Table 4 Computational tools for cancer transcriptomics

Spliced alignment

TopHat

http://tophat.cbcb.umd.edu/

[61, 69]

MapSplice

http://www.netlab.uky.edu/p/bioinfo/MapSplice

[62]

SpliceMap

http://www.stanford.edu/group/wonglab/SpliceMap/

[63]

GSNAP

http://research-pub.gene.com/gmap/

[64]

STAR

http://gingeraslab.cshl.edu/STAR/

[65]

Differential expression

CuffDiff

http://cufflinks.cbcb.umd.edu/

[68, 69]

EdgeR

http://www.bioconductor.org/packages/2.11/bioc/html/edgeR.html

[67]

DESeq

http://www-huber.embl.de/users/anders/DESeq/

[66]

Myrna

http://bowtie-bio.sourceforge.net/myrna/index.shtml

[81]

Alternative splicing

CuffDiff

http://cufflinks.cbcb.umd.edu/

[68, 69]

MISO

http://genes.mit.edu/burgelab/miso/

[71]

DEXseq

http://watson.nci.nih.gov/bioc_mirror/packages/2.9/bioc/html/DEXSeq.html

[82]

Alexa-seq

http://www.alexaplatform.org/alexa_seq/

[70]

Gene fusion

SOAPfusion

http://soap.genomics.org.cn/SOAPfusion.html

TopHat-Fusion

http://tophat.cbcb.umd.edu/fusion_index.html

[72]

BreakFusion

http://bioinformatics.mdanderson.org/main/BreakFusion

[73]

FusionHunter

http://bioen-compbio.bioen.illinois.edu/FusionHunter/

[74]

deFuse

http://sourceforge.net/apps/mediawiki/defuse/

[75]

FusionAnalyser

http://www.ilte-cml.org/FusionAnalyser/

[76]