Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
☆464Apr 11, 2026Updated 4 months ago
Alternatives and similar repositories for cNMF
Users that are interested in cNMF are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Methods to discover gene programs on single-cell data☆207Jul 21, 2026Updated 3 weeks ago
- ☆158Mar 20, 2026Updated 4 months ago
- NicheNet: predict active ligand-target links between interacting cells☆673Jun 1, 2026Updated 2 months ago
- Code for reproducing the analysis in Gavish et al. "The transcriptional hallmarks of intra-tumor heterogeneity across a thousand tumors".☆137Sep 6, 2024Updated last year
- R package implementation of Milo for testing for differential abundance in KNN graphs☆443May 11, 2026Updated 3 months ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…☆195Aug 12, 2025Updated last year
- Inferring CNV from Single-Cell RNA-Seq☆680Nov 14, 2025Updated 9 months ago
- Interpretation of cell states using reference single-cell maps☆323Dec 19, 2025Updated 7 months ago
- A package to help convert different single-cell data formats to each other☆470Feb 20, 2026Updated 5 months ago
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆335Nov 1, 2022Updated 3 years ago
- CellRank: dynamics from multi-view single-cell data☆455Aug 3, 2026Updated 2 weeks ago
- A Bayesian model for compositional single-cell data analysis☆199Jan 13, 2026Updated 7 months ago
- High dimensional weighted gene co-expression network analysis☆491Jun 16, 2026Updated 2 months ago
- CytoTRACE 2 is an interpretable AI method for predicting cellular potency and absolute developmental potential from scRNA-seq data.☆265Jul 8, 2026Updated last month
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- ☆301Jun 16, 2026Updated 2 months ago
- Clone Calling from Visium Spatial Transcriptomics of Cancer samples☆101Dec 8, 2022Updated 3 years ago
- Python package to find communication-driven intercellular flows from single-cell RNA-sequencing and spatial transcriptomics data.☆89Mar 19, 2026Updated 4 months ago
- AUCell: score single cells with gene regulatory networks☆201Mar 9, 2024Updated 2 years ago
- Methods for detecting doublets in single-cell sequencing data☆260Jul 7, 2026Updated last month
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆632Jun 26, 2025Updated last year
- Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.☆196Aug 10, 2026Updated last week
- This is the alpha version of the CellOracle package☆482Apr 30, 2026Updated 3 months ago
- Implements *CellAnnotator (aka *CAT/starCAT), annotating scRNA-Seq with predefined gene expression programs☆108Jul 13, 2026Updated last month
- 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.
- ☆134Mar 27, 2022Updated 4 years ago
- Reference mapping for single-cell genomics☆406Jun 26, 2026Updated last month
- R package for integrating and analyzing multiple single-cell datasets☆432Feb 4, 2026Updated 6 months ago
- Scissor package☆273May 10, 2024Updated 2 years ago
- R package to infer biological activities from omics data using a collection of methods.☆304Dec 16, 2025Updated 8 months ago
- reticulate-free single cell format conversion☆218Jul 10, 2026Updated last month
- STARTRAC(Single T-cell Analysis by Rna-seq and Tcr TRACking)☆124Apr 26, 2025Updated last year
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data☆195Mar 27, 2025Updated last year
- ☆63Dec 27, 2023Updated 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.
- A tool for semi-automatic cell type classification☆500May 22, 2026Updated 2 months ago
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data☆793Jan 6, 2024Updated 2 years ago
- Cell type prioritization in single-cell data☆148Mar 26, 2026Updated 4 months ago
- Assessing the purity of single cell population☆155Jun 3, 2022Updated 4 years ago
- Python package to perform enrichment analysis from omics data.☆289Updated this week
- MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological …☆388Oct 3, 2024Updated last year
- Convert between AnnData and SingleCellExperiment☆151Aug 11, 2026Updated last week