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SCO2
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pnrobinson committed Jan 6, 2024
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Expand Up @@ -27,6 +27,7 @@ were mainly created using the Python library [pyphetools](https://github.com/mon
| [PTPN11](https://github.com/monarch-initiative/phenopacket-store/tree/main/notebooks/PTPN11){:target="_blank"} | 42 phenopackets; [LEOPARD syndrome 1](https://omim.org/entry/151100){:target="_blank"}, [Metachondromatosis](https://omim.org/entry/156250){:target="_blank"}, [Noonan syndrome 1](https://omim.org/entry/163950){:target="_blank"} |
| [RPGRIP1]() | 229 phenopackets; [Cone-rod dystrophy 13](https://omim.org/entry/608194){:target="_blank"}, [Leber congenital amaurosis 6](https://omim.org/entry/613826){:target="_blank"} |
| [SCN2A](https://github.com/monarch-initiative/phenopacket-store/blob/main/notebooks/SCN2A/Crawford_SCN2A.ipynb){:target="_blank"} | 394 phenopackets; [Developmental and epileptic encephalopathy 11](https://omim.org/entry/613721){:target="_blank"}, [Seizures, benign familial infantile, 3](https://omim.org/entry/607745){:target="_blank"} |
| [SCO2](https://github.com/monarch-initiative/phenopacket-store/blob/main/notebooks/SCO2){:target="_blank"} | 36 phenopackets |
| [SETD2](https://github.com/monarch-initiative/phenopacket-store/tree/main/notebooks/SETD2){:target="_blank"} | 29 phenopackets; [Rabin-Pappas syndrome](https://omim.org/entry/620155){:target="_blank"}, [Rabin-Pappas syndrome](https://omim.org/entry/620155){:target="_blank"}, [Intellectual developmental disorder, autosomal dominant 70](https://omim.org/entry/620157){:target="_blank"}, [Luscan-Lumish syndrome](https://omim.org/entry/616831){:target="_blank"} |
| [SLC45A2](https://github.com/monarch-initiative/phenopacket-store/blob/main/notebooks/SLC45A2/SLC45A2_Moreno2022PMID_36553465.ipynb){:target="_blank"} | 30 phenopackets; [Albinism, oculocutaneous, type IV](https://omim.org/entry/606574){:target="_blank"} |
| [SMARCB1](https://github.com/monarch-initiative/phenopacket-store/tree/main/notebooks/SMARCB1){:target="_blank"} | 17 phenopackets; [Coffin-Siris syndrome 3](https://omim.org/entry/614608){:target="_blank"}, [Rhabdoid tumor predisposition syndrome-1](https://omim.org/entry/609322){:target="_blank"} |
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15 changes: 15 additions & 0 deletions docs/developers.md
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phenopacket-store has a small python package that facilitates exporting all available phenopackets. See
[GetPhenopackets](https://github.com/monarch-initiative/phenopacket-store/blob/main/GetPhenopackets.ipynb){:target="_blank"} for details.

## Running the notebooks locally

There are several ways of doing this. We prefer the following method. First, create a virtual environment (shown here as my_venv, but choose any name you like) and activiate it. Then, install pyphetools and some packages required to run Jupyter notebooks. Use the ipykernel package to enable the use of the virtual environment in a notebook. Finally, open or create a notebook and choose the kernel

```
python3 -m venv my_venv
source my_venv/bin/activate
pip install --upgrade pip
pip install pyphetools jupyter ipykernel
python -m ipykernel install --name my_venv --user
jupyter-notebook
```

Make sure to choose the kernel called 'my_venv' in the notebook.

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