Multi-sample multi-group scRNA-seq analysis tools
☆229Apr 28, 2026Updated 3 weeks ago
Alternatives and similar repositories for muscat
Users that are interested in muscat are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A toolkit for single-cell immune profiling☆368May 12, 2026Updated last week
- TRAjectory-based Differential Expression analysis for SEQuencing data☆295Jun 17, 2025Updated 11 months ago
- MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…☆186Aug 12, 2025Updated 9 months ago
- Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data☆241May 8, 2023Updated 3 years ago
- Interpretation of cell states using reference single-cell maps☆319Dec 19, 2025Updated 5 months ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- R package for integrating and analyzing multiple single-cell datasets☆429Feb 4, 2026Updated 3 months ago
- R package implementation of Milo for testing for differential abundance in KNN graphs☆432May 11, 2026Updated last week
- distinct: a method for differential analyses via hierarchical permutation tests☆13Dec 4, 2023Updated 2 years ago
- Easy single cell analysis platform for enrichment☆223Apr 3, 2026Updated last month
- Interactively analyze single cell genomic data☆187Jan 14, 2026Updated 4 months ago
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆327Nov 1, 2022Updated 3 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.☆300May 11, 2026Updated last week
- Coarse-graining of large single-cell RNA-seq data into metacells☆102Apr 16, 2026Updated last month
- Functions for identifying and characterizing continuous developmental trajectories in single-cell data.☆334Apr 23, 2024Updated 2 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Color blindness friendly visualization of single-cell and bulk RNA-sequencing data☆215Dec 10, 2025Updated 5 months ago
- Analysis of cell-cell communication at single-cell resolution☆107Sep 10, 2024Updated last year
- Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets☆125Apr 16, 2025Updated last year
- Spatial omics analysis toolbox☆374May 15, 2026Updated last week
- AUCell: score single cells with gene regulatory networks☆191Mar 9, 2024Updated 2 years ago
- Methods for detecting doublets in single-cell sequencing data☆251Updated this week
- R package to infer biological activities from omics data using a collection of methods.☆295Dec 16, 2025Updated 5 months ago
- Automated, probabilistic assignment of cell types in scRNA-seq data☆213Jan 9, 2023Updated 3 years ago
- Conversion between scRNA-seq objects☆209May 5, 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.
- High dimensional weighted gene co-expression network analysis☆473Mar 13, 2026Updated 2 months ago
- Tools and methods for analysis of single cell assay data in R☆263Oct 17, 2025Updated 7 months ago
- Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆457Jan 22, 2026Updated 4 months ago
- NicheNet: predict active ligand-target links between interacting cells☆646Nov 12, 2025Updated 6 months ago
- Methods to discover gene programs on single-cell data☆184Apr 1, 2026Updated last month
- R package for modeling single cell UMI expression data using regularized negative binomial regression☆261Jan 10, 2026Updated 4 months ago
- ☆183May 4, 2026Updated 2 weeks ago
- Cell type prioritization in single-cell data☆141Mar 26, 2026Updated last month
- R package for the joint analysis of multiple single-cell RNA-seq datasets☆225Apr 26, 2026Updated 3 weeks ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- R package for pathway analysis in scRNA-seq data☆80Aug 17, 2024Updated last year
- Scissor package☆263May 10, 2024Updated 2 years ago
- R-package for the analysis of single-cell TCR/BCR data in the Seurat ecosystem☆21Apr 14, 2025Updated last year
- ☆12May 14, 2024Updated 2 years ago
- Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).☆88Dec 4, 2025Updated 5 months ago
- CellRank: dynamics from multi-view single-cell data☆449May 4, 2026Updated 2 weeks ago
- Framework for clustering, phenotyping, pseudotiming and inferring gene regulatory networks from single cell data☆109Jul 3, 2023Updated 2 years ago