saeyslab / nichenetrView external linksLinks
NicheNet: predict active ligand-target links between interacting cells
☆615Nov 12, 2025Updated 3 months ago
Alternatives and similar repositories for nichenetr
Users that are interested in nichenetr are comparing it to the libraries listed below
Sorting:
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data☆760Jan 6, 2024Updated 2 years ago
- MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…☆180Aug 12, 2025Updated 6 months ago
- ☆358Dec 9, 2021Updated 4 years ago
- R package implementation of Milo for testing for differential abundance in KNN graphs☆414Sep 4, 2025Updated 5 months ago
- LIANA: a LIgand-receptor ANalysis frAmework☆231Aug 7, 2024Updated last year
- R package for detecting doublets in single-cell RNA sequencing data☆523Mar 21, 2025Updated 10 months ago
- CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.☆464Jun 6, 2025Updated 8 months ago
- Methods for detecting doublets in single-cell sequencing data☆230Dec 15, 2025Updated last month
- SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.☆478Apr 5, 2024Updated last year
- A package to help convert different single-cell data formats to each other☆454Feb 28, 2024Updated last year
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆311Nov 1, 2022Updated 3 years ago
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics☆540Oct 7, 2025Updated 4 months ago
- Inferring CNV from Single-Cell RNA-Seq☆650Nov 14, 2025Updated 2 months ago
- Community-provided extensions to Seurat☆355Jan 30, 2026Updated 2 weeks ago
- A toolkit for single-cell immune profiling☆362Jan 27, 2026Updated 2 weeks ago
- CellRank: dynamics from multi-view single-cell data☆420Jan 22, 2026Updated 3 weeks ago
- AUCell: score single cells with gene regulatory networks☆183Mar 9, 2024Updated last year
- Scissor package☆250May 10, 2024Updated last year
- Tools and methods for analysis of single cell assay data in R☆260Oct 17, 2025Updated 3 months ago
- High dimensional weighted gene co-expression network analysis☆465Jan 7, 2026Updated last month
- ☆438Jan 8, 2026Updated last month
- Functions for identifying and characterizing continuous developmental trajectories in single-cell data.☆324Apr 23, 2024Updated last year
- R package to infer biological activities from omics data using a collection of methods.☆285Dec 16, 2025Updated last month
- Interpretation of cell states using reference single-cell maps☆309Dec 19, 2025Updated last month
- R client for the OmniPath web service☆153Feb 4, 2026Updated last week
- R package for integrating and analyzing multiple single-cell datasets☆425Feb 4, 2026Updated last week
- Fast, sensitive and accurate integration of single-cell data with Harmony☆620Oct 10, 2025Updated 4 months ago
- Quantifying metabolism activity at the single-cell resolution☆151Jun 27, 2025Updated 7 months ago
- Spatial omics analysis toolbox☆360Updated this week
- RNA velocity estimation in R☆194Sep 14, 2023Updated 2 years ago
- ☆269Oct 13, 2025Updated 4 months ago
- Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data☆407Aug 22, 2025Updated 5 months ago
- Reference mapping for single-cell genomics☆398Dec 2, 2025Updated 2 months ago
- Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕☆185Jun 24, 2021Updated 4 years ago
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)☆416Jan 19, 2026Updated 3 weeks ago
- Signature Analysis and Visualization for Single-Cell RNA-seq☆175Jun 10, 2024Updated last year
- inferring cell-cell communication from scRNA-seq of ligand-receptor☆85Oct 6, 2023Updated 2 years ago
- Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆438Jan 22, 2026Updated 3 weeks ago
- A tool for semi-automatic cell type classification☆451Jan 31, 2026Updated last week