Metadata-Version: 2.1
Name: scvi
Version: 0.6.6
Summary: Single-cell Variational Inference
Home-page: https://github.com/YosefLab/scVI
Author: Romain Lopez, Jeffrey Regier, Maxime Langevin, Edouard Mehlman, Yining Liu, Achille Nazaret, Gabriel Misrachi, Oscar Clivio, Pierre Boyeau, Adam Gayoso
Author-email: romain_lopez@berkeley.edu
License: MIT license
Description: ========================================
        scVI - Single cell Variational Inference
        ========================================
        
        |Stars| |PyPI| |BioConda| |Docs| |Build Status| |Coverage| |Code Style| |Downloads|
        
        .. |Stars| image:: https://img.shields.io/github/stars/YosefLab/scVI?logo=GitHub&color=yellow
           :target: https://github.com/YosefLab/scVI/stargazers
        .. |PyPI| image:: https://img.shields.io/pypi/v/scVI.svg
            :target: https://pypi.org/project/scvi
        .. |BioConda| image:: https://img.shields.io/conda/vn/bioconda/scVI
           :target: https://bioconda.github.io/recipes/scvi/README.html
        .. |Docs| image:: https://readthedocs.org/projects/scvi/badge/?version=latest
            :target: https://scvi.readthedocs.io/en/stable/?badge=stable
            :alt: Documentation Status
        .. |Build Status| image:: https://travis-ci.org/YosefLab/scVI.svg?branch=master
            :target: https://travis-ci.org/YosefLab/scVI
        .. |Coverage| image:: https://codecov.io/gh/YosefLab/scVI/branch/master/graph/badge.svg
            :target: https://codecov.io/gh/YosefLab/scVI
        .. |Code Style| image:: https://img.shields.io/badge/code%20style-black-000000.svg
            :target: https://github.com/python/black
        .. |Downloads| image:: https://pepy.tech/badge/scvi
           :target: https://pepy.tech/project/scvi
        
        scVI is a package for end-to-end analysis of single-cell omics data. The package is composed of several deep generative models for omics data analysis, namely:
        
        * scVI_ for analysis of single-cell RNA-seq data, as well as its improved differential expression framework_
        * scANVI_ for cell annotation of scRNA-seq data using semi-labeled examples
        * totalVI_ for analysis of CITE-seq data
        * gimVI_ for imputation of missing genes in spatial transcriptomics from scRNA-seq data
        * AutoZI_ for assessing gene-specific levels of zero-inflation in scRNA-seq data
        * LDVAE_ for an interpretable linear factor model version of scVI
        
        Tutorials and API reference are available in the documentation_.
        Please use the issues here to discuss usage, or submit bug reports.
        If you'd like to contribute, please check out our `contributing guide`_.
        If you find a model useful for your research, please consider citing the corresponding publication (linked above).
        
        .. _documentation: https://scvi.readthedocs.io
        .. _`contributing guide`: https://scvi.readthedocs.io/en/stable/contributing.html
        .. _scVI: https://rdcu.be/bdHYQ
        .. _scANVI: https://www.biorxiv.org/content/biorxiv/early/2019/01/29/532895.full.pdf
        .. _totalVI: https://www.biorxiv.org/content/10.1101/2020.05.08.083337v1.full.pdf
        .. _AutoZI: https://www.biorxiv.org/content/biorxiv/early/2019/10/10/794875.full.pdf
        .. _LDVAE: https://www.biorxiv.org/content/10.1101/737601v1.full.pdf
        .. _gimVI: https://arxiv.org/pdf/1905.02269.pdf
        .. _framework: https://www.biorxiv.org/content/biorxiv/early/2019/10/04/794289.full.pdf
        
        
        
        =======
        History
        =======
        0.6.6 (2020-7-08)
        -----------------
        * add tqdm to within cluster DE genes `@adam`_
        * restore tqdm to use simple bar instead of ipywidget `@adam`_
        * move to numpydoc for doctstrings `@adam`_
        * update issues templates `@adam`_
        * Poisson variable gene selection `@valentine-svensson`_
        * BrainSmallDataset set defualt save_path_10X `@gokcen-eraslan`_
        * train_size must be float between 0.0 and 1.0 `@galen`_
        * bump dependency versions `@galen`_
        * remove reproducibility notebook `@galen`_
        * fix scanVI dataloading `@pierre`_
        
        0.6.5 (2020-5-10)
        ------------------
        * updates to totalVI posterior functions and notebooks `@adam`_
        * update seurat v3 HVG selection now using skmisc loess  `@adam`_
        
        0.6.4 (2020-4-14)
        ------------------
        * add back Python 3.6 support `@adam`_
        * get_sample_scale() allows gene selection `@valentine-svensson`_
        * bug fix to the dataset to anndata method with how cell measurements are stored `@adam`_
        * fix requirements `@adam`_
        
        0.6.3 (2020-4-01)
        ------------------
        * bug in version for Louvian in setup.py `@adam`_
        
        0.6.2 (2020-4-01)
        ------------------
        * update highly variable gene selection to handle sparse matrices `@adam`_
        * update DE docstrings `@pierre`_
        * improve posterior save load to also handle subclasses `@pierre`_
        * Create NB and ZINB distributions with torch and refactor code accordingly `@pierre`_
        * typos in autozivae `@achille`_
        * bug in csc sparse matrices in anndata data loader `@adam`_
        
        0.6.1 (2020-3-13)
        ------------------
        * handles gene and cell attributes with the same name `@han-yuan`_
        * fixes anndata overwriting when loading `@adam`_, `@pierre`_
        * formatting in basic tutorial `@adam`_
        
