Table 1.
Computational tools for GRN inference using single-cell data. Each method is categorized according to the core model they use to construct the GRN. 
Tools with a web-based interface. 
Tools provided as scripts that are executable in the command line. 
Tools distributed as stand-alone packages. (*) Inference Snapshot provides a mixture of scripts written in C++ and Matlab. This requires users to switch between the two environments to finish any single analysis. Tools with an undeclared license (None) are free for noncommercial use without redistribution. (**) SCENIC is free for noncommercial use and has its own license agreement. The usability of each software ranges from 1 (
) to 5 (
). This score indicates how easy it is for users to analyze an scRNA-seq dataset using a tool. The higher the score (and the darker the color), the easier it is to use. A method with a score of 5 means that it is very easy to start an analysis with the method
| Method | Availability | Code | Pkg. | Ref. | Year | Cit. | License | Usability |
|---|---|---|---|---|---|---|---|---|
| Boolean model | ||||||||
| Boolean Pseudotime | https://github.com/fionahamey/Pseudotime-network-inference | Python |
|
[34] | 2017 | 23 | Apache 2.0 |
|
| BTR | https://cran.r-project.org/package=BTR | R |
|
[35] | 2016 | 23 | GPL-3 |
|
| SCNS | https://github.com/swoodhouse/SCNS-GUI | F# |
|
[36] | 2018 | 5 | MIT |
|
| Differential equation | ||||||||
| Inference Snapshot | https://www.helmholtz-muenchen.de/fileadmin/ICB/software /inferenceSnapshot.zip | C++/Matlab | * | [37] | 2015 | 80 | None |
|
| SCODE | https://github.com/hmatsu1226/SCODE | R/Julia/Ruby |
|
[38] | 2017 | 34 | MIT |
|
| SCOUP | https://github.com/hmatsu1226/SCOUP | C++ |
|
[39] | 2016 | 24 | MIT |
|
| Gene correlation | ||||||||
| Empirical Bayes | https://github.com/ananth-pallaseni/EmpiricalBayes.jl | Julia |
|
[40] | 2018 | 2 | MIT |
|
| Information Measures | https://github.com/Tchanders/InformationMeasures.jl | Julia |
|
[41] | 2017 | 61 | MIT |
|
| NLNET | https://cran.r-project.org/package=nlnet | R |
|
[42] | 2016 | 1 | GPL 2 |
|
| SINCERA | https://research.cchmc.org/pbge/sincera.html | R |
|
[43] | 2015 | 115 | GPL-3 |
|
| SCENIC | https://github.com/aertslab/SCENIC | R/Python |
|
[44] | 2017 | 149 | Free
|
|
| Correlation ensemble over pseudotime | ||||||||
| LEAP | https://cran.r-project.org/package=LEAP | R |
|
[45] | 2016 | 18 | GPL-2 |
|
| SINCERITIES | http://www.cabsel.ethz.ch/tools/sincerities.html | R/Matlab |
|
[46] | 2017 | 20 | BSD |
|
| SCIMITAR | https://github.com/dimenwarper/scimitar | Python |
|
[47] | 2017 | 8 | None |
|
| SCINGE | https://github.com/gitter-lab/SCINGE | Matlab |
|
[48] | 2019 | 1 | MIT |
|