data and model repository for single-cell data
☆135Dec 21, 2023Updated 2 years ago
Alternatives and similar repositories for sfaira
Users that are interested in sfaira are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Reference mapping for single-cell genomics☆404Mar 21, 2026Updated last month
- Benchmarking analysis of data integration tools☆413Updated this week
- kallisto index tag extractor☆20Jul 6, 2019Updated 6 years ago
- CellRank: dynamics from multi-view single-cell data☆443Apr 24, 2026Updated last week
- Formalizing and benchmarking open problems in single-cell genomics☆427Apr 21, 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.
- Spatial Single Cell Analysis in Python☆566Updated this week
- muon is a multimodal omics Python framework☆266Mar 16, 2026Updated last month
- Learning motif contributions to cell transitions using sequence features and graphs.☆27Aug 30, 2024Updated last year
- Differential expression analysis for single-cell RNA-seq data.☆206Oct 21, 2025Updated 6 months ago
- A flexible and extensible API for annotated 2D matrix data stored in multiple underlying formats.☆84Apr 20, 2026Updated last week
- scMatch: a single-cell gene expression profile annotation tool using reference datasets☆21Aug 11, 2020Updated 5 years ago
- R package for integrating and analyzing multiple single-cell datasets☆428Feb 4, 2026Updated 2 months ago
- Convert between AnnData and SingleCellExperiment☆149Updated this week
- Comparison of single cell normalization strategies☆11Aug 13, 2021Updated 4 years ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- Single-cell perturbation analysis☆309Updated this week
- Tutorials for Squidpy☆34Dec 18, 2025Updated 4 months ago
- Models and datasets for perturbational single-cell omics☆176Aug 19, 2022Updated 3 years ago
- Single-cell analysis in Python. Scales to >100M cells.☆2,432Updated this week
- Code used to benchmark Xenium☆81Apr 10, 2026Updated 3 weeks ago
- A Bayesian model for compositional single-cell data analysis☆196Jan 13, 2026Updated 3 months ago
- Flexible, probablistic metrics for quality control of scRNA-seq data☆21Jan 4, 2023Updated 3 years ago
- PROGENY Python implementation☆12Apr 5, 2022Updated 4 years ago
- Information-based dimensionality reduction☆29Dec 14, 2024Updated last year
- 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.
- Quantifying experimental perturbations at single cell resolution☆115Sep 27, 2024Updated last year
- Discovering novel cell types across heterogenous single-cell experiments☆123Dec 8, 2022Updated 3 years ago
- Panoramic stitching of single cell data☆295Jul 14, 2025Updated 9 months ago
- An interface for Nested Stochastic Block Model for single cell analysis☆37Sep 30, 2025Updated 7 months ago
- A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…☆245Mar 14, 2026Updated last month
- Automatically use the latest “vX.X.X” tag as version in your Python package☆13Updated this week
- Detect doublets in single-cell RNA-seq data☆86Jul 3, 2019Updated 6 years ago
- Deep probabilistic analysis of single-cell and spatial omics data☆1,607Apr 24, 2026Updated last week
- Companion repository to Lause, Berens & Kobak (2021): "Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data", Gen…☆40May 6, 2022Updated 3 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Single cell perturbation prediction☆342Dec 5, 2024Updated last year
- Multimodal Data (.h5mu) implementation for Python☆119Updated this week
- Code associated with the manuscript Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in t…☆22Aug 19, 2022Updated 3 years ago
- A toolkit for single-cell immune profiling☆367Apr 24, 2026Updated last week
- Filtering of Poison noise on a single-cell RNA-seq UMI count matrix☆81Dec 4, 2025Updated 4 months ago
- RNA Velocity generalized through dynamical modeling☆497Feb 25, 2026Updated 2 months ago
- Deep count autoencoder for denoising scRNA-seq data☆271Mar 21, 2024Updated 2 years ago