R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
☆769Jan 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
Sorting:
- NicheNet: predict active ligand-target links between interacting cells☆630Nov 12, 2025Updated 4 months ago
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics☆559Mar 4, 2026Updated 2 weeks ago
- CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.☆470Jun 6, 2025Updated 9 months ago
- ☆361Dec 9, 2021Updated 4 years ago
- R package for detecting doublets in single-cell RNA sequencing data☆533Mar 21, 2025Updated last year
- Fast, sensitive and accurate integration of single-cell data with Harmony☆623Oct 10, 2025Updated 5 months ago
- SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.☆479Apr 5, 2024Updated last year
- Inferring CNV from Single-Cell RNA-Seq☆658Nov 14, 2025Updated 4 months ago
- A toolkit for single-cell immune profiling☆365Mar 9, 2026Updated last week
- R package implementation of Milo for testing for differential abundance in KNN graphs☆423Sep 4, 2025Updated 6 months ago
- R toolkit for single cell genomics☆2,682Mar 13, 2026Updated last week
- Functions for identifying and characterizing continuous developmental trajectories in single-cell data.☆326Apr 23, 2024Updated last year
- High dimensional weighted gene co-expression network analysis☆466Mar 13, 2026Updated last week
- Methods for detecting doublets in single-cell sequencing data☆233Feb 12, 2026Updated last month
- A package to help convert different single-cell data formats to each other☆460Feb 20, 2026Updated last month
- Interpretation of cell states using reference single-cell maps☆313Dec 19, 2025Updated 3 months ago
- ☆446Jan 8, 2026Updated 2 months ago
- Analysis of cell-cell communication at single-cell resolution☆106Sep 10, 2024Updated last year
- Community-provided extensions to Seurat☆358Feb 17, 2026Updated last month
- LIANA: a LIgand-receptor ANalysis frAmework☆234Aug 7, 2024Updated last year
- R toolkit for the analysis of single-cell chromatin data☆410Jan 20, 2026Updated 2 months ago
- R package for integrating and analyzing multiple single-cell datasets☆427Feb 4, 2026Updated last month
- Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data☆238May 8, 2023Updated 2 years ago
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆317Nov 1, 2022Updated 3 years ago
- ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)☆448Feb 18, 2025Updated last year
- 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
- R package to infer biological activities from omics data using a collection of methods.☆286Dec 16, 2025Updated 3 months ago
- Inference of cell-cell communication from single-cell RNAseq data☆49Apr 21, 2025Updated 10 months ago
- TRAjectory-based Differential Expression analysis for SEQuencing data☆291Jun 17, 2025Updated 9 months ago
- inferring cell-cell communication from scRNA-seq of ligand-receptor☆88Oct 6, 2023Updated 2 years ago
- Spatial Transcriptomics Capture Location Deconvolution☆203Oct 20, 2025Updated 5 months ago
- SingleR: Single-cell RNA-seq cell types Recognition (legacy version)☆329Jul 28, 2020Updated 5 years ago
- MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…☆182Aug 12, 2025Updated 7 months ago
- Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕☆185Jun 24, 2021Updated 4 years ago
- Fast Wilcoxon and auROC☆206Nov 8, 2024Updated last year
- RNA Velocity generalized through dynamical modeling☆494Feb 25, 2026Updated 3 weeks ago
- Gene set variation analysis☆235Updated this week
- AUCell: score single cells with gene regulatory networks☆189Mar 9, 2024Updated 2 years ago
- ☆65Aug 2, 2019Updated 6 years ago