Table 3 Computational methods for cancer genome interpretation

Cancer gene prioritization

ActiveDriver

http://individual.utoronto.ca/reimand/ActiveDriver/

[73]

ContrastRank

http://snps.biofold.org/contrastrank/

[75]

DrGaP

https://code.google.com/p/drgap/

[70]

MuSiC

http://gmt.genome.wustl.edu/packages/genome-music/

[68]

MuSigCV

http://www.broadinstitute.org/cancer/cga/mutsig

[69]

OncodriveCLUST

http://bg.upf.edu/oncodriveclust

[74]

OncodriveFM

http://bg.upf.edu/oncodrivefm

[64]

Simon's tool

http://linus.nci.nih.gov/Data/YounA/software.zip

[71]

Cancer variant annotation tools

CanPredict

http://goo.gl/UK9lbv

[91]

CHASM

http://wiki.chasmsoftware.org/

[90]

DrCancer

http://snps.biofold.org/drcancer/

[89]

FATHMM

http://fathmm.biocompute.org.uk/cancer.html

[92]

MutationAssessor

http://mutationassessor.org

[78]

TransFIC

http://bg.upf.edu/transfic/

[93]

Pathway and network analysis

Dendrix

http://compbio.cs.brown.edu/projects/dendrix/

[113]

HotNet2

http://compbio.cs.brown.edu/projects/hotnet2/

[115]

MDPFinder

http://zhangroup.aporc.org/ShiHuaZhang

[107]

MEMo

http://cbio.mskcc.org/memo

[105]

PathScan

http://genome.wustl.edu/software/pathscan

[114]

PARADIGM

http://sbenz.github.com/Paradigm

[116]

Classification of tumor subclonal variants

ABSOLUTE

http://www.broadinstitute.org/cancer/cga/absolute

[122]

BTP

http://compbio.cs.brown.edu/projects/btp/

[123]

CloneHD

https://github.com/andrej-fischer/cloneHD/

[126]

PhyloSub

https://github.com/morrislab/phylosub/

[124]

PyClones

http://compbio.bccrc.ca/software/pyclone/

[125]