SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
☆501Apr 5, 2024Updated 2 years ago
Alternatives and similar repositories for SCENIC
Users that are interested in SCENIC 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…☆649Jun 26, 2025Updated last year
- A scalable SCENIC workflow for single-cell gene regulatory network analysis☆185Dec 8, 2022Updated 3 years ago
- Fast, sensitive and accurate integration of single-cell data with Harmony☆676Oct 15, 2026Updated 2 weeks ago
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data☆790Jan 6, 2024Updated 2 years ago
- NicheNet: predict active ligand-target links between interacting cells☆683Oct 23, 2026Updated last week
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- R package for detecting doublets in single-cell RNA sequencing data☆574Mar 21, 2025Updated last year
- Inferring CNV from Single-Cell RNA-Seq☆686Updated this week
- Functions for identifying and characterizing continuous developmental trajectories in single-cell data.☆348Apr 23, 2024Updated 2 years ago
- RNA velocity estimation in R☆196Sep 14, 2023Updated 3 years ago
- R toolkit for single cell genomics☆2,811Updated this week
- High dimensional weighted gene co-expression network analysis☆493Jun 16, 2026Updated 4 months ago
- AUCell: score single cells with gene regulatory networks☆207Mar 9, 2024Updated 2 years ago
- ☆363Dec 9, 2021Updated 4 years ago
- SingleR: Single-cell RNA-seq cell types Recognition (legacy version)☆347Jul 28, 2020Updated 6 years 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.
- SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…☆269Jan 16, 2026Updated 9 months ago
- RNA velocity estimation in Python☆177Oct 7, 2025Updated last year
- CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.☆491Jun 6, 2025Updated last year
- R package implementation of Milo for testing for differential abundance in KNN graphs☆450Aug 25, 2026Updated 2 months ago
- Assessing the purity of single cell population☆157Jun 3, 2022Updated 4 years ago
- This is the alpha version of the CellOracle package☆508Apr 30, 2026Updated 6 months ago
- A package to help convert different single-cell data formats to each other☆471Feb 20, 2026Updated 8 months ago
- ☆469Sep 22, 2026Updated last month
- ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)☆468Feb 18, 2025Updated last year
- 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.
- Community-provided extensions to Seurat☆372Oct 8, 2026Updated 3 weeks ago
- RNA Velocity generalized through dynamical modeling☆514Feb 25, 2026Updated 8 months ago
- ☆317Nov 10, 2024Updated last year
- CellRank: dynamics from multi-view single-cell data☆459Oct 14, 2026Updated 2 weeks ago
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics☆689Mar 4, 2026Updated 7 months ago
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆347Nov 1, 2022Updated 3 years ago
- Tools and methods for analysis of single cell assay data in R☆266Oct 17, 2025Updated last year
- R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters an…☆48Apr 8, 2022Updated 4 years ago
- An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.☆683Mar 11, 2026Updated 7 months ago
- 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.
- Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.☆3,887Updated this week
- R package for integrating and analyzing multiple single-cell datasets☆435Aug 18, 2026Updated 2 months ago
- Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data☆484Apr 11, 2026Updated 6 months ago
- Create cisTarget databases☆65Jun 18, 2025Updated last year
- Mapping out the coarse-grained connectivity structures of complex manifolds.☆248May 23, 2020Updated 6 years ago
- R package for single cell and other data analysis using diffusion maps☆114Oct 21, 2026Updated last week
- Quantifying metabolism activity at the single-cell resolution☆201Aug 20, 2026Updated 2 months ago