Deep probabilistic analysis of single-cell and spatial omics data
☆1,607Apr 24, 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.☆2,432Updated this week
- Reference mapping for single-cell genomics☆404Mar 21, 2026Updated last month
- CellRank: dynamics from multi-view single-cell data☆443Updated this week
- Annotated data.☆735Updated this week
- Spatial Single Cell Analysis in Python☆566Updated this week
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.☆3,718Apr 13, 2026Updated 2 weeks ago
- Deep count autoencoder for denoising scRNA-seq data☆271Mar 21, 2024Updated 2 years ago
- RNA Velocity generalized through dynamical modeling☆497Feb 25, 2026Updated 2 months ago
- Benchmarking analysis of data integration tools☆413Updated this week
- Single cell perturbation prediction☆342Dec 5, 2024Updated last year
- Panoramic stitching of single cell data☆295Jul 14, 2025Updated 9 months ago
- Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …☆490Apr 23, 2026Updated last week
- muon is a multimodal omics Python framework☆266Mar 16, 2026Updated last month
- Reproducing the experiments of the paper "Deep generative modeling for single-cell transcriptomics"☆57Dec 15, 2018Updated 7 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- A tool for semi-automatic cell type classification☆473Mar 21, 2026Updated last month
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆600Jun 26, 2025Updated 10 months ago
- A package to help convert different single-cell data formats to each other☆465Feb 20, 2026Updated 2 months ago
- Differential expression analysis for single-cell RNA-seq data.☆206Oct 21, 2025Updated 6 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…☆1,561Dec 11, 2022Updated 3 years ago
- ☆1,552Updated this week
- R toolkit for single cell genomics☆2,715Apr 22, 2026Updated last week
- Graph-linked unified embedding for single-cell multi-omics data integration☆464Feb 9, 2026Updated 2 months ago
- A Bayesian model for compositional single-cell data analysis☆196Jan 13, 2026Updated 3 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)☆429Updated this week
- Fast, sensitive and accurate integration of single-cell data with Harmony☆642Apr 21, 2026Updated last week
- Formalizing and benchmarking open problems in single-cell genomics☆427Apr 21, 2026Updated last week
- This is the alpha version of the CellOracle package☆447Feb 3, 2026Updated 2 months ago
- CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.☆470Jun 6, 2025Updated 10 months ago
- https://www.sc-best-practices.org☆1,201Updated this week
- CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.☆392Jul 30, 2025Updated 9 months ago
- 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
- R package implementation of Milo for testing for differential abundance in KNN graphs☆428Apr 23, 2026Updated last week
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Batch balanced KNN☆178Oct 11, 2023Updated 2 years ago
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data☆187Mar 27, 2025Updated last year
- An interactive explorer for single-cell transcriptomics data☆763Apr 24, 2026Updated last week
- Spatial alignment of single cell transcriptomic data.☆361Jul 1, 2025Updated 9 months ago
- Single cell trajectory detection☆309Apr 21, 2026Updated last week
- Mapping out the coarse-grained connectivity structures of complex manifolds.☆239May 23, 2020Updated 5 years ago
- Single-cell epigenomics analysis tools☆315Mar 13, 2026Updated last month