Bibliography

1

Simon Anders and Wolfgang Huber.
Differential expression analysis for sequence count data.
Genome Biology, 11:R106, 2010.
URL: http://genomebiology.com/2010/11/10/R106.

2

Mark D. Robinson and Gordon K. Smyth.
Moderated statistical tests for assessing differences in tag abundance.
Bioinformatics, 23:2881, 2007.
URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/21/2881, http://arxiv.org/abs/http://bioinformatics.oxfordjournals.org/cgi/reprint/23/21/2881.pdf arXiv:http://bioinformatics.oxfordjournals.org/cgi/reprint/23/21/2881.pdf, http://dx.doi.org/10.1093/bioinformatics/btm453 doi:10.1093/bioinformatics/btm453.

3

Simon Anders, Alejandro Reyes, and Wolfgang Huber.
Detecting differential usage of exons from RNA-seq data.
Genome Research, 22:2008, 2012.
http://dx.doi.org/10.1101/gr.133744.111 doi:10.1101/gr.133744.111.

4

Alexander Dobin, Carrie A. Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, and Thomas R. Gingeras.
STAR: ultrafast universal RNA-seq aligner.
Bioinformatics, 29(1):15-21, 2013.
URL: http://bioinformatics.oxfordjournals.org/content/29/1/15.abstract, http://arxiv.org/abs/http://bioinformatics.oxfordjournals.org/content/29/1/15.full.pdf+html arXiv:http://bioinformatics.oxfordjournals.org/content/29/1/15.full.pdf+html, http://dx.doi.org/10.1093/bioinformatics/bts635 doi:10.1093/bioinformatics/bts635.

5

Thomas D. Wu and Serban Nacu.
Fast and SNP-tolerant detection of complex variants and splicing in short reads.
Bioinformatics, 26(7):873-881, 2010.
URL: http://bioinformatics.oxfordjournals.org/content/26/7/873.abstract, http://arxiv.org/abs/http://bioinformatics.oxfordjournals.org/content/26/7/873.full.pdf+html arXiv:http://bioinformatics.oxfordjournals.org/content/26/7/873.full.pdf+html, http://dx.doi.org/10.1093/bioinformatics/btq057 doi:10.1093/bioinformatics/btq057.

6

Daehwan Kim, Geo Pertea, Cole Trapnell, Harold Pimentel, Ryan Kelley, and Steven Salzberg.
Tophat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.
Genome Biology, 14(4):R36, 2013.
URL: http://genomebiology.com/2013/14/4/R36, http://dx.doi.org/10.1186/gb-2013-14-4-r36 doi:10.1186/gb-2013-14-4-r36.

7

McCarthy DJ Robinson MD and Smyth GK.
edger: a bioconductor package for differential expression analysis of digital gene expression data.
Bioinformatics, 26:139-140, 2010.

8

Davis J. McCarthy, Yunshun Chen, and Gordon K. Smyth.
Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.
Nucleic Acids Research, 40:4288-4297, 2012.