MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
☆182Aug 12, 2025Updated 6 months ago
Alternatives and similar repositories for multinichenetr
Users that are interested in multinichenetr are comparing it to the libraries listed below
Sorting:
- LIANA: a LIgand-receptor ANalysis frAmework☆232Aug 7, 2024Updated last year
- NicheNet: predict active ligand-target links between interacting cells☆620Nov 12, 2025Updated 3 months ago
- R package implementation of Milo for testing for differential abundance in KNN graphs☆420Sep 4, 2025Updated 5 months ago
- Multi-sample multi-group scRNA-seq analysis tools☆218Feb 16, 2026Updated last week
- Analysis of cell-cell communication at single-cell resolution☆106Sep 10, 2024Updated last year
- R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.☆289Feb 18, 2026Updated last week
- High dimensional weighted gene co-expression network analysis☆465Feb 13, 2026Updated 2 weeks ago
- A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression☆223May 29, 2025Updated 9 months ago
- Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆438Jan 22, 2026Updated last month
- Multiview Intercellular SpaTial modeling framework☆71Jan 15, 2026Updated last month
- A package to help convert different single-cell data formats to each other☆458Feb 20, 2026Updated last week
- A Toolbox for Spatial Transcriptomics Analysis☆166May 6, 2025Updated 9 months ago
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics☆543Feb 19, 2026Updated last week
- Methods to discover gene programs on single-cell data☆174Sep 26, 2025Updated 5 months ago
- Coarse-graining of large single-cell RNA-seq data into metacells☆94Updated this week
- A tool for semi-automatic cell type classification☆453Updated this week
- R package to infer biological activities from omics data using a collection of methods.☆285Dec 16, 2025Updated 2 months ago
- CellRank: dynamics from multi-view single-cell data☆430Updated this week
- A python-based package and software to predict metabolite mediated cell-cell communications by single-cell RNA-seq data☆79Jul 25, 2025Updated 7 months ago
- AUCell: score single cells with gene regulatory networks☆185Mar 9, 2024Updated last year
- DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…☆118Jan 22, 2024Updated 2 years ago
- Spatial Transcriptomics Capture Location Deconvolution☆201Oct 20, 2025Updated 4 months ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆70Nov 2, 2025Updated 3 months ago
- Generate high quality, publication ready visualizations for single cell transcriptomics data.☆217Updated this week
- Easy single cell analysis platform for enrichment☆214Jan 4, 2026Updated last month
- ☆182May 6, 2025Updated 9 months ago
- Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data☆412Aug 22, 2025Updated 6 months ago
- ☆131Apr 24, 2024Updated last year
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆152Feb 12, 2026Updated 2 weeks ago
- Methods for detecting doublets in single-cell sequencing data☆231Feb 12, 2026Updated 2 weeks ago
- Quantifying metabolism activity at the single-cell resolution☆153Feb 18, 2026Updated last week
- R client for the OmniPath web service☆154Feb 12, 2026Updated 2 weeks ago
- Spatial omics analysis toolbox☆362Feb 12, 2026Updated 2 weeks ago
- ☆63Aug 26, 2025Updated 6 months ago
- This is the alpha version of the CellOracle package☆421Feb 3, 2026Updated 3 weeks ago
- Assessing the purity of single cell population☆142Jun 3, 2022Updated 3 years ago
- BANKSY: spatial clustering☆137Oct 15, 2025Updated 4 months ago
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆313Nov 1, 2022Updated 3 years ago
- Some tools for plotting single-cell data☆178May 17, 2025Updated 9 months ago