]
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# ## Parameters
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# Specify the PRIDE identifier and file to be downloaded
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# - and where to store intermediate files.
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# and where to store intermediate files.
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# %% tags=["parameters"]
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pxd_id: str = "PXD008541" # PRIDE identifier

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