SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
☆261Jan 16, 2026Updated 6 months ago
Alternatives and similar repositories for scenicplus
Users that are interested in scenicplus are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.☆82Jul 9, 2026Updated last week
- This is the alpha version of the CellOracle package☆478Apr 30, 2026Updated 2 months ago
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆625Jun 26, 2025Updated last year
- Context specific and dynamic gene regulatory network reconstruction and analysis☆129Updated this week
- ☆132Jul 11, 2026Updated last week
- 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.
- R package implementation of Milo for testing for differential abundance in KNN graphs☆440May 11, 2026Updated 2 months ago
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data☆192Mar 27, 2025Updated last year
- CellRank: dynamics from multi-view single-cell data☆454Updated this week
- ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)☆461Feb 18, 2025Updated last year
- Multi-omic velocity inference☆120Oct 23, 2024Updated last year
- Functional Inference of Gene Regulation☆54Jul 5, 2024Updated 2 years ago
- Analysis of cell-cell communication at single-cell resolution☆107Sep 10, 2024Updated last year
- Single-cell epigenomics analysis tools☆323Jul 13, 2026Updated last week
- SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.☆491Apr 5, 2024Updated 2 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.☆70Jul 9, 2026Updated last week
- Aligning gene expression trajectories of single-cell reference and query systems☆89Aug 10, 2025Updated 11 months ago
- scOpen: single-cell open chromatin analysis via NMF modelling☆28Feb 4, 2023Updated 3 years ago
- A python-based package and software to predict metabolite mediated cell-cell communications by single-cell RNA-seq data☆83Jul 25, 2025Updated 11 months ago
- A package to help convert different single-cell data formats to each other☆473Feb 20, 2026Updated 5 months ago
- ☆155Mar 20, 2026Updated 4 months ago
- Graph-linked unified embedding for single-cell multi-omics data integration☆472Feb 9, 2026Updated 5 months ago
- Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆472Jan 22, 2026Updated 6 months ago
- CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.☆406Jun 16, 2026Updated last month
- 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.
- A tool for semi-automatic cell type classification☆496May 22, 2026Updated 2 months ago
- R package for pathway analysis in scRNA-seq data☆82Aug 17, 2024Updated last year
- ☆68Apr 22, 2026Updated 3 months ago
- AUCell: score single cells with gene regulatory networks☆199Mar 9, 2024Updated 2 years ago
- CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for desi…☆75Jul 3, 2026Updated 2 weeks ago
- pycistarget is a python module to perform motif enrichment analysis in sets of regions with different tools and identify high confidence …☆20Apr 14, 2026Updated 3 months ago
- R toolkit for the analysis of single-cell chromatin data☆424Updated this week
- ☆15Jun 4, 2023Updated 3 years ago
- LIANA: a LIgand-receptor ANalysis frAmework☆245Aug 7, 2024Updated last year
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- All code associated with manuscript detailing scATAC and scRNA-seq following stimulus of PBMCs☆42Mar 20, 2023Updated 3 years ago
- A tool for detecting somatic variants in single cell data☆224Sep 15, 2024Updated last year
- Scissor package☆271May 10, 2024Updated 2 years ago
- Reference mapping for single-cell genomics☆406Jun 26, 2026Updated 3 weeks ago
- Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms☆201Jan 30, 2026Updated 5 months ago
- RNA Velocity generalized through dynamical modeling☆507Feb 25, 2026Updated 4 months ago
- ☆16Sep 1, 2023Updated 2 years ago