A scalable SCENIC workflow for single-cell gene regulatory network analysis
☆174Dec 8, 2022Updated 3 years ago
Alternatives and similar repositories for SCENICprotocol
Users that are interested in SCENICprotocol are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆594Jun 26, 2025Updated 9 months ago
- SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.☆481Apr 5, 2024Updated 2 years ago
- A package to help convert different single-cell data formats to each other☆462Feb 20, 2026Updated last month
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data☆776Jan 6, 2024Updated 2 years ago
- Algorithms for single-cell analysis☆29Jul 19, 2021Updated 4 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- RNA Velocity generalized through dynamical modeling☆495Feb 25, 2026Updated last month
- Create cisTarget databases☆57Jun 18, 2025Updated 9 months ago
- Convert between AnnData and SingleCellExperiment☆148Updated this week
- Interfaces for HDF5-based Single Cell File Formats☆176Nov 4, 2023Updated 2 years ago
- R package for detecting doublets in single-cell RNA sequencing data☆538Mar 21, 2025Updated last year
- CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data☆139Feb 20, 2025Updated last year
- NicheNet: predict active ligand-target links between interacting cells☆636Nov 12, 2025Updated 4 months ago
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data☆184Mar 27, 2025Updated last year
- ☆361Dec 9, 2021Updated 4 years 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.
- R package implementation of Milo for testing for differential abundance in KNN graphs☆424Sep 4, 2025Updated 7 months ago
- Batch balanced KNN☆179Oct 11, 2023Updated 2 years ago
- Fast, sensitive and accurate integration of single-cell data with Harmony☆631Mar 23, 2026Updated 2 weeks ago
- Mapping out the coarse-grained connectivity structures of complex manifolds.☆238May 23, 2020Updated 5 years ago
- CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.☆470Jun 6, 2025Updated 10 months ago
- Reference mapping for single-cell genomics☆401Mar 21, 2026Updated 3 weeks ago
- Single-cell Transcriptome and Regulome Analysis Pipeline☆307Mar 6, 2023Updated 3 years ago
- MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological …☆379Oct 3, 2024Updated last year
- R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets☆248Apr 1, 2026Updated last week
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- Detect doublets in single-cell RNA-seq data☆168Dec 29, 2020Updated 5 years ago
- Tools and methods for analysis of single cell assay data in R☆262Oct 17, 2025Updated 5 months ago
- A Bayesian model for compositional single-cell data analysis☆194Jan 13, 2026Updated 2 months ago
- Python implementation of the Loom file format - http://loompy.org☆148Dec 16, 2024Updated last year
- Benchmarking analysis of data integration tools☆409Sep 17, 2025Updated 6 months ago
- RNA velocity estimation in R☆196Sep 14, 2023Updated 2 years ago
- Inferring CNV from Single-Cell RNA-Seq☆662Nov 14, 2025Updated 4 months ago
- A tool for semi-automatic cell type classification☆464Mar 21, 2026Updated 2 weeks ago
- Ordering gene-expression and functional events in single-cell experiments☆30Mar 7, 2026Updated last month
- 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.
- ☆132Nov 17, 2023Updated 2 years ago
- Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data☆423Mar 30, 2026Updated last week
- Mapping the Functional Landscape of TCR Repertoire☆36Oct 8, 2021Updated 4 years ago
- A scanpy extension to analyse single-cell TCR and BCR data.☆246Updated this week
- Community-provided extensions to Seurat☆359Feb 17, 2026Updated last month
- Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕☆185Jun 24, 2021Updated 4 years ago
- R package for distinguishing cells from background barcodes in droplet-based single-cell RNA-seq data☆11Apr 19, 2023Updated 2 years ago