data and model repository for single-cell data
☆136Dec 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
Sorting:
- Reference mapping for single-cell genomics☆399Dec 2, 2025Updated 3 months ago
- Benchmarking analysis of data integration tools☆407Sep 17, 2025Updated 5 months ago
- kallisto index tag extractor☆20Jul 6, 2019Updated 6 years ago
- CellRank: dynamics from multi-view single-cell data☆430Updated this week
- muon is a multimodal omics Python framework☆262Jan 19, 2026Updated last month
- Spatial Single Cell Analysis in Python☆553Updated this week
- A flexible and extensible API for annotated 2D matrix data stored in multiple underlying formats.☆83Updated this week
- Formalizing and benchmarking open problems in single-cell genomics☆420Nov 26, 2025Updated 3 months ago
- Learning motif contributions to cell transitions using sequence features and graphs.☆28Aug 30, 2024Updated last year
- Models and datasets for perturbational single-cell omics☆172Aug 19, 2022Updated 3 years ago
- Single-cell perturbation analysis☆289Feb 23, 2026Updated last week
- Tutorials for Squidpy☆34Dec 18, 2025Updated 2 months ago
- PROGENY Python implementation☆12Apr 5, 2022Updated 3 years ago
- Convert between AnnData and SingleCellExperiment☆144Updated this 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
- Differential expression analysis for single-cell RNA-seq data.☆206Oct 21, 2025Updated 4 months ago
- A Bayesian model for compositional single-cell data analysis☆188Jan 13, 2026Updated last month
- R package for integrating and analyzing multiple single-cell datasets☆424Feb 4, 2026Updated 3 weeks ago
- Quantifying experimental perturbations at single cell resolution☆113Sep 27, 2024Updated last year
- Detect doublets in single-cell RNA-seq data☆86Jul 3, 2019Updated 6 years ago
- Discovering novel cell types across heterogenous single-cell experiments☆123Dec 8, 2022Updated 3 years ago
- Panoramic stitching of single cell data☆295Jul 14, 2025Updated 7 months ago
- Workflow for the Association of T-cell receptors from 3' single-cell RNA-seq (WAT3R)☆21Jan 15, 2023Updated 3 years ago
- Single-cell analysis in Python. Scales to >100M cells.☆2,359Updated this week
- RNA Velocity generalized through dynamical modeling☆488Updated this week
- scMatch: a single-cell gene expression profile annotation tool using reference datasets☆21Aug 11, 2020Updated 5 years ago
- Deep probabilistic analysis of single-cell and spatial omics data☆1,573Updated this week
- Bench-marking classification tools for scRNA-seq data☆194Jun 9, 2022Updated 3 years ago
- A toolkit for single-cell immune profiling☆363Updated this week
- A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…☆234Jan 2, 2026Updated 2 months ago
- Single-Cell Clustering Assessment Framework☆108Oct 27, 2023Updated 2 years ago
- Single cell perturbation prediction☆335Dec 5, 2024Updated last year
- netNMF-sc: A network regularization algorithm for dimensionality reduction and imputation of single-cell expression data☆23Apr 19, 2021Updated 4 years ago
- Flexible, probablistic metrics for quality control of scRNA-seq data☆21Jan 4, 2023Updated 3 years ago
- Multimodal Data (.h5mu) implementation for Python☆109Feb 23, 2026Updated last week
- Filtering of Poison noise on a single-cell RNA-seq UMI count matrix☆80Dec 4, 2025Updated 2 months ago
- Episcanpy: Epigenomics Single Cell Analysis in Python☆150Dec 5, 2024Updated last year
- Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey a…☆161Jan 27, 2026Updated last month
- Comparison of single cell normalization strategies☆10Aug 13, 2021Updated 4 years ago