Simulating Gene Regulatory Networks for Validation of scRNA-seq Data Alignment Methods

Inferring Gene Regulatory Networks in Stem Cells: Methods and Applications.

Uncovering Cellular Resolution in scRNAseq via Unbiased Cell and Gene Network Analysis

The results indicate that GmGM provides a unified, reproducible framework for joint cell clustering and gene-network inference, capable of revealing cellular structure beyond that captured by conventional pipelines.

scFlowReport: A Reproducible Workflow for Comparative Downstream Biological Analysis of Single-Cell RNA-seq Data

Application of scFlowReport to a publicly available Atopic Dermatitis scRNA-seq dataset demonstrated its utility by enabling researchers to obtain complementary biological evidence from multiple established downstream analyses.

Benchmarking methods for inferring single-cell transcription factor activity using large-scale perturbation sequencing data

A comprehensive evaluation of eight mainstream TFA inference methods using large-scale, high-quality single-cell perturbation sequencing (Perturb-seq) datasets shows that metaTF, which employs an integrated GRN, achieves the best performance across multiple metrics, including TF coverage, predictive accuracy for pertur...

scGraphVerse: a modular workflow for single-cell gene network inference

Abstract Motivation Inferring gene networks from single-cell RNA sequencing data is challenging due to high sparsity, dimensionality, and technical noise. Current pipelines lack the multi-dataset integration and comprehensive post-processing analysis. Results scGraphVerse is an R package that integrates multiple algori...

FERRET: Framework to Evaluate Robustness in Regulatory Networks Using Heterogeneous Cell Types

This work validate FERRET using experimentally derived ChIP-seq networks from B lymphocytes and fibroblasts as positive controls and randomly generated networks as negative controls, showing that biologically related networks receive high robustness scores whereas randomly generated networks receive scores consistent w...