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Contents
- 1
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Stephen W Hartley and James C Mullikin.
Qorts: a comprehensive toolset for quality control and data
processing of rna-seq experiments.
BMC bioinformatics, 16(1):224, 2015.
URL: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4506620/.
- 2
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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.
- 3
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Simon Anders Michael I Love, Wolfgang Huber.
Moderated estimation of fold change and dispersion for rna-seq data
with deseq2.
Genome Biology, 15:550, 2014.
URL: http://www.genomebiology.com/content/15/12/550.
- 4
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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.
- 5
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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.
- 6
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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.
- 7
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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.
- 8
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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.
- 9
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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.
- 10
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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.
Dr Stephen William Hartley
2016-06-14