R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
☆689Mar 4, 2026Updated 7 months 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 data☆790Jan 6, 2024Updated 2 years ago
- CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.☆491Jun 6, 2025Updated last year
- NicheNet: predict active ligand-target links between interacting cells☆683Oct 23, 2026Updated last week
- CytoTRACE 2 is an interpretable AI method for predicting cellular potency and absolute developmental potential from scRNA-seq data.☆270Jul 8, 2026Updated 3 months ago
- ☆469Sep 22, 2026Updated last month
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…☆203Aug 12, 2025Updated last year
- High dimensional weighted gene co-expression network analysis☆493Jun 16, 2026Updated 4 months ago
- Methods for detecting doublets in single-cell sequencing data☆276Oct 18, 2026Updated last week
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆649Jun 26, 2025Updated last year
- An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.☆683Mar 11, 2026Updated 7 months ago
- Quantifying metabolism activity at the single-cell resolution☆201Aug 20, 2026Updated 2 months ago
- LIANA: a LIgand-receptor ANalysis frAmework☆253Aug 7, 2024Updated 2 years ago
- R package for detecting doublets in single-cell RNA sequencing data☆574Mar 21, 2025Updated last year
- BANKSY: spatial clustering☆170Updated this week
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- A tool for semi-automatic cell type classification☆517May 22, 2026Updated 5 months ago
- Inferring CNV from Single-Cell RNA-Seq☆686Updated this week
- Scissor package☆279May 10, 2024Updated 2 years ago
- Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆491Jan 22, 2026Updated 9 months ago
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)☆465Oct 19, 2026Updated last week
- Gene set scoring for single-cell data☆214Sep 8, 2026Updated last month
- Methods to discover gene programs on single-cell data☆212Oct 12, 2026Updated 2 weeks ago
- R toolkit for single cell genomics☆2,811Updated this week
- A package to help convert different single-cell data formats to each other☆471Feb 20, 2026Updated 8 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.
- R package to infer biological activities from omics data using a collection of methods.☆313Dec 16, 2025Updated 10 months ago
- CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.☆427Sep 12, 2026Updated last month
- SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.☆501Apr 5, 2024Updated 2 years ago
- ☆230Oct 23, 2026Updated last week
- R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.☆314Jun 30, 2026Updated 4 months ago
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆347Nov 1, 2022Updated 3 years ago
- Fast, sensitive and accurate integration of single-cell data with Harmony☆676Oct 15, 2026Updated 2 weeks ago
- A Toolbox for Spatial Transcriptomics Analysis☆172May 6, 2025Updated last year
- Assessing the purity of single cell population☆157Jun 3, 2022Updated 4 years 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.
- R package implementation of Milo for testing for differential abundance in KNN graphs☆450Aug 25, 2026Updated 2 months ago
- Spatial omics analysis toolbox☆394Updated this week
- ☆314Jun 16, 2026Updated 4 months ago
- LIANA+: an all-in-one framework for cell-cell communication☆324Oct 9, 2026Updated 3 weeks ago
- scGSVA: Perform GSVA for single cell RNA seq☆87Sep 5, 2026Updated last month
- Spatial Transcriptomics Capture Location Deconvolution☆216Oct 20, 2025Updated last year
- A toolkit for single-cell immune profiling☆377Oct 16, 2026Updated 2 weeks ago