qwerty239qwe/scTenifoldpy

R/MATLAB package to perform virtual knockout experiments on single-cell gene regulatory networks.

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.

Gene knockout inference with variational graph autoencoder learning single-cell gene regulatory networks

Multiome GRN inference.

Metacells - Single-cell RNA Sequencing Analysis

Manifold learning to detect cell-cell interactions.

GeneCompass

Single-cell analysis in Python. Scales to >100M cells.