R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
☆794Jan 6, 2024Updated 2 years ago
Alternatives and similar repositories for CellChat
Users that are interested in CellChat 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 toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics☆636Mar 4, 2026Updated 4 months ago
- NicheNet: predict active ligand-target links between interacting cells☆665Jun 1, 2026Updated last month
- R toolkit for single cell genomics☆2,770Jul 14, 2026Updated last week
- R package for detecting doublets in single-cell RNA sequencing data☆554Mar 21, 2025Updated last year
- CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.☆477Jun 6, 2025Updated last year
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Fast, sensitive and accurate integration of single-cell data with Harmony☆665Jun 5, 2026Updated last month
- ☆364Dec 9, 2021Updated 4 years ago
- SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.☆490Apr 5, 2024Updated 2 years ago
- Inferring CNV from Single-Cell RNA-Seq☆677Nov 14, 2025Updated 8 months ago
- Functions for identifying and characterizing continuous developmental trajectories in single-cell data.☆342Apr 23, 2024Updated 2 years ago
- ☆461May 26, 2026Updated last month
- R package implementation of Milo for testing for differential abundance in KNN graphs☆439May 11, 2026Updated 2 months ago
- A toolkit for single-cell immune profiling☆372Jul 9, 2026Updated last week
- High dimensional weighted gene co-expression network analysis☆487Jun 16, 2026Updated last month
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- Methods for detecting doublets in single-cell sequencing data☆258Jul 7, 2026Updated 2 weeks ago
- Analysis of cell-cell communication at single-cell resolution☆107Sep 10, 2024Updated last year
- Interpretation of cell states using reference single-cell maps☆323Dec 19, 2025Updated 7 months ago
- A package to help convert different single-cell data formats to each other☆473Feb 20, 2026Updated 5 months ago
- R toolkit for the analysis of single-cell chromatin data☆423Jul 2, 2026Updated 2 weeks ago
- Community-provided extensions to Seurat☆367Jun 29, 2026Updated 3 weeks ago
- LIANA: a LIgand-receptor ANalysis frAmework☆245Aug 7, 2024Updated last year
- Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data☆243May 8, 2023Updated 3 years ago
- R package for integrating and analyzing multiple single-cell datasets☆431Feb 4, 2026Updated 5 months ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆335Nov 1, 2022Updated 3 years ago
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆624Jun 26, 2025Updated last year
- TRAjectory-based Differential Expression analysis for SEQuencing data☆306Jun 17, 2025Updated last year
- ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)☆461Feb 18, 2025Updated last year
- MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…☆194Aug 12, 2025Updated 11 months ago
- AUCell: score single cells with gene regulatory networks☆199Mar 9, 2024Updated 2 years ago
- RNA Velocity generalized through dynamical modeling☆507Feb 25, 2026Updated 4 months ago
- SingleR: Single-cell RNA-seq cell types Recognition (legacy version)☆346Jul 28, 2020Updated 5 years ago
- R package to infer biological activities from omics data using a collection of methods.☆301Dec 16, 2025Updated 7 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- CellRank: dynamics from multi-view single-cell data☆454Updated this week
- Inference of cell-cell communication from single-cell RNAseq data☆48Apr 21, 2025Updated last year
- Gene set variation analysis☆247Updated this week
- Gene set scoring for single-cell data☆203Apr 29, 2026Updated 2 months ago
- ☆298Jun 16, 2026Updated last month
- Easy single cell analysis platform for enrichment☆228Apr 3, 2026Updated 3 months ago
- Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕☆187Jun 24, 2021Updated 5 years ago