Package: scvi
scVI - Single cell Variational InferencescVI 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:scVIfor analysis of single-cell RNA-seq data, as well as its improved differential expressionframeworkscANVIfor cell annotation of scRNA-seq data using semi-labeled examplestotalVIfor analysis of CITE-seq datagimVIfor imputation of missing genes in spatial transcriptomics from scRNA-seq dataAutoZIfor assessing gene-specific levels of zero-inflation in scRNA-seq dataLDVAEfor an interpretable linear factor model version of scVITutorials and API reference are available in thedocumentation.
Please use the issues here to discuss usage, or submit bug reports.
If you’d like to contribute, please check out ourcontributing guide.
If you find a model useful for your research, please consider citing the corresponding publication (linked above).Package transitionscviis transitioning toscvi-tools. If you’re looking forscvisource code, please use the branch tags.scviis still available via pypi and bioconda, but there will be no future releases past0.6.8. An alpha-release ofscvi-toolswill be available shortly.History0.6.8 (2020-9-16)scvi is now deprecated, please uninstall and install scvi-tools (available shortly)0.6.7 (2020-8-05)downgrade anndata>=0.7 and scanpy>=1.4.6@galenmake loompy optional, raise sckmisc import error@adamfix PBMCDataset download bug@galenfix AnnDatasetFromAnnData _X in adata.obs bug@galen0.6.6 (2020-7-08)add tqdm to within cluster DE genes@adamrestore tqdm to use simple bar instead of ipywidget@adammove to numpydoc for doctstrings@adamupdate issues templates@adamPoisson variable gene selection@valentine-svenssonBrainSmallDataset set defualt save_path_10X@gokcen-eraslantrain_size must be float between 0.0 and 1.0@galenbump dependency versions@galenremove reproducibility notebook@galenfix scanVI dataloading@pierre0.6.5 (2020-5-10)updates to totalVI posterior functions and notebooks@adamupdate seurat v3 HVG selection now using skmisc loess@adam0.6.4 (2020-4-14)add back Python 3.6 support@adamget_sample_scale() allows gene selection@valentine-svenssonbug fix to the dataset to anndata method with how cell measurements are stored@adamfix requirements@adam0.6.3 (2020-4-01)bug in version for Louvian in setup.py@adam0.6.2 (2020-4-01)update highly variable gene selection to handle sparse matrices@adamupdate DE docstrings@pierreimprove posterior save load to also handle subclasses@pierreCreate NB and ZINB distributions with torch and refactor code accordingly@pierretypos in autozivae@achillebug in csc sparse matrices in anndata data loader@adam0.6.1 (2020-3-13)handles gene and cell attributes with the same name@han-yuanfixes anndata overwriting when loading@adam,@pierreformatting in basic tutorial@adam0.6.0 (2020-2-28)updates on TotalVI and LDVAE@adamfix documentation, compatibility and diverse bugs@adam,@pierre@romainfix for external module on scanpy@galen0.5.0 (2019-10-17)do not automatically upper case genes@adamAutoZI@oscarMade the intro tutorial more user friendly@adamTests for LDVAE notebook@adamblack codebase@achille@gabriel@adamfix compatibility issues with sklearn and numba@romainfix Anndata@francesco-brundudocstring, totalVI, totalVI notebook and CITE-seq data@adamfix type@eduardo-beltramefixing installation guide@jeffimproved error message for dispersion@stephen-flemming0.4.1 (2019-08-03)docstring@achilledifferential expression@oscar@pierre0.4.0 (2019-07-25)gimVI@achillesynthetic correlated datasets, fixed bug in marginal log likelihood@oscarautotune, dataset enhancements@gabrieldocumentation@jeffmore consistent posterior API, docstring, validation set@adamfix anndataset@michael-raevskylinearly decoded VAE@valentine-svenssonsupport for scanpy, fixed bugs, dataset enhancements@achillefix filtering bug, synthetic correlated datasets, docstring, differential expression@pierrebetter docstring@jamie-mortonclassifier based on library size for doublet detection@david-kelley0.3.0 (2019-05-03)corrected notebook@julesadded UMAP and updated harmonization code@chenling@romainsupport for batch indices in csvdataset@primoz-godecspeeding up likelihood computations@william-yangbetter anndata interop@casey-greeneearly stopping based on classifier accuracy@david-kelley0.2.4 (2018-12-20)updated to torch v1@julesadded stress tests for harmonization@chenlingfixed autograd breaking@romainmake removal of empty cells more efficient@john-reidswitch to os.path.join@casey-greene0.2.2 (2018-11-08)added baselines and datasets for sMFISH imputation@julesadded harmonization content@chenlingfixing bugs on DE@romain0.2.0 (2018-09-04)annotation notebook@eddieMemory footprint management@jeffupdated early stopping@maxdocstring@james-webber0.1.6 (2018-08-08)MMD and adversarial inference wrapper@eddieDocumentation@jeffsmFISH data imputation@max0.1.5 (2018-07-24)Dataset additions@eddieDocumentation@yiningupdated early stopping@max0.1.3 (2018-06-22)Notebook enhancement@yiningSemi-supervision@eddie0.1.2 (2018-06-13)First release on PyPiSkeleton code & dependencies@jeffUnit tests@maxPyTorch implementation of scVI@eddie@maxDataset preprocessing@eddie@max@yining0.1.0 (2017-09-05)First scVI TensorFlow version@romain