GeneSPIDER

GeneSPIDER (Generation and Simulation Package for Informative Data ExploRation) is a Matlab toolbox for gene regulatory network inference and benchmarking with controlled network and data properties. It supplies essential components that have been missing to existing network inference methods in common use and wrappers for a selected number of inference methods. GeneSPIDER contains tools for controlling and evaluating network topology (random, small-world, scale-free), stability of linear time-invariant systems, signal to noise ratio (SNR), and network interampatteness, properties that has been shown to play a major role in the ability to infer a good network that can explain the data. GeneSPIDER2 is a new version of GeneSPIDER that allows simulating single-cell gene expression data. Other improvments and functions have been implemented as well, such as large scale-free GRN generator, new inference methods, integration with NestBoot and detailed tutorials accessed via https://sonnhammer-tutorials.bitbucket.io/genespider.html. GeneSPIDER2 is publicly available at https://bitbucket.org/sonnhammergrni/genespider/.