R package to infer biological activities from omics data using a collection of methods.
☆285Dec 16, 2025Updated 2 months ago
Alternatives and similar repositories for decoupleR
Users that are interested in decoupleR are comparing it to the libraries listed below
Sorting:
- R client for the OmniPath web service☆155Updated this week
- Generate high quality, publication ready visualizations for single cell transcriptomics data.☆217Updated this week
- R package implementation of Milo for testing for differential abundance in KNN graphs☆421Sep 4, 2025Updated 5 months ago
- LIANA: a LIgand-receptor ANalysis frAmework☆232Aug 7, 2024Updated last year
- Python package to perform enrichment analysis from omics data.☆257Updated this week
- Methods for detecting doublets in single-cell sequencing data☆231Feb 12, 2026Updated 2 weeks ago
- High dimensional weighted gene co-expression network analysis☆465Feb 13, 2026Updated 2 weeks ago
- TRAjectory-based Differential Expression analysis for SEQuencing data☆290Jun 17, 2025Updated 8 months ago
- AUCell: score single cells with gene regulatory networks☆185Mar 9, 2024Updated last year
- Interpretation of cell states using reference single-cell maps☆312Dec 19, 2025Updated 2 months ago
- Gene regulatory network containing signed transcription factor-target gene interactions☆99May 27, 2025Updated 9 months ago
- NicheNet: predict active ligand-target links between interacting cells☆620Nov 12, 2025Updated 3 months ago
- Functions for identifying and characterizing continuous developmental trajectories in single-cell data.☆324Apr 23, 2024Updated last year
- Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆438Jan 22, 2026Updated last month
- MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…☆182Aug 12, 2025Updated 6 months ago
- A Toolbox for Spatial Transcriptomics Analysis☆166May 6, 2025Updated 9 months ago
- IOBR is an R package to perform comprehensive analysis of tumor microenvironment and signatures for immuno-oncology.☆276Jan 3, 2026Updated 2 months ago
- An R package for visualising cell-cell interactions☆46Aug 14, 2024Updated last year
- R package for integrating and analyzing multiple single-cell datasets☆424Feb 4, 2026Updated 3 weeks ago
- Methods to discover gene programs on single-cell data☆174Sep 26, 2025Updated 5 months ago
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data☆765Jan 6, 2024Updated 2 years ago
- R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.☆289Updated this week
- Easy single cell analysis platform for enrichment☆215Jan 4, 2026Updated last month
- A toolkit for single-cell immune profiling☆363Updated this week
- Gene set variation analysis☆231Updated this week
- Visualise Clusterings at Different Resolutions☆252Jun 21, 2025Updated 8 months ago
- Spatial Transcriptomics Capture Location Deconvolution☆201Oct 20, 2025Updated 4 months ago
- Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)☆310Feb 10, 2026Updated 3 weeks ago
- Signature Analysis and Visualization for Single-Cell RNA-seq☆175Jun 10, 2024Updated last year
- R toolkit for the analysis of single-cell chromatin data☆406Jan 20, 2026Updated last month
- Spatial omics analysis toolbox☆362Feb 12, 2026Updated 2 weeks ago
- Multi-sample multi-group scRNA-seq analysis tools☆218Feb 16, 2026Updated 2 weeks ago
- An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.☆627Nov 28, 2025Updated 3 months ago
- Conversion between scRNA-seq objects☆200Jan 12, 2026Updated last month
- R package for the joint analysis of multiple single-cell RNA-seq datasets☆219Feb 26, 2024Updated 2 years ago
- Bayesian model for clustering and enhancing the resolution of spatial gene expression experiments.☆167Jan 8, 2026Updated last month
- A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…☆521Jan 5, 2026Updated last month
- Multiview Intercellular SpaTial modeling framework☆71Jan 15, 2026Updated last month
- Some tools for plotting single-cell data☆178May 17, 2025Updated 9 months ago