https://github.com/jhsmit/hdxms-datasets
Download and parse curated HDX-MS datasets
https://github.com/jhsmit/hdxms-datasets
Last synced: about 1 month ago
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Download and parse curated HDX-MS datasets
- Host: GitHub
- URL: https://github.com/jhsmit/hdxms-datasets
- Owner: Jhsmit
- License: mit
- Created: 2022-10-25T14:23:20.000Z (over 2 years ago)
- Default Branch: master
- Last Pushed: 2025-01-21T09:56:28.000Z (4 months ago)
- Last Synced: 2025-03-28T17:48:05.376Z (about 2 months ago)
- Language: Python
- Homepage: https://jhsmit.github.io/hdxms-datasets/
- Size: 1.15 MB
- Stars: 2
- Watchers: 2
- Forks: 0
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.rst
- License: LICENSE
- Authors: AUTHORS.rst
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README
# HDXMS Datasets
* Free software: MIT license
### Installation
```bash
$ pip install hdxms-datasets
```
### HDX-MS database
Currently a beta test database is set up at:
https://github.com/Jhsmit/HDX-MS-datasets
### Example code
```python
from pathlib import Path
from hdxms_datasets import DataVault
# local path the download datasets to
cache_dir = Path('.cache')
# create a vault with local cache dir, set `remote_url` to connect to a different database
vault = DataVault(cache_dir=cache_dir)
# Download a specific HDX dataset
vault.fetch_dataset("20221007_1530_SecA_Krishnamurthy")
# Load the dataset
ds = vault.load_dataset("20221007_1530_SecA_Krishnamurthy")
# Load the FD control of the first 'state' in the dataset.
fd_control = ds.load_peptides(0, "FD_control")
# Load the corresponding experimental peptides.
peptides = ds.load_peptides(0, "experiment")
```