pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
☆617Jun 26, 2025Updated last year
Alternatives and similar repositories for pySCENIC
Users that are interested in pySCENIC are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.☆488Apr 5, 2024Updated 2 years ago
- A scalable SCENIC workflow for single-cell gene regulatory network analysis☆180Dec 8, 2022Updated 3 years ago
- SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…☆260Jan 16, 2026Updated 5 months ago
- CellRank: dynamics from multi-view single-cell data☆453Jun 24, 2026Updated last week
- CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.☆475Jun 6, 2025Updated last year
- 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.
- ☆364Dec 9, 2021Updated 4 years ago
- This is the alpha version of the CellOracle package☆470Apr 30, 2026Updated 2 months ago
- Single-cell analysis in Python. Scales to >100M cells.☆2,493Updated this week
- A Bayesian model for compositional single-cell data analysis☆199Jan 13, 2026Updated 5 months ago
- Inferring CNV from Single-Cell RNA-Seq☆675Nov 14, 2025Updated 7 months ago
- R package for detecting doublets in single-cell RNA sequencing data☆552Mar 21, 2025Updated last year
- RNA Velocity generalized through dynamical modeling☆506Feb 25, 2026Updated 4 months ago
- Reference mapping for single-cell genomics☆406Updated this week
- NicheNet: predict active ligand-target links between interacting cells☆662Jun 1, 2026Updated last month
- 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.
- Fast, sensitive and accurate integration of single-cell data with Harmony☆661Jun 5, 2026Updated 3 weeks ago
- CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.☆403Jun 16, 2026Updated 2 weeks ago
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data☆791Jan 6, 2024Updated 2 years ago
- AUCell: score single cells with gene regulatory networks☆196Mar 9, 2024Updated 2 years ago
- A package to help convert different single-cell data formats to each other☆470Feb 20, 2026Updated 4 months ago
- Differential expression analysis for single-cell RNA-seq data.☆206Oct 21, 2025Updated 8 months ago
- CytoTRACE 2 is an interpretable AI method for predicting cellular potency and absolute developmental potential from scRNA-seq data.☆259Jun 19, 2026Updated last week
- Deep probabilistic analysis of single-cell and spatial omics data☆1,649Updated this week
- Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data☆449Apr 11, 2026Updated 2 months ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- ☆456May 26, 2026Updated last month
- Episcanpy: Epigenomics Single Cell Analysis in Python☆151Dec 5, 2024Updated last year
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics☆630Mar 4, 2026Updated 3 months ago
- trajectory inference☆109Jan 27, 2025Updated last year
- Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …☆503Updated this week
- A tool for semi-automatic cell type classification☆491May 22, 2026Updated last month
- Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.☆3,771Jun 23, 2026Updated last week
- High dimensional weighted gene co-expression network analysis☆481Jun 16, 2026Updated 2 weeks ago
- Python package to perform enrichment analysis from omics data.☆272Jun 22, 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.
- Convert between AnnData and SingleCellExperiment☆151Updated this week
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆332Nov 1, 2022Updated 3 years ago
- R toolkit for single cell genomics☆2,757Updated this week
- Functions for identifying and characterizing continuous developmental trajectories in single-cell data.☆339Apr 23, 2024Updated 2 years ago
- Methods for detecting doublets in single-cell sequencing data☆254Jun 23, 2026Updated last week
- Mapping out the coarse-grained connectivity structures of complex manifolds.☆244May 23, 2020Updated 6 years ago
- ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)☆458Feb 18, 2025Updated last year