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README.md
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@@ -10,7 +10,7 @@ short_description: Probabilistic modeling and analysis of single-cell omics dat
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# **scvi-tools**
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Welcome to the **scvi-tools** organization. We provide state-of-the-art probabilistic models tailored for analyzing single-cell omics data
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These models provide a consistent API making it easy to integrate it into your current analysis pipeline. **scvi-tools** is part of [scverse](https://scverse.org).
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This is an open science initiative, please contribute your own models to allow the single-cell community to leverage your reference datasets. Learn how to upload your model in our [HubModel tutorials](https://docs.scvi-tools.org/en/stable/tutorials/notebooks/hub/scvi_hub_upload_and_large_files.html).
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### **Current HubModels**
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- **[scVI](https://docs.scvi-tools.org/en/stable/user_guide/models/scvi.html)**:
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- A variational autoencoder for dimensionality reduction, batch correction, and clustering.
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- Ideal for processing single-cell RNA-seq data.
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- **[scANVI](https://docs.scvi-tools.org/en/stable/user_guide/models/scanvi.html)**:
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- A semi-supervised model designed for label prediction, especially in cases of partially labeled data.
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- **[totalVI](https://docs.scvi-tools.org/en/stable/user_guide/models/totalvi.html)**:
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- A multi-modal model for joint analysis of RNA and protein data, additionally allowing imputation of missing protein data.
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- **[MultiVI](https://docs.scvi-tools.org/en/stable/user_guide/models/multivi.html)**:
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- A multi-modal model for joint analysis of RNA, ATAC and protein data, enabling integrative insights from diverse omics data.
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- **[DestVI](https://docs.scvi-tools.org/en/stable/user_guide/models/destvi.html)**:
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- A deconvolution model for prediction of single-cell profiles given subcellular spatial transcriptomics data. We provide here pre-trained single cell models (CondSCVI).
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- **[Stereoscope](https://docs.scvi-tools.org/en/stable/user_guide/models/stereoscope.html)**:
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These models have been applied to a wide array of biological questions, such as:
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- Batch correction across experiments.
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- Identification of rare cell populations.
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- Multi-modal integration of single-cell RNA,
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- Differential expression and abundance analysis in disease contexts.
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For hands-on examples, refer to our **[tutorials](https://docs.scvi-tools.org/en/stable/tutorials/index.html)**.
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## **Publications**
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- **[Original scvi-tools Paper](https://www.nature.com/articles/s41587-021-01206-w)**:
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- Published in *Nature Biotechnology*, this paper introduces the foundational principles
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- **[scvi-hub Preprint](https://www.biorxiv.org/content/10.1101/2024.03.01.582887v1)**:
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- This manuscript showcases real-world applications of scvi-hub in diverse biological contexts and provides building blocks
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- to apply these models in your own research
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## **How to Get Started**
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1. Visit our **[official documentation](https://docs.scvi-tools.org)** to get started with installation and explore our API.
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2. Follow our **[tutorials](https://docs.scvi-tools.org/en/stable/tutorials/index.html)** for step-by-step guides on using scvi-tools effectively.
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3. Dive into our **[models](https://docs.scvi-tools.org/en/stable/user_guide/index.html)** to see how
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---
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# **scvi-tools**
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Welcome to the **scvi-tools** organization. We provide state-of-the-art probabilistic models tailored for analyzing single-cell omics data. Those enable researchers to gain biological insights with scalable algorithms.
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These models provide a consistent API making it easy to integrate it into your current analysis pipeline. **scvi-tools** is part of [scverse](https://scverse.org).
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This is an open science initiative, please contribute your own models to allow the single-cell community to leverage your reference datasets. Learn how to upload your model in our [HubModel tutorials](https://docs.scvi-tools.org/en/stable/tutorials/notebooks/hub/scvi_hub_upload_and_large_files.html).
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### **Current HubModels**
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- **[scVI](https://docs.scvi-tools.org/en/stable/user_guide/models/scvi.html)**:
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- A variational autoencoder for dimensionality reduction, batch correction, and clustering.
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- **[scANVI](https://docs.scvi-tools.org/en/stable/user_guide/models/scanvi.html)**:
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- A semi-supervised model designed for label prediction, especially in cases of partially labeled data.
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- **[totalVI](https://docs.scvi-tools.org/en/stable/user_guide/models/totalvi.html)**:
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- A multi-modal model for joint analysis of RNA and protein data, additionally allowing imputation of missing protein data.
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<!---
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- **[MultiVI](https://docs.scvi-tools.org/en/stable/user_guide/models/multivi.html)**:
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- A multi-modal model for joint analysis of RNA, ATAC and protein data, enabling integrative insights from diverse omics data.
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-->
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- **[DestVI](https://docs.scvi-tools.org/en/stable/user_guide/models/destvi.html)**:
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- A deconvolution model for prediction of single-cell profiles given subcellular spatial transcriptomics data. We provide here pre-trained single cell models (CondSCVI).
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- **[Stereoscope](https://docs.scvi-tools.org/en/stable/user_guide/models/stereoscope.html)**:
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These models have been applied to a wide array of biological questions, such as:
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- Batch correction across experiments.
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- Identification of rare cell populations.
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- Multi-modal integration of single-cell RNA, and protein data.
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- Differential expression and abundance analysis in disease contexts.
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For hands-on examples, refer to our **[tutorials](https://docs.scvi-tools.org/en/stable/tutorials/index.html)**.
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## **Publications**
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- **[Original scvi-tools Paper](https://www.nature.com/articles/s41587-021-01206-w)**:
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- Published in *Nature Biotechnology*, this paper introduces the foundational principles of scvi-tools.
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- **[scvi-hub Preprint](https://www.biorxiv.org/content/10.1101/2024.03.01.582887v1)**:
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- This manuscript showcases real-world applications of scvi-hub in diverse biological contexts and provides building blocks
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- to apply these models in your own research
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## **How to Get Started**
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1. Visit our **[official documentation](https://docs.scvi-tools.org)** to get started with installation and explore our API.
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2. Follow our **[tutorials](https://docs.scvi-tools.org/en/stable/tutorials/index.html)** for step-by-step guides on using scvi-tools effectively.
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3. Dive into our **[models](https://docs.scvi-tools.org/en/stable/user_guide/index.html)** to see how to apply them to your single-cell analysis.
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