1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
|
@Article{Anders:2010:GB,
url = {http://genomebiology.com/2010/11/10/R106},
author = {Simon Anders and Wolfgang Huber},
Title = {{D}ifferential expression analysis for sequence
count data},
Journal = {Genome Biology},
Year = 2010,
Volume = 11,
Pages = {R106},
}
@article{DEXSeqPaper,
author = {Simon Anders and Alejandro Reyes and Wolfgang Huber},
title = {Detecting differential usage of exons from {RNA-seq}
data},
year = 2012,
journal = {Genome Research},
Volume = 22,
Pages = "2008",
doi = {10.1101/gr.133744.111},
}
@article{Brooks2010,
author = {Angela N. Brooks and Li Yang and Michael O. Duff and Kasper D. Hansen and
Jung W. Park and Sandrine Dudoit and Steven E. Brenner and Brenton R. Graveley},
doi = {10.1101/gr.108662.110},
issn = {1088},
journal = {Genome Research},
volume = {21},
pages = {193--202},
title = {{Conservation of an RNA regulatory map between
Drosophila and mammals}},
url =
{http://genome.cshlp.org/cgi/doi/10.1101/gr.108662.110},
year = 2011
}
@article{edgeR,
author = {Robinson, Mark D. and Smyth, Gordon K.},
title = {Moderated statistical tests for assessing
differences in tag abundance},
journal = {Bioinformatics},
volume = 23,
pages = {2881},
doi = {10.1093/bioinformatics/btm453},
year = 2007,
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/21/2881},
eprint = {http://bioinformatics.oxfordjournals.org/cgi/reprint/23/21/2881.pdf}
}
@article{edgeR_GLM,
author = {McCarthy, Davis J. and Chen, Yunshun and Smyth, Gordon K.},
year = {2012},
title = {Differential expression analysis of multifactor {RNA-Seq} experiments with respect to biological variation},
journal = {Nucleic Acids Research},
volume = {40},
pages = {4288-4297}
}
@misc{pasillaVignette,
title = {Data preprocessing and creation of the data objects {pasillaGenes} and {pasillaExons}},
author = {Alejandro Reyes},
year = {2013},
howpublished = {Vignette to Bioconductor data package \emph{pasilla}, \url{http://bioconductor.org/packages/release/data/experiment/html/pasilla.html}}
}
@article{DEProt,
title = {Count-based differential expression analysis of {RNA} sequencing data using {R} and {Bioconductor}},
author = {Simon Anders and Davis J. McCarthy and Yunshen Chen and Michal Okoniewski and Gordon K. Smyth and Wolfgang Huber and Mark D. Robinson},
year = {2013},
journal = {Nature Protocols},
volume = {8},
pages = {1765},
doi = {10.1038/nprot.2013.099}
}
@misc{parathyroidSEVignette,
title = {{SummarizedExperiment for RNA-Seq of primary cultures of parathyroid tumors by Haglund et al., J Clin Endocrinol Metab 2012}},
author = {Michael Love},
year = {2013},
howpublished = {Vignette to Bioconductor data package \emph{parathyroidSE}, \url{http://bioconductor.org/packages/release/data/experiment/html/parathyroidSE.html}}
}
@article{parathyroidPaper,
author = {Haglund, Felix and Ma, Ran and Huss, Mikael and Sulaiman, Luqman and Lu, Ming and Nilsson, Inga-Lena and H\"o\"og, Anders and Juhlin, C. Christofer and Hartman, Johan and Larsson, Catharina},
title = {Evidence of a Functional Estrogen Receptor in Parathyroid Adenomas},
volume = {97},
number = {12},
year = {2012},
doi = {10.1210/jc.2012-2484},
URL = {http://jcem.endojournals.org/content/97/12/4631.abstract},
eprint = {http://jcem.endojournals.org/content/97/12/4631.full.pdf+html},
journal = {Journal of Clinical Endocrinology \& Metabolism}
}
@article{TopHat2,
AUTHOR = {Kim, Daehwan and Pertea, Geo and Trapnell, Cole and Pimentel, Harold and Kelley, Ryan and Salzberg, Steven},
TITLE = {TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions},
JOURNAL = {Genome Biology},
VOLUME = {14},
YEAR = {2013},
NUMBER = {4},
PAGES = {R36},
URL = {http://genomebiology.com/2013/14/4/R36},
DOI = {10.1186/gb-2013-14-4-r36},
}
@article{GSNAP,
author = {Wu, Thomas D. and Nacu, Serban},
title = {Fast and {SNP}-tolerant detection of complex variants and splicing in short reads},
volume = {26},
number = {7},
pages = {873-881},
year = {2010},
doi = {10.1093/bioinformatics/btq057},
URL = {http://bioinformatics.oxfordjournals.org/content/26/7/873.abstract},
eprint = {http://bioinformatics.oxfordjournals.org/content/26/7/873.full.pdf+html},
journal = {Bioinformatics}
}
@article{STAR,
author = {Dobin, Alexander and Davis, Carrie A. and Schlesinger, Felix and Drenkow, Jorg and Zaleski, Chris and Jha, Sonali and Batut, Philippe and Chaisson, Mark and Gingeras, Thomas R.},
title = {{STAR}: ultrafast universal {RNA-seq} aligner},
volume = {29},
number = {1},
pages = {15-21},
year = {2013},
doi = {10.1093/bioinformatics/bts635},
URL = {http://bioinformatics.oxfordjournals.org/content/29/1/15.abstract},
eprint = {http://bioinformatics.oxfordjournals.org/content/29/1/15.full.pdf+html},
journal = {Bioinformatics}
}
@misc{ExpressionSet,
title = {An Introduction to {Bioconductor's} {ExpressionSet} Class},
author = {Seth Falcon and Martin Morgan and Robert Gentleman},
year = {2007},
howpublished = {Vignette, provided with Bioconductor package \emph{Biobase}, \url{http://http://www.bioconductor.org/packages/release/bioc/vignettes/Biobase/inst/doc/ExpressionSetIntroduction.pdf}}
}
@article{hwriter,
title={The hwriter Package},
author={Gregoire Pau and Wolfgang Huber},
journal={The R Journal},
volume={1},
issue={1},
pages={22},
url={http://journal.r-project.org/archive/2009-1/RJournal_2009-1_Pau+Huber.pdf},
year=2009
}
@article{deseq2,
author = {Michael I Love and Wolfgang Huber and Simon Anders},
title = {{Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2}},
year = {2014},
doi = {10.1101/002832},
URL = {http://biorxiv.org/content/early/2014/02/19/002832},
eprint = {http://biorxiv.org/content/early/2014/02/19/002832.full.pdf},
journal = {bioRxiv}
}
@Article{soneson2015,
author="Soneson, Charlotte
and Matthes, Katarina L.
and Nowicka, Malgorzata
and Law, Charity W.
and Robinson, Mark D.",
title="Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage",
journal="Genome Biology",
year="2016",
volume="17",
number="1",
pages="1--15",
issn="1474-760X",
doi="10.1186/s13059-015-0862-3",
url="http://dx.doi.org/10.1186/s13059-015-0862-3"
}
|
