SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
☆498Apr 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…☆638Jun 26, 2025Updated last year
- A scalable SCENIC workflow for single-cell gene regulatory network analysis☆183Dec 8, 2022Updated 3 years ago
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data☆793Jan 6, 2024Updated 2 years ago
- R package for detecting doublets in single-cell RNA sequencing data☆565Mar 21, 2025Updated last year
- Fast, sensitive and accurate integration of single-cell data with Harmony☆672Jun 5, 2026Updated 3 months ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- NicheNet: predict active ligand-target links between interacting cells☆679Jun 1, 2026Updated 3 months ago
- Inferring CNV from Single-Cell RNA-Seq☆685Nov 14, 2025Updated 10 months ago
- Functions for identifying and characterizing continuous developmental trajectories in single-cell data.☆349Apr 23, 2024Updated 2 years ago
- R toolkit for single cell genomics☆2,801Updated this week
- RNA velocity estimation in R☆197Sep 14, 2023Updated 3 years ago
- ☆363Dec 9, 2021Updated 4 years ago
- RNA velocity estimation in Python☆177Oct 7, 2025Updated 11 months ago
- Community-provided extensions to Seurat☆372Jun 29, 2026Updated 2 months ago
- High dimensional weighted gene co-expression network analysis☆494Jun 16, 2026Updated 3 months ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- AUCell: score single cells with gene regulatory networks☆204Mar 9, 2024Updated 2 years ago
- SingleR: Single-cell RNA-seq cell types Recognition (legacy version)☆347Jul 28, 2020Updated 6 years ago
- R package implementation of Milo for testing for differential abundance in KNN graphs☆448Aug 25, 2026Updated 3 weeks ago
- SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…☆264Jan 16, 2026Updated 8 months ago
- A package to help convert different single-cell data formats to each other☆470Feb 20, 2026Updated 7 months ago
- RNA Velocity generalized through dynamical modeling☆512Feb 25, 2026Updated 6 months ago
- Create cisTarget databases☆63Jun 18, 2025Updated last year
- Tools and methods for analysis of single cell assay data in R☆264Oct 17, 2025Updated 11 months ago
- CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.☆487Jun 6, 2025Updated last year
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics☆671Mar 4, 2026Updated 6 months ago
- ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)☆465Feb 18, 2025Updated last year
- This is the alpha version of the CellOracle package☆499Apr 30, 2026Updated 4 months ago
- An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.☆675Mar 11, 2026Updated 6 months ago
- Quantifying metabolism activity at the single-cell resolution☆196Aug 20, 2026Updated last month
- Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.☆3,857Sep 7, 2026Updated 2 weeks ago
- Signature Analysis and Visualization for Single-Cell RNA-seq☆185Jun 10, 2024Updated 2 years ago
- ☆294Jul 15, 2022Updated 4 years ago
- Assessing the purity of single cell population☆156Jun 3, 2022Updated 4 years ago
- 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.
- CellRank: dynamics from multi-view single-cell data☆456Updated this week
- ☆468Sep 9, 2026Updated last week
- 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
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆343Nov 1, 2022Updated 3 years ago
- R package for integrating and analyzing multiple single-cell datasets☆432Aug 18, 2026Updated last month
- Panoramic stitching of single cell data☆295Jul 14, 2025Updated last year
- RcisTarget: Transcription factor binding motif enrichment☆50Mar 4, 2024Updated 2 years ago