Table 1.

Computational biology tools to map Transcriptional Regulatory Networks.

Tools	Full names (when available)	Links to tool (when available)	Approaches and data used	References
ARACNe-AP	Algorithm for the Reconstruction of Accurate Cellular Networks	http://sourceforge.net/projects/aracne-ap	Information theory, bulk transcriptomics, tested on single-cell RNA-seq	[56], [60]
CLR	Context Likelihood of Relatedness		Information theory, bulk transcriptomics, tested on single-cell RNA-seq	[57]
ANOVerence		http://www2.bio.ifi.lmu.de/~kueffner/anova.tar.gz	Correlation, bulk transcriptomics	[58]
CoExpNetViz		http://bioinformatics.psb.ugent.be/webtools/coexpr/	Information theory, bulk transcriptomics	[59]
GeneXPress	Module Networks algorithm	https://pypi.org/project/GeneXpress/#files	Regression, bulk transcriptomics	[38]
GENIE3	GEne Network Inference with Ensemble of trees	https://bioconductor.org/packages/release/bioc/html/GENIE3.html	Regression, bulk transcriptomics, tested on single-cell RNA-seq	[39]
GRNBoost	Gene Regulatory Networks Boost	http://arboreto.readthedocs.io	Regression, bulk transcriptomics, tested on single-cell RNA-seq	[40]
TIGRESS	Trustful Inference of Gene REgulation using Stability Selection	http://cbio.ensmp.fr/tigress	Regression, bulk transcriptomics	[42]
LiPLike	Linear Profile Likelihood	https://gitlab.com/Gustafsson-lab/liplike	Regression, bulk transcriptomics	[41]
Banjo	Bayesian Network Inference with Java Objects	Source code and simulated data are available upon request	Bayesian inference, bulk transcriptomics	[63]
LeMoNe		http://bioinformatics.psb.ugent.be/software	Bayesian inference, bulk transcriptomics	[64]
TWNs	Transcriptome-Wide Networks	https://github.com/battle-lab/twn_tsn	Bayesian inference, splicing isoforms, bulk transcriptomics	[66]
NIR	Network Identification by multiple Regression		ODEs, bulk transcriptomics	[67]
Inferelator		freely available upon request	ODEs, bulk transcriptomics	[68]
GINsim	Gene Interaction Network simulation suite	http://ginsim.org/	Logical modelling, bulk transcriptomics	[70], [71]
GNA	Genetic Network Analyzer	http://www-helix.inrialpes.fr/gna	Piecewise linear equations, bulk transcriptomics	[72]
Network Deconvolution	Network Deconvolution	http://compbio.mit.edu/nd/index.html	Network deconvolution, bulk transcriptomics	[73]
RegulonDB		http://regulondb.ccg.unam.mx	TF regulatory information, relational database, bulk transcriptomics	[34], [28]
GRAM	Genetic Regulatory Modules		TF regulatory information, bulk transcriptomics	[26]
DISTILLER	Data Integration System to Identify Links in Expression Regulation		TF regulatory information, bulk transcriptomics	[35]
SEREND	SEmi-supervised REgulatory Network Discoverer	http://sb.cs.cmu.edu/ecoli/	TF regulatory information, logistic regression, bulk transcriptomics	[36]
DeMAND	Detecting Mechanism of Action by Network Dysregulation	Bioconductor package or web based geWorkbench module	TF regulatory information, logistic regression, bulk transcriptomics	[37]
SIRENE	Supervised Inference of REgulatory NEtworks	http://projects.cbio.mines-paristech.fr/sirene/	TF regulatory information, SNV classifiers, bulk transcriptomics	[33]
DREM	Dynamic Regulatory Events Miner	http://sb.cs.cmu.edu/drem/	TF regulatory information, HMM based, bulk transcriptomics	[32], [29]
Flynet		http://compbio.mit.edu/flynet/	Evolutionary conserved sequence motifs integrated with TF binding and chromatin modification data	[77]
SCENIC	Single-CEll regulatory Network Inference and Clustering	https://aertslab.org/#scenic	Single-cell RNA-seq, based on GENIE3 and GENEBoost	[62]
SCINET	Single-Cell Imputation and NETwork construction	https://github.com/shmohammadi86/SCINET	Single-cell RNA-seq and a reference global interactome	[85]
PIDC	Partial Information Decomposition and Context		Single-cell RNA-seq, information theory, bulk transcriptomics, partial information decomposition	[86]
SCNS toolkit	Single-Cell Network synthesis	http://scns.stemcells.cam.ac.uk/	Single-cell RNA-seq, boolean logical rules	[87]
SCODE	scRNA-seq performed on differentiating cells by integrating the transformation of linear ODEs and linear regression	https://github.com/hmatsu1226/SCODE	Single-cell RNA-seq via regulatory dynamics based on ODEs	[88]
CSHMM-TF	Continuous-State Hidden Markov Models TF	https://github.com/jessica1338/CSHMM-TF-for-time-series-scRNA-Seq	Single-cell RNA-seq and TF-gene interaction, Continuous-State Hidden Markov Models	[89]
MARINa	Master Regulator Inference Algorithm	http://califano.c2b2.columbia.edu/marina-license	Differential expression and protein-protein interactions	[93]
GNAT		http://mostafavilab.stat.ubc.ca/gnat/	Bulk transcriptomics using hierarchy of tissues, Gaussian Markov Random Fields	[95]
CRCmapper	Core transcriptional Regulatory Circuitry mapper	https://github.com/ViolaineSaint-Andre/CRCmapper	Graph theory, enhancer information (H3K27ac or relevant TF ChIP-seq) and optionally expression and/or ATAC-seq data	[15]