πΌ Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
β271Apr 26, 2026Updated last month
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 Harmonyβ656Updated this week
- Batch balanced KNNβ178Oct 11, 2023Updated 2 years ago
- Panoramic stitching of single cell dataβ295Jul 14, 2025Updated 10 months ago
- Python implementation of the Slingshot pseudotime algorithmβ77Oct 28, 2025Updated 7 months ago
- Python package to perform enrichment analysis from omics data.β269Updated this week
- Wordpress hosting with auto-scaling - Free Trial Offer β’ AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Episcanpy: Epigenomics Single Cell Analysis in Pythonβ151Dec 5, 2024Updated last year
- A scanpy extension to analyse single-cell TCR and BCR data.β256Updated this week
- CellRank: dynamics from multi-view single-cell dataβ451Updated this week
- RNA Velocity generalized through dynamical modelingβ502Feb 25, 2026Updated 3 months ago
- Convert between AnnData and SingleCellExperimentβ151Jun 1, 2026Updated last week
- Detect doublets in single-cell RNA-seq dataβ177Dec 29, 2020Updated 5 years ago
- Python library for plotting Cellphonedb results. Ported from ktplots R package.β57May 29, 2026Updated last week
- Port of symphony algorithm of single-cell reference atlas mapping to Pythonβ34May 19, 2026Updated 3 weeks ago
- muon is a multimodal omics Python frameworkβ269May 8, 2026Updated last month
- Managed Kubernetes at scale on DigitalOcean β’ AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- A package to help convert different single-cell data formats to each otherβ468Feb 20, 2026Updated 3 months ago
- Python implementation of Milo for differential abundance testing on KNN graphβ84Feb 17, 2025Updated last year
- Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction β¦β501Apr 23, 2026Updated last month
- Gene Set Enrichment Analysis in Pythonβ701Jun 4, 2026Updated last week
- An implementation of MNN (Mutual Nearest Neighbors) correct in python.β77Jan 9, 2023Updated 3 years ago
- This is the alpha version of the CellOracle packageβ462Apr 30, 2026Updated last month
- Differential expression analysis for single-cell RNA-seq data.β206Oct 21, 2025Updated 7 months ago
- CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.β400May 6, 2026Updated last month
- Single-cell analysis in Python. Scales to >100M cells.β2,482Updated this week
- Deploy to Railway using AI coding agents - Free Credits Offer β’ AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Single-cell perturbation analysisβ322Jun 3, 2026Updated last week
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics dataβ190Mar 27, 2025Updated last year
- Annotated data.β750Updated this week
- LIANA+: an all-in-one framework for cell-cell communicationβ294May 26, 2026Updated 2 weeks ago
- Reference mapping for single-cell genomicsβ405Mar 21, 2026Updated 2 months ago
- Harmony framework for connecting scRNA-seq data from discrete time pointsβ54Dec 1, 2025Updated 6 months ago
- Deep probabilistic analysis of single-cell and spatial omics dataβ1,638Updated this week
- Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.β191Jun 1, 2026Updated last week
- A novel machine learning pipeline to analyse spatial transcriptomics dataβ249May 5, 2026Updated last month
- Deploy to Railway using AI coding agents - Free Credits Offer β’ AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Benchmarking analysis of data integration toolsβ421Apr 27, 2026Updated last month
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)β439Jun 2, 2026Updated last week
- An open and interoperable data framework for spatial omics dataβ378Updated this week
- Single-cell epigenomics analysis toolsβ319May 19, 2026Updated 3 weeks ago
- Multimodal Data (.h5mu) implementation for Pythonβ122Jun 2, 2026Updated last week
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) whichβ¦β612Jun 26, 2025Updated 11 months ago
- Spatial alignment of single cell transcriptomic data.β368Jul 1, 2025Updated 11 months ago