NicheNet: predict active ligand-target links between interacting cells
☆656Jun 1, 2026Updated 2 weeks ago
Alternatives and similar repositories for nichenetr
Users that are interested in nichenetr 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☆789Jan 6, 2024Updated 2 years ago
- ☆364Dec 9, 2021Updated 4 years ago
- MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…☆188Aug 12, 2025Updated 10 months ago
- CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.☆475Jun 6, 2025Updated last year
- LIANA: a LIgand-receptor ANalysis frAmework☆242Aug 7, 2024Updated last year
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- R package implementation of Milo for testing for differential abundance in KNN graphs☆434May 11, 2026Updated last month
- R package for detecting doublets in single-cell RNA sequencing data☆548Mar 21, 2025Updated last year
- Methods for detecting doublets in single-cell sequencing data☆253Updated this week
- 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
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics☆623Mar 4, 2026Updated 3 months ago
- A package to help convert different single-cell data formats to each other☆469Feb 20, 2026Updated 3 months ago
- Community-provided extensions to Seurat☆365Feb 17, 2026Updated 3 months ago
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆331Nov 1, 2022Updated 3 years ago
- CellRank: dynamics from multi-view single-cell data☆454Updated this week
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Inferring CNV from Single-Cell RNA-Seq☆674Nov 14, 2025Updated 7 months ago
- AUCell: score single cells with gene regulatory networks☆195Mar 9, 2024Updated 2 years ago
- Scissor package☆267May 10, 2024Updated 2 years ago
- A toolkit for single-cell immune profiling☆369May 12, 2026Updated last month
- High dimensional weighted gene co-expression network analysis☆476Mar 13, 2026Updated 3 months ago
- Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data☆447Apr 11, 2026Updated 2 months ago
- Functions for identifying and characterizing continuous developmental trajectories in single-cell data.☆339Apr 23, 2024Updated 2 years ago
- RNA velocity estimation in R☆197Sep 14, 2023Updated 2 years ago
- ☆454May 26, 2026Updated 2 weeks ago
- 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.
- R package to infer biological activities from omics data using a collection of methods.☆297Dec 16, 2025Updated 5 months ago
- Interpretation of cell states using reference single-cell maps☆321Dec 19, 2025Updated 5 months ago
- Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕☆186Jun 24, 2021Updated 4 years ago
- R client for the OmniPath web service☆166Apr 29, 2026Updated last month
- inferring cell-cell communication from scRNA-seq of ligand-receptor☆88Oct 6, 2023Updated 2 years ago
- Spatial omics analysis toolbox☆376Jun 2, 2026Updated last week
- Quantifying metabolism activity at the single-cell resolution☆181Feb 18, 2026Updated 3 months ago
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆614Jun 26, 2025Updated 11 months ago
- Fast, sensitive and accurate integration of single-cell data with Harmony☆658Jun 5, 2026Updated last week
- 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.
- ☆290Oct 13, 2025Updated 8 months ago
- R package for integrating and analyzing multiple single-cell datasets☆432Feb 4, 2026Updated 4 months ago
- Tools and methods for analysis of single cell assay data in R☆264Oct 17, 2025Updated 7 months ago
- ☆67Aug 2, 2019Updated 6 years ago
- Signature Analysis and Visualization for Single-Cell RNA-seq☆181Jun 10, 2024Updated 2 years ago
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)☆440Jun 2, 2026Updated last week
- Reference mapping for single-cell genomics☆405Mar 21, 2026Updated 2 months ago