Fast, sensitive and accurate integration of single-cell data with Harmony
☆656Jun 5, 2026Updated this week
Alternatives and similar repositories for harmony
Users that are interested in harmony are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- R package for detecting doublets in single-cell RNA sequencing data☆548Mar 21, 2025Updated last year
- R package for integrating and analyzing multiple single-cell datasets☆430Feb 4, 2026Updated 4 months ago
- R toolkit for single cell genomics☆2,746May 29, 2026Updated last week
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data☆789Jan 6, 2024Updated 2 years ago
- Inferring CNV from Single-Cell RNA-Seq☆674Nov 14, 2025Updated 6 months ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.☆486Apr 5, 2024Updated 2 years ago
- ☆454May 26, 2026Updated 2 weeks ago
- ☆364Dec 9, 2021Updated 4 years ago
- 🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.☆271Apr 26, 2026Updated last month
- Panoramic stitching of single cell data☆295Jul 14, 2025Updated 10 months ago
- SingleR: Single-cell RNA-seq cell types Recognition (legacy version)☆338Jul 28, 2020Updated 5 years ago
- A tool for semi-automatic cell type classification☆485May 22, 2026Updated 2 weeks ago
- A package to help convert different single-cell data formats to each other☆468Feb 20, 2026Updated 3 months ago
- Automated, probabilistic assignment of cell types in scRNA-seq data☆213Jan 9, 2023Updated 3 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data☆241May 8, 2023Updated 3 years ago
- AUCell: score single cells with gene regulatory networks☆193Mar 9, 2024Updated 2 years ago
- Functions for identifying and characterizing continuous developmental trajectories in single-cell data.☆338Apr 23, 2024Updated 2 years ago
- R package for the joint analysis of multiple single-cell RNA-seq datasets☆225Apr 26, 2026Updated last month
- Community-provided extensions to Seurat☆365Feb 17, 2026Updated 3 months ago
- ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)☆455Feb 18, 2025Updated last year
- NicheNet: predict active ligand-target links between interacting cells☆655Jun 1, 2026Updated last week
- Tools and methods for analysis of single cell assay data in R☆264Oct 17, 2025Updated 7 months ago
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆612Jun 26, 2025Updated 11 months ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Efficient and precise single-cell reference atlas mapping with Symphony☆121May 24, 2026Updated 2 weeks ago
- R package for modeling single cell UMI expression data using regularized negative binomial regression☆264Jan 10, 2026Updated 4 months ago
- R toolkit for the analysis of single-cell chromatin data☆417Apr 20, 2026Updated last month
- Fast Wilcoxon and auROC☆212May 5, 2026Updated last month
- R package implementation of Milo for testing for differential abundance in KNN graphs☆434May 11, 2026Updated 3 weeks ago
- RNA Velocity generalized through dynamical modeling☆502Feb 25, 2026Updated 3 months ago
- A toolkit for single-cell immune profiling☆369May 12, 2026Updated 3 weeks ago
- High dimensional weighted gene co-expression network analysis☆476Mar 13, 2026Updated 2 months ago
- Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.☆3,744Jun 1, 2026Updated last week
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Reference mapping for single-cell genomics☆405Mar 21, 2026Updated 2 months ago
- STARTRAC(Single T-cell Analysis by Rna-seq and Tcr TRACking)☆122Apr 26, 2025Updated last year
- CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.☆474Jun 6, 2025Updated last year
- Single-cell analysis in Python. Scales to >100M cells.☆2,482Updated this week
- A Bayesian model for compositional single-cell data analysis☆198Jan 13, 2026Updated 4 months ago
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆329Nov 1, 2022Updated 3 years ago
- Detect doublets in single-cell RNA-seq data☆177Dec 29, 2020Updated 5 years ago