cailab-tamu/scTenifoldKnk

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.

Single-cell perturbation analysis

Easy single cell analysis platform for enrichment

State is a machine learning model that predicts cellular perturbation response across diverse contexts

Modeling complex perturbations with CellFlow

Fast Wilcoxon and auROC

Combined RNA and ATAC Footprint Training of Gene Regulatory Network

Methods to discover gene programs on single-cell data

Agentic design of virtual cell models