Table 2. Driver prediction algorithms.

Name	Ref.	Repository	Level	Principles
20/20plus	[6]	https://github.com/KarchinLab/2020plus	gene	Machine learning, trained on Cancer Genome Landscapes (20/20 rule); Nonsynonymous/Synonymous, clustering, conservation (uses UCSC’s 46-way vertebrate alignment and SNVBox), impact (uses VEST), network (uses BioGrid), expression, chromatin, replication (uses MutSigCV)
ANDRIF	This paper	https://github.com/belikov-av/ANDRIF	Chromosomal arm, chromosome	Recurrence
CHASMplus	[7]	https://github.com/KarchinLab/CHASMplus	mutation	Machine learning, trained on TCGA; clustering (uses HotMAPS 1D), conservation (uses UCSC Multiz-100-way and SNV box), network (uses Interactome Insider)
CompositeDriver	[8]	https://github.com/mil2041/CompositeDriver	gene	Recurrence, impact (uses FunSeq2)
dNdScv	[2]	https://github.com/im3sanger/dndscv	gene	Nonsynonymous/Synonymous
DriverNet	[9]	https://github.com/shahcompbio/drivernet https://bioconductor.org/packages/release/bioc/html/DriverNet.html	gene	Network (uses MGSA and a human functional protein interaction network), impact (uses gene expression outliers)
HotMAPS	[10]	https://github.com/karchinlab/HotMAPS	mutation	3D clustering (uses Protein Data Bank and ModPipe)
OncodriveCLUSTL	[11]	http://bbglab.irbbarcelona.org/oncodriveclustl/analysis https://bitbucket.org/bbglab/oncodriveclustl/src/master/	gene	Clustering
OncodriveFML	[12]	http://bbglab.irbbarcelona.org/oncodrivefml/analysis https://bitbucket.org/bbglab/oncodrivefml/src/master/	gene	Recurrence, Impact (uses CADD and RNAsnp)
SNADRIF	This paper	https://github.com/belikov-av/SNADRIF	gene	Nonsynonymous/Synonymous
Bailey et al, 2018	[8]	https://www.cell.com/cell/fulltext/S0092-8674(18)30237-X	gene	Consensus driver gene list from 26 algorithms applied to PanCanAtlas data
COSMIC Cancer Gene Census	[14]	https://cancer.sanger.ac.uk/cosmic/census?tier=1	gene	Manually curated list of cancer driver genes, current “gold standard”