scVI - Single cell Variational Inference
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).
Package transition
scvi
is transitioning to
scvi-tools
. If you’re looking for
scvi
source code, please use the branch tags.
scvi
is still available via pypi and bioconda, but there will be no future releases past
0.6.8
. An alpha-release of
scvi-tools
will be available shortly.
History
0.6.8 (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
@galen
make loompy optional, raise sckmisc import error
@adam
fix PBMCDataset download bug
@galen
fix AnnDatasetFromAnnData _X in adata.obs bug
@galen
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
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