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
| Â |
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] |