Table 1 A brief overview of available methodologies to construct network models

GENIE3³²/

GRNBoost2³³

O

X

X

O

X

X

Python

and R

https://github.com/aertslab

SINCERETIES⁷⁹

O

X

O

X

X

X

R and

MATLAB

https://github.com/CABSEL/SINCERITIES

PIDC³⁴

O

X

X

X

X

X

Julia

https://github.com/Tchanders/NetworkInference.jl

LEAP³⁵

O

X

O

O

X

X

R

R package LEAP available on CRAN

SCENIC³⁶

O

X

O

O

X

cisTarget

Python

and R

https://scenic.aertslab.org/

SCENIC+³⁷

O

O

O

O

X

cisTarget

Python

and R

https://github.com/aertslab/scenicplus

scMTNI⁸⁰

O

O

X

O

X

CIS-BP

C++

https://github.com/Roy-lab/scMTNI

Pando³⁸

O

O

O

X

X

CIS-BP

R

https://github.com/quadbio/Pando

CellOracle⁴⁰

O

O

O

O

X

CIS-BP

Python

https://github.com/morris-lab/CellOracle

FigR⁸¹

O

O

O

X

X

CIS-BP

R

https://github.com/buenrostrolab/FigR

Dictys³⁹

O

O

O

O

X

HOCOMOCO

Python

https://github.com/pinellolab/dictys

scTenifoldKnk⁴⁶

O

X

O

O

X

X

R and

MATLAB

https://github.com/cailab-tamu/scTenifoldKnk

BTR⁴¹

O

X

O

X

O

X

R

https://github.com/cheeyeelim/btr

SCNS⁴²

O

X

O

X

O

X

F# and

Javascript

https://github.com/swoodhouse/SCNS-GUI

SCODE⁴⁴

O

X

O

O

O

X

R and

Julia

https://github.com/hmatsu1226/SCODE

SCOUP⁴⁵

O

X

O

X

O

X

C++

https://github.com/hmatsu1226/SCOUP