        0.6.0 (2020-2-28)
        ------------------
        * updates on TotalVI and LDVAE `@adam`_
        * fix documentation, compatibility and diverse bugs `@adam`_, `@pierre`_ `@romain`_
        * fix for external module on scanpy `@galen`_
        
        0.5.0 (2019-10-17)
        ------------------
        * do not automatically upper case genes `@adam`_
        * AutoZI `@oscar`_
        * Made the intro tutorial more user friendly `@adam`_
        * Tests for LDVAE notebook `@adam`_
        * black codebase `@achille`_ `@gabriel`_ `@adam`_
        * fix compatibility issues with sklearn and numba `@romain`_
        * fix Anndata `@francesco-brundu`_
        * docstring, totalVI, totalVI notebook and CITE-seq data `@adam`_
        * fix type `@eduardo-beltrame`_
        * fixing installation guide `@jeff`_
        * improved error message for dispersion `@stephen-flemming`_
        
        0.4.1 (2019-08-03)
        ------------------
        
        * docstring `@achille`_
        * differential expression `@oscar`_ `@pierre`_
        
        0.4.0 (2019-07-25)
        ------------------
        
        * gimVI `@achille`_
        * synthetic correlated datasets, fixed bug in marginal log likelihood `@oscar`_
        * autotune, dataset enhancements `@gabriel`_
        * documentation `@jeff`_
        * more consistent posterior API, docstring, validation set `@adam`_
        * fix anndataset `@michael-raevsky`_
        * linearly decoded VAE `@valentine-svensson`_
        * support for scanpy, fixed bugs, dataset enhancements `@achille`_
        * fix filtering bug, synthetic correlated datasets, docstring, differential expression `@pierre`_
        * better docstring `@jamie-morton`_
        * classifier based on library size for doublet detection `@david-kelley`_
        
        0.3.0 (2019-05-03)
        ------------------
        
        * corrected notebook `@jules`_
        * added UMAP and updated harmonization code `@chenling`_ `@romain`_
        * support for batch indices in csvdataset `@primoz-godec`_
        * speeding up likelihood computations `@william-yang`_
        * better anndata interop `@casey-greene`_
        * early stopping based on classifier accuracy `@david-kelley`_
        
        0.2.4 (2018-12-20)
        ------------------
        
        * updated to torch v1 `@jules`_
        * added stress tests for harmonization `@chenling`_
        * fixed autograd breaking `@romain`_
        * make removal of empty cells more efficient `@john-reid`_
        * switch to os.path.join `@casey-greene`_
        
        
        0.2.2 (2018-11-08)
        ------------------
        
        * added baselines and datasets for sMFISH imputation `@jules`_
        * added harmonization content `@chenling`_
        * fixing bugs on DE `@romain`_
        
        
        0.2.0 (2018-09-04)
        ------------------
        
        * annotation notebook `@eddie`_
        * Memory footprint management `@jeff`_
        * updated early stopping `@max`_
        * docstring `@james-webber`_
        
        0.1.6 (2018-08-08)
        ------------------
        
        * MMD and adversarial inference wrapper `@eddie`_
        * Documentation `@jeff`_
        * smFISH data imputation `@max`_
        
        0.1.5 (2018-07-24)
        ------------------
        
        * Dataset additions `@eddie`_
        * Documentation `@yining`_
        * updated early stopping `@max`_
        
        
        0.1.3 (2018-06-22)
        ------------------
        
        * Notebook enhancement `@yining`_
        * Semi-supervision `@eddie`_
        
        0.1.2 (2018-06-13)
        ------------------
        
        * First release on PyPi
        * Skeleton code & dependencies `@jeff`_
        * Unit tests `@max`_
        * PyTorch implementation of scVI `@eddie`_ `@max`_
        * Dataset preprocessing `@eddie`_ `@max`_ `@yining`_
        
        0.1.0 (2017-09-05)
        ------------------
        
        * First scVI TensorFlow version `@romain`_
        
        .. _`@romain`: https://github.com/romain-lopez
        .. _`@adam`: https://github.com/adamgayoso
        .. _`@eddie`: https://github.com/Edouard360
        .. _`@jeff`: https://github.com/jeff-regier
        .. _`@pierre`: https://github.com/PierreBoyeau
        .. _`@max`: https://github.com/maxime1310
        .. _`@yining`: https://github.com/imyiningliu
        .. _`@gabriel`: https://github.com/gabmis
        .. _`@achille`: https://github.com/ANazaret
        .. _`@chenling`: https://github.com/chenlingantelope
        .. _`@jules`: https://github.com/jules-samaran
        .. _`@david-kelley`: https://github.com/davek44
        .. _`@william-yang`: https://github.com/triyangle
        .. _`@oscar`: https://github.com/oscarclivio
        .. _`@casey-greene`: https://github.com/cgreene
        .. _`@jamie-morton`: https://github.com/mortonjt
        .. _`@valentine-svensson`: https://github.com/vals
        .. _`@stephen-flemming`: https://github.com/sjfleming
        .. _`@michael-raevsky`: https://github.com/raevskymichail
        .. _`@james-webber`: https://github.com/jamestwebber
        .. _`@galen`: https://github.com/galenxing
        .. _`@francesco-brundu`: https://github.com/fbrundu
        .. _`@primoz-godec`: https://github.com/PrimozGodec
        .. _`@eduardo-beltrame`: https://github.com/Munfred
        .. _`@john-reid`: https://github.com/JohnReid
        .. _`@han-yuan`: https://github.com/hy395
        .. _`@gokcen-eraslan`: https://github.com/gokceneraslan
        
Keywords: scvi
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Provides-Extra: notebooks
Provides-Extra: docs
Provides-Extra: test
