GeneSPIDER2: large scale GRN simulation and benchmarking with perturbed single-cell data.

ABSTRACT: Single-cell data is increasingly used for gene regulatory network (GRN) inference, and benchmarks for this have been developed based on simulated data. However, existing single-cell simulators cannot model the effects of gene perturbations. A further challenge lies in generating large-scale GRNs that often struggle with computational and stability issues. We present GeneSPIDER2, an update of the GeneSPIDER MATLAB toolbox for GRN benchmarking, inference, and analysis. Several software modules have improved capabilities and performance, and new functionalities have been added. A major improvement is the ability to generate large GRNs with biologically realistic topological properties in terms of scale-free degree distribution and modularity. Another major addition is a simulation of single-c

SUBMITTER: Garbulowski M 

PROVIDER: S-EPMC11409065 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature