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psmyth94 authored Nov 18, 2024
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<p align="center">
$${\Huge{\textbf{\textsf{\color{#2E8B57}Bio\color{#4682B4}fit}}}}$$
$${\Huge{\textbf{\textsf{\color{#2E8B57}Bio\color{red}fit}}}}$$
<br/>
<br/>
</p>
<p align="center">
<a href="https://github.com/psmyth94/biosets/actions/workflows/ci_cd_pipeline.yml?query=branch%3Amain"><img alt="Build" src="https://github.com/psmyth94/biosets/actions/workflows/ci_cd_pipeline.yml/badge.svg?branch=main"></a>
<a href="https://github.com/psmyth94/biosets/blob/main/LICENSE"><img alt="GitHub" src="https://img.shields.io/github/license/psmyth94/biosets.svg?color=blue"></a>
<a href="https://github.com/psmyth94/biosets/tree/main/docs"><img alt="Documentation" src="https://img.shields.io/website/http/github/psmyth94/biosets/tree/main/docs.svg?down_color=red&down_message=offline&up_message=online"></a>
<a href="https://github.com/psmyth94/biosets/releases"><img alt="GitHub release" src="https://img.shields.io/github/release/psmyth94/biosets.svg"></a>
<a href="https://github.com/psmyth94/biofit/actions/workflows/ci_cd_pipeline.yml?query=branch%3Amain"><img alt="Build" src="https://github.com/psmyth94/biofit/actions/workflows/ci_cd_pipeline.yml/badge.svg?branch=main"></a>
<a href="https://github.com/psmyth94/biofit/blob/main/LICENSE"><img alt="GitHub" src="https://img.shields.io/github/license/psmyth94/biofit.svg?color=blue"></a>
<a href="https://github.com/psmyth94/biofit/tree/main/docs"><img alt="Documentation" src="https://img.shields.io/website/http/github/psmyth94/biofit/tree/main/docs.svg?down_color=red&down_message=offline&up_message=online"></a>
<a href="https://github.com/psmyth94/biofit/releases"><img alt="GitHub release" src="https://img.shields.io/github/release/psmyth94/biofit.svg"></a>
<a href="CODE_OF_CONDUCT.md"><img alt="Contributor Covenant" src="https://img.shields.io/badge/Contributor%20Covenant-2.0-4baaaa.svg"></a>
<a href="https://zenodo.org/records/14028772"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.14028772.svg" alt="DOI"></a>
</p>
Expand All @@ -29,7 +29,7 @@ and configurable processing pipelines. Here are some of the main features of Bio
- [CSR (SciPy)](https://github.com/scipy/scipy)
- [Arrow](https://github.com/apache/arrow)
- 🤗 [Datasets](https://github.com/huggingface/datasets)
- [Biosets](https://github.com/psmyth94/biosets)
- [biofit](https://github.com/psmyth94/biofit)
- **Machine Learning Models:** Supports a wide range of machine learning models, including:
- [Scikit-learn](https://github.com/scikit-learn/scikit-learn)
- [Random Forest](https://scikit-learn.org/stable/modules/generated/sklearn.ensemble.RandomForestClassifier.html)
Expand Down Expand Up @@ -98,11 +98,11 @@ print(preprocessor)
preprocessed_data = preprocessor.fit_transform(dataset)
```

Biofit is made with Biosets in mind. You can pass the loaded dataset instead of a string
Biofit is made with biofit in mind. You can pass the loaded dataset instead of a string
to load the preprocessors:

```python
from biosets import load_dataset
from biofit import load_dataset

dataset = load_dataset("csv", data_files="my_file.csv", experiment_type="snp")

Expand All @@ -120,7 +120,7 @@ Biofit allows you to create custom preprocessing pipelines using the
`sklearn` and Biofit in a single operation:

```python
from biosets import load_dataset
from biofit import load_dataset
from biofit.preprocessing import LogTransformer, PreprocessorPipeline
from sklearn.preprocessing import StandardScaler

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