🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
☆259Feb 13, 2026Updated last month
Alternatives and similar repositories for harmonypy
Users that are interested in harmonypy are comparing it to the libraries listed below
Sorting:
- Fast, sensitive and accurate integration of single-cell data with Harmony☆625Oct 10, 2025Updated 5 months ago
- Batch balanced KNN☆178Oct 11, 2023Updated 2 years ago
- Panoramic stitching of single cell data☆297Jul 14, 2025Updated 8 months ago
- Python implementation of the Slingshot pseudotime algorithm☆71Oct 28, 2025Updated 4 months ago
- Python package to perform enrichment analysis from omics data.☆263Updated this week
- Episcanpy: Epigenomics Single Cell Analysis in Python☆151Dec 5, 2024Updated last year
- A scanpy extension to analyse single-cell TCR and BCR data.☆246Updated this week
- CellRank: dynamics from multi-view single-cell data☆433Mar 9, 2026Updated last week
- Convert between AnnData and SingleCellExperiment☆147Updated this week
- RNA Velocity generalized through dynamical modeling☆494Feb 25, 2026Updated 3 weeks ago
- Detect doublets in single-cell RNA-seq data☆166Dec 29, 2020Updated 5 years ago
- Python library for plotting Cellphonedb results. Ported from ktplots R package.☆57Updated this week
- Port of symphony algorithm of single-cell reference atlas mapping to Python☆33Updated this week
- muon is a multimodal omics Python framework☆264Jan 19, 2026Updated 2 months ago
- A package to help convert different single-cell data formats to each other☆460Feb 20, 2026Updated last month
- Python implementation of Milo for differential abundance testing on KNN graph☆82Feb 17, 2025Updated last year
- Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …☆488Updated this week
- This is the alpha version of the CellOracle package☆429Feb 3, 2026Updated last month
- Gene Set Enrichment Analysis in Python☆694Mar 10, 2026Updated last week
- An implementation of MNN (Mutual Nearest Neighbors) correct in python.☆77Jan 9, 2023Updated 3 years ago
- Differential expression analysis for single-cell RNA-seq data.☆206Oct 21, 2025Updated 5 months ago
- CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.☆384Jul 30, 2025Updated 7 months ago
- Single-cell perturbation analysis☆295Updated this week
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data☆181Mar 27, 2025Updated 11 months ago
- Annotated data.☆720Updated this week
- Single-cell analysis in Python. Scales to >100M cells.☆2,379Updated this week
- Reference mapping for single-cell genomics☆400Dec 2, 2025Updated 3 months ago
- Deep probabilistic analysis of single-cell and spatial omics data☆1,585Updated this week
- Harmony framework for connecting scRNA-seq data from discrete time points☆53Dec 1, 2025Updated 3 months ago
- Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.☆183Updated this week
- LIANA+: an all-in-one framework for cell-cell communication☆276Jan 24, 2026Updated last month
- Benchmarking analysis of data integration tools☆408Sep 17, 2025Updated 6 months ago
- A novel machine learning pipeline to analyse spatial transcriptomics data☆242Mar 12, 2026Updated last week
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆585Jun 26, 2025Updated 8 months ago
- Multimodal Data (.h5mu) implementation for Python☆109Updated this week
- Spatial alignment of single cell transcriptomic data.☆358Jul 1, 2025Updated 8 months ago
- Python package to perform normalization and variance-stabilization of single-cell data☆27Jul 17, 2025Updated 8 months ago
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)☆422Updated this week
- CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data☆138Feb 20, 2025Updated last year