https://github.com/cellgeni/cloupe
Cloupe reader
https://github.com/cellgeni/cloupe
10x-genomics loupe reader single-cell
Last synced: 5 months ago
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Cloupe reader
- Host: GitHub
- URL: https://github.com/cellgeni/cloupe
- Owner: cellgeni
- License: agpl-3.0
- Created: 2024-09-28T17:38:35.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-01-13T00:12:41.000Z (over 1 year ago)
- Last Synced: 2025-09-09T23:51:33.768Z (9 months ago)
- Topics: 10x-genomics, loupe, reader, single-cell
- Language: Python
- Homepage:
- Size: 209 KB
- Stars: 1
- Watchers: 2
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# cloupe
Loupe Browser is a powerful visualization software that provides the intuitive functionality you need to explore and analyze 10x Genomics Chromium and Visium data. This is a PoC parser to read CLOUPE files using python.
# Install
```shell
pip install git+https://github.com/cellgeni/cloupe.git
```
# Run
```python
from cloupe import Cloupe
# parse file
c = Cloupe("/path/to/file.cloupe")
# extract barcodes, features and projections to CSVs
c.to_csv(outdir="/path/to/out")
# create anndata with the same name as input file but `.h5ad` extension
c.to_anndata()
```
### Command line
Export barcodes, features and projections to CSV in current folder
```shell
cloupe --cloupe /path/to/file.cloupe --csv
```