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scvi-tools(single-cell variational inference tools) is a package for end-to-end analysis of single-cell omics data primarily developed and maintained by the Yosef Lab at UC Berkeley and the Weizman...
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Python
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2026-03-03 21:20:16
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Documentation — scvi-tools Skip to main content Back to top Ctrl + K GitHub Discourse Model hub Installation Tutorials Quick start Introduction to scvi-tools Data loading and preparation Using Python in R with reticulate scRNA-seq Atlas-level integration of lung data Integrating datasets with scVI in R Integration and label transfer with Tabula Muris Reference mapping with scvi-tools Querying the Human Lung Cell Atlas Seed labeling with scANVI Linearly decoded VAE Identification of zero-inflated genes Annotation with CellAssign Topic Modeling with Amortized LDA Differential expression on C. elegans data Isolating perturbation-induced variations with contrastiveVI Benchmarking the scANVI fix ATAC-seq PeakVI: Analyzing scATACseq data ATAC-seq analysis in R ScBasset: Analyzing scATACseq data scBasset: Batch correction of scATACseq data PoissonVI: Analyzing quantitative scATAC-seq fragment counts Multimodal CITE-seq anal...
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