Deep probabilistic analysis of single-cell and spatial omics data
☆1,623May 14, 2026Updated last week
Alternatives and similar repositories for scvi-tools
Users that are interested in scvi-tools are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Single-cell analysis in Python. Scales to >100M cells.☆2,452May 13, 2026Updated last week
- Reference mapping for single-cell genomics☆404Mar 21, 2026Updated 2 months ago
- CellRank: dynamics from multi-view single-cell data☆449May 4, 2026Updated 2 weeks ago
- Annotated data.☆741Updated this week
- Spatial Single Cell Analysis in Python☆571Updated this week
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.☆3,735May 2, 2026Updated 2 weeks ago
- Deep count autoencoder for denoising scRNA-seq data☆271Mar 21, 2024Updated 2 years ago
- RNA Velocity generalized through dynamical modeling☆499Feb 25, 2026Updated 2 months ago
- Benchmarking analysis of data integration tools☆415Apr 27, 2026Updated 3 weeks ago
- Single cell perturbation prediction☆343Dec 5, 2024Updated last year
- Panoramic stitching of single cell data☆295Jul 14, 2025Updated 10 months ago
- Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …☆495Apr 23, 2026Updated 3 weeks ago
- muon is a multimodal omics Python framework☆267May 8, 2026Updated last week
- Reproducing the experiments of the paper "Deep generative modeling for single-cell transcriptomics"☆57Dec 15, 2018Updated 7 years ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- A tool for semi-automatic cell type classification☆476Updated this week
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆606Jun 26, 2025Updated 10 months ago
- A package to help convert different single-cell data formats to each other☆465Feb 20, 2026Updated 3 months ago
- Differential expression analysis for single-cell RNA-seq data.☆206Oct 21, 2025Updated 7 months ago
- Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq an…☆1,566Dec 11, 2022Updated 3 years ago
- ☆1,566Apr 29, 2026Updated 3 weeks ago
- R toolkit for single cell genomics☆2,724Updated this week
- A Bayesian model for compositional single-cell data analysis☆196Jan 13, 2026Updated 4 months ago
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)☆434Updated this week
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Graph-linked unified embedding for single-cell multi-omics data integration☆466Feb 9, 2026Updated 3 months ago
- Fast, sensitive and accurate integration of single-cell data with Harmony☆650May 12, 2026Updated last week
- Formalizing and benchmarking open problems in single-cell genomics☆428May 7, 2026Updated 2 weeks ago
- This is the alpha version of the CellOracle package☆453Apr 30, 2026Updated 3 weeks ago
- CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.☆471Jun 6, 2025Updated 11 months ago
- CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.☆394May 6, 2026Updated 2 weeks ago
- https://www.sc-best-practices.org☆1,194May 13, 2026Updated last week
- MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological …☆381Oct 3, 2024Updated last year
- Batch balanced KNN☆178Oct 11, 2023Updated 2 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- R package implementation of Milo for testing for differential abundance in KNN graphs☆432May 11, 2026Updated last week
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data☆188Mar 27, 2025Updated last year
- An interactive explorer for single-cell transcriptomics data☆767May 9, 2026Updated last week
- Spatial alignment of single cell transcriptomic data.☆365Jul 1, 2025Updated 10 months ago
- Single cell trajectory detection☆311Apr 21, 2026Updated last month
- Mapping out the coarse-grained connectivity structures of complex manifolds.☆242May 23, 2020Updated 5 years ago
- NicheNet: predict active ligand-target links between interacting cells☆646Nov 12, 2025Updated 6 months ago