πΌ Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
β266Apr 26, 2026Updated this week
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 Harmonyβ643Apr 21, 2026Updated last week
- Batch balanced KNNβ178Oct 11, 2023Updated 2 years ago
- Panoramic stitching of single cell dataβ295Jul 14, 2025Updated 9 months ago
- Python implementation of the Slingshot pseudotime algorithmβ75Oct 28, 2025Updated 6 months ago
- Python package to perform enrichment analysis from omics data.β266Apr 21, 2026Updated last week
- Deploy on Railway without the complexity - Free Credits Offer β’ AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Episcanpy: Epigenomics Single Cell Analysis in Pythonβ151Dec 5, 2024Updated last year
- A scanpy extension to analyse single-cell TCR and BCR data.β249Updated this week
- CellRank: dynamics from multi-view single-cell dataβ443Apr 24, 2026Updated last week
- Convert between AnnData and SingleCellExperimentβ149Updated this week
- RNA Velocity generalized through dynamical modelingβ497Feb 25, 2026Updated 2 months ago
- Detect doublets in single-cell RNA-seq dataβ173Dec 29, 2020Updated 5 years ago
- Python library for plotting Cellphonedb results. Ported from ktplots R package.β57Updated this week
- Port of symphony algorithm of single-cell reference atlas mapping to Pythonβ33Mar 16, 2026Updated last month
- muon is a multimodal omics Python frameworkβ266Mar 16, 2026Updated last month
- Bare Metal GPUs on DigitalOcean Gradient AI β’ AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- A package to help convert different single-cell data formats to each otherβ465Feb 20, 2026Updated 2 months ago
- Python implementation of Milo for differential abundance testing on KNN graphβ83Feb 17, 2025Updated last year
- Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction β¦β490Apr 23, 2026Updated last week
- Gene Set Enrichment Analysis in Pythonβ696Updated this week
- An implementation of MNN (Mutual Nearest Neighbors) correct in python.β76Jan 9, 2023Updated 3 years ago
- This is the alpha version of the CellOracle packageβ447Feb 3, 2026Updated 2 months ago
- Differential expression analysis for single-cell RNA-seq data.β206Oct 21, 2025Updated 6 months ago
- CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.β392Jul 30, 2025Updated 9 months ago
- Single-cell perturbation analysisβ309Updated this week
- Bare Metal GPUs on DigitalOcean Gradient AI β’ AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics dataβ187Mar 27, 2025Updated last year
- Annotated data.β735Updated this week
- Single-cell analysis in Python. Scales to >100M cells.β2,432Updated this week
- LIANA+: an all-in-one framework for cell-cell communicationβ283Jan 24, 2026Updated 3 months ago
- Reference mapping for single-cell genomicsβ404Mar 21, 2026Updated last month
- Harmony framework for connecting scRNA-seq data from discrete time pointsβ54Dec 1, 2025Updated 5 months ago
- Deep probabilistic analysis of single-cell and spatial omics dataβ1,607Apr 24, 2026Updated last week
- Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.β189Updated this week
- Benchmarking analysis of data integration toolsβ413Updated 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.
- A novel machine learning pipeline to analyse spatial transcriptomics dataβ245Apr 17, 2026Updated 2 weeks ago
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) whichβ¦β600Jun 26, 2025Updated 10 months ago
- Multimodal Data (.h5mu) implementation for Pythonβ119Updated this week
- Spatial alignment of single cell transcriptomic data.β361Jul 1, 2025Updated 10 months ago
- Python package to perform normalization and variance-stabilization of single-cell dataβ28Jul 17, 2025Updated 9 months ago
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)β429Updated this week
- CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics dataβ141Feb 20, 2025Updated last year