🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
☆281Apr 26, 2026Updated 2 months ago
Alternatives and similar repositories for harmonypy
Users that are interested in harmonypy are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Fast, sensitive and accurate integration of single-cell data with Harmony☆665Jun 5, 2026Updated last month
- Batch balanced KNN☆179Oct 11, 2023Updated 2 years ago
- Panoramic stitching of single cell data☆295Jul 14, 2025Updated last year
- Python implementation of the Slingshot pseudotime algorithm☆76Oct 28, 2025Updated 8 months ago
- Episcanpy: Epigenomics Single Cell Analysis in Python☆151Dec 5, 2024Updated last year
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- Python package to perform enrichment analysis from omics data.☆284Updated this week
- A scanpy extension to analyse single-cell TCR and BCR data.☆262Updated this week
- 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
- Detect doublets in single-cell RNA-seq data☆180Dec 29, 2020Updated 5 years ago
- Python library for plotting Cellphonedb results. Ported from ktplots R package.☆57Jun 29, 2026Updated 3 weeks ago
- Port of symphony algorithm of single-cell reference atlas mapping to Python☆34May 19, 2026Updated 2 months ago
- muon is a multimodal omics Python framework☆273Updated 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.
- A package to help convert different single-cell data formats to each other☆473Feb 20, 2026Updated 5 months ago
- Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …☆504Jul 1, 2026Updated 3 weeks ago
- Python implementation of Milo for differential abundance testing on KNN graph☆85Feb 17, 2025Updated last year
- An implementation of MNN (Mutual Nearest Neighbors) correct in python.☆77Jan 9, 2023Updated 3 years ago
- Gene Set Enrichment Analysis in Python☆706Jul 9, 2026Updated last week
- This is the alpha version of the CellOracle package☆478Apr 30, 2026Updated 2 months ago
- Differential expression analysis for single-cell RNA-seq data.☆206Oct 21, 2025Updated 9 months ago
- CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.☆406Jun 16, 2026Updated last month
- Harmony framework for connecting scRNA-seq data from discrete time points☆54Dec 1, 2025Updated 7 months ago
- 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.
- LIANA+: an all-in-one framework for cell-cell communication☆305Updated this week
- Single-cell analysis in Python. Scales to >100M cells.☆2,522Updated this week
- Annotated data.☆759Updated this week
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data☆192Mar 27, 2025Updated last year
- Reference mapping for single-cell genomics☆406Jun 26, 2026Updated 3 weeks ago
- Deep probabilistic analysis of single-cell and spatial omics data☆1,663Updated this week
- Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.☆193Updated this week
- A novel machine learning pipeline to analyse spatial transcriptomics data☆253Jul 12, 2026Updated last week
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)☆450Jul 13, 2026Updated last week
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Benchmarking analysis of data integration tools☆425Apr 27, 2026Updated 2 months ago
- Single-cell epigenomics analysis tools☆323Jul 13, 2026Updated last week
- An open and interoperable data framework for spatial omics data☆382Updated this week
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆624Jun 26, 2025Updated last year
- Multimodal Data (.h5mu) implementation for Python☆127Updated this week
- Spatial alignment of single cell transcriptomic data.☆370Jul 1, 2025Updated last year
- rapids-singlecell: GPU-accelerated framework for scRNA analysis☆386Updated this week