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nebfield authored Mar 22, 2024
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# `pgscatalog-utils`

This convenience package bundles every PGS Catalog application.
This convenience package bundles every PGS Catalog application, including:

| Application | Description | Link |
|------------------------------|------------------------------------------------------------------------|-------------------------------------------------------------------------------------|
| `pgscatalog-download` | Download scoring files from the PGS Catalog in specific genome builds | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/download.html) |
| `pgscatalog-combine` | Combine multiple scoring files into a consistent structure | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/combine.html) |
| `pgscatalog-relabel` | Relabel values in a column based on values in a column in another file | [README](pgscatalog.core/README.md) |
| `pgscatalog-match` | Match structured scoring file to variants in target genomes | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/match.html) |
| `pgscatalog-matchmerge` | Merge variant match results, useful on larger datasets | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/match.html) |
| `pgscatalog-aggregate` | Aggregate calculated PGS split across multiple files | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/aggregate.html) |
| `pgscatalog-ancestry-adjust` | Adjust calculated PGS in the context of genetic ancestry | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/ancestry.html) |

Please note `v1.0.0` contains breaking changes: CLI applications have been renamed and the package has been significantly refactored.

See https://github.com/PGScatalog/pygscatalog for more details.

## Installation

```
$ pip install pgscatalog-utils
```

## Documentation

Documentation is available at https://pygscatalog.readthedocs.io/.

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