A scalable SCENIC workflow for single-cell gene regulatory network analysis
☆182Dec 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…☆631Jun 26, 2025Updated last year
- SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.☆494Apr 5, 2024Updated 2 years ago
- A package to help convert different single-cell data formats to each other☆470Feb 20, 2026Updated 5 months ago
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data☆793Jan 6, 2024Updated 2 years ago
- Algorithms for single-cell analysis☆29Jul 19, 2021Updated 5 years ago
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- RNA Velocity generalized through dynamical modeling☆506Feb 25, 2026Updated 5 months ago
- Create cisTarget databases☆61Jun 18, 2025Updated last year
- Interfaces for HDF5-based Single Cell File Formats☆178Nov 4, 2023Updated 2 years ago
- Convert between AnnData and SingleCellExperiment☆152Aug 4, 2026Updated last week
- R package for detecting doublets in single-cell RNA sequencing data☆557Mar 21, 2025Updated last year
- NicheNet: predict active ligand-target links between interacting cells☆670Jun 1, 2026Updated 2 months ago
- CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data☆152Feb 20, 2025Updated last year
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data☆194Mar 27, 2025Updated last year
- ☆364Dec 9, 2021Updated 4 years 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 implementation of Milo for testing for differential abundance in KNN graphs☆442May 11, 2026Updated 2 months ago
- Fast, sensitive and accurate integration of single-cell data with Harmony☆667Jun 5, 2026Updated 2 months ago
- Batch balanced KNN☆180Oct 11, 2023Updated 2 years ago
- Reference mapping for single-cell genomics☆407Jun 26, 2026Updated last month
- CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.☆479Jun 6, 2025Updated last year
- Mapping out the coarse-grained connectivity structures of complex manifolds.☆246May 23, 2020Updated 6 years ago
- MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological …☆387Oct 3, 2024Updated last year
- Single-cell Transcriptome and Regulome Analysis Pipeline☆312Mar 6, 2023Updated 3 years ago
- R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets☆257Jun 28, 2026Updated last month
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Tools and methods for analysis of single cell assay data in R☆265Oct 17, 2025Updated 9 months ago
- A Bayesian model for compositional single-cell data analysis☆199Jan 13, 2026Updated 6 months ago
- Detect doublets in single-cell RNA-seq data☆180Dec 29, 2020Updated 5 years ago
- Python implementation of the Loom file format - http://loompy.org☆150Dec 16, 2024Updated last year
- R package for single-cell comparative regulatory analysis☆12Jun 26, 2021Updated 5 years ago
- RNA velocity estimation in R☆196Sep 14, 2023Updated 2 years ago
- Inferring CNV from Single-Cell RNA-Seq☆680Nov 14, 2025Updated 8 months ago
- Ordering gene-expression and functional events in single-cell experiments☆33Jul 6, 2026Updated last month
- Benchmarking analysis of data integration tools☆426Apr 27, 2026Updated 3 months 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.
- ☆134Nov 17, 2023Updated 2 years ago
- A tool for semi-automatic cell type classification☆500May 22, 2026Updated 2 months ago
- BEELINE: evaluation of algorithms for gene regulatory network inference☆215Jul 11, 2026Updated 3 weeks ago
- Mapping the Functional Landscape of TCR Repertoire☆36Oct 8, 2021Updated 4 years ago
- A scanpy extension to analyse single-cell TCR and BCR data.☆264Updated this week
- Community-provided extensions to Seurat☆370Jun 29, 2026Updated last month
- Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data☆463Apr 11, 2026Updated 3 months ago