Annotated data.
☆759Jul 21, 2026Updated this week
Alternatives and similar repositories for anndata
Users that are interested in anndata 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.☆2,522Updated this week
- Deep probabilistic analysis of single-cell and spatial omics data☆1,666Updated this week
- Spatial Single Cell Analysis in Python☆585Updated this week
- Multimodal Data (.h5mu) implementation for Python☆127Updated this week
- muon is a multimodal omics Python framework☆273Updated this week
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- CellRank: dynamics from multi-view single-cell data☆454Updated this week
- RNA Velocity generalized through dynamical modeling☆507Feb 25, 2026Updated 4 months ago
- Convert between AnnData and SingleCellExperiment☆152Updated this week
- Differential expression analysis for single-cell RNA-seq data.☆206Oct 21, 2025Updated 9 months ago
- An open and interoperable data framework for spatial omics data☆382Updated this week
- Reference mapping for single-cell genomics☆406Jun 26, 2026Updated 3 weeks ago
- ☆100Jul 2, 2026Updated 2 weeks ago
- Python package to perform enrichment analysis from omics data.☆286Updated this week
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆625Jun 26, 2025Updated last year
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- A scanpy extension to analyse single-cell TCR and BCR data.☆263Updated this week
- Benchmarking analysis of data integration tools☆425Apr 27, 2026Updated 2 months ago
- rapids-singlecell: GPU-accelerated framework for scRNA analysis☆388Updated this week
- 🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.☆281Apr 26, 2026Updated 2 months ago
- Episcanpy: Epigenomics Single Cell Analysis in Python☆151Dec 5, 2024Updated last year
- A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.☆759Updated this week
- Single-cell perturbation analysis☆339Updated this week
- A user-friendly library that brings familiar DataFrame-style operations to AnnData objects with a simple and expressive API.☆18Updated this week
- Cookiecutter template for scverse☆89Updated this week
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- R toolkit for single cell genomics☆2,772Jul 14, 2026Updated last week
- LIANA+: an all-in-one framework for cell-cell communication☆305Updated this week
- Batch balanced KNN☆180Oct 11, 2023Updated 2 years ago
- An interactive explorer for single-cell transcriptomics data☆782Updated this week
- Gene Set Enrichment Analysis in Python☆706Updated this week
- Python implementation of the Loom file format - http://loompy.org☆149Dec 16, 2024Updated last year
- Formalizing and benchmarking open problems in single-cell genomics☆437Jun 30, 2026Updated 3 weeks ago
- Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq an…☆1,580Dec 11, 2022Updated 3 years ago
- Configure Vitessce using existing Scverse plotting APIs☆25Updated this week
- 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.
- Mapping out the coarse-grained connectivity structures of complex manifolds.☆246May 23, 2020Updated 6 years ago
- Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …☆504Jul 1, 2026Updated 3 weeks ago
- Scanpy Tutorials.☆241Updated this week
- Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.☆3,811Jul 14, 2026Updated last week
- CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.☆406Jun 16, 2026Updated last month
- AnnData interoperability in R☆192Updated this week
- Fast array utilities☆15Updated this week