scvi-tools (single-cell variational inference tools) 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, API reference, and installation guides are available in the documentation. Please use the issues here to submit bug reports. For discussion of usage, checkout out our forum. If you’d like to contribute, check out our development guide. If you find a model useful for your research, please consider citing the corresponding publication (linked above).
Package transition
scvi is now 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. Documentation for scvi is available at the same documentation website.
3 maintainers
Release files for scvi-tools 0.7.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| scvi-tools-0.7.1.tar.gz | 123.6 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| scvi_tools-0.7.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 280.9 kB
Release files / scvi-tools-0.7.1.tar.gz
| Download URL | scvi-tools-0.7.1.tar.gz |
|---|---|
| Size | 123.6 kB |
| Tags | Source |
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SHA-256 checksum How to use checksums |
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Release files / scvi_tools-0.7.1-py3-none-any.whl
| Download URL | scvi_tools-0.7.1-py3-none-any.whl |
|---|---|
| Size | 157.3 kB |
| Tags | Python 3 |
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poetry/1.0.10 CPython/3.7.6 Darwin/19.6.0
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