-
Notifications
You must be signed in to change notification settings - Fork 10
/
bibliography.bib
executable file
·324 lines (287 loc) · 10.4 KB
/
bibliography.bib
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
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
%
% List of publications / Leo Lahti.
% http://www.iki.fi/Leo.Lahti/work/pubs/
@Manual{Caballero_2013,
title = {df2json: Convert a dataframe to JSON},
author = {Nacho Caballero},
year = {2013},
note = {R package version 0.0.2},
url = {http://CRAN.R-project.org/package=df2json},
}
@Article{Chessel_2004,
title = {The ade4 package-{I}- {O}ne-table methods},
author = {D. Chessel and A.B. Dufour and J. Thioulouse},
journal = {R News},
year = {2004},
volume = {4},
pages = {5-10},
}
@Manual{Couture-Beil_2014,
title = {rjson: JSON for R},
author = {Alex Couture-Beil},
year = {2014},
note = {R package version 0.2.15},
url = {http://CRAN.R-project.org/package=rjson},
}
@Manual{Dejean_2014,
title = {mixOmics: Omics Data Integration Project},
author = {Sebastien Dejean and Ignacio Gonzalez and Kim-Anh Le Cao with contributions from Pierre Monget and Jeff Coquery and FangZou Yao and Benoit Liquet and Florian Rohart},
year = {2014},
note = {R package version 5.0-3},
url = {http://CRAN.R-project.org/package=mixOmics},
}
@Article{Dray_2007,
title = {The ade4 package: implementing the duality diagram for ecologists},
author = {S. Dray and A.B. Dufour},
journal = {Journal of Statistical Software},
year = {2007},
volume = {22},
pages = {1-20},
number = {4},
}
@Article{Dray_2007a,
title = {The ade4 package-{II}: {T}wo-table and {K}-table methods.},
author = {S. Dray and A.B. Dufour and D. Chessel},
journal = {R News},
year = {2007},
volume = {7},
number = {2},
pages = {47-52},
}
@article{HalfvarsonNatMicro,
author = {Jonas Halfvarson and Colin J. Brislawn and Regina Lamendella and
Yoshiki Vázquez-Baeza and William A. Walters and Lisa M. Bramer
and Mauro D'Amato and Ferdinando Bonfiglio and Daniel McDonald
and Antonio Gonzalez and Erin E. McClure and Mitchell F. Dunklebarger
and Rob Knight and Janet K. Jansson},
title = {Dynamics of the human gut microbiome in inflammatory bowel disease},
journal = {{Nature Microbiology}},
year = 2017,
volume = 2,
number = 17004,
month = {Feb.},
doi = {doi:10.1038/nmicrobiol.2017.4},
url = {http://www.nature.com/articles/nmicrobiol20174},
}
@article{Halfvarson_2017,
title = {Dynamics of the human gut microbiome in inflammatory bowel disease},
author = {Jonas Halfvarson and Colin J. Brislawn and Regina Lamendella and
Yoshiki Vázquez-Baeza and William A. Walters and Lisa M. Bramer
and Mauro D'Amato and Ferdinando Bonfiglio and Daniel McDonald
and Antonio Gonzalez and Erin E. McClure and Mitchell F. Dunklebarger
and Rob Knight and Janet K. Jansson},
journal = {{Nature Microbiology}},
year = {2017},
volume = {2},
month = {Feb.},
doi = {doi:10.1038/nmicrobiol.2017.4},
url = {http://www.nature.com/articles/nmicrobiol20174},
}
@article{Lahti11rpa,
author = {Leo Lahti and Laura L. Elo and Tero Aittokallio and
Samuel Kaski},
title = {Probabilistic Analysis of Probe Reliability in
Differential Gene Expression Studies with Short
Oligonucleotide Arrays},
journal = {{IEEE/ACM Transactions on Computational Biology and
Bioinformatics}},
year = 2011,
volume = 8,
number = 1,
pages = {217--225},
month = {Jan.-Mar.},
doi = {doi:10.1109/TCBB.2009.38},
url =
{http://www.computer.org/portal/web/csdl/doi/10.1109/TCBB.2009.38},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
annote = {Open source implementation:
http://bioconductor.org/packages/release/bioc/html/RPA.html}
}
@Article{Lahti13nar,
author = {Leo Lahti and Aurora Torrente and Laura L Elo and
Alvis Brazma and Johan Rung},
title = {A fully scalable online pre-processing algorithm for
short oligonucleotide microarray atlases},
journal = {Nucleic Acids Research},
volume = 41,
number = 10,
year = 2013,
pages = {e110},
doi = {10.1093/nar/gkt229},
note = {Implementation available through Bioconductor RPA package.}
}
@Article{Lahti13provasI,
author = {Leo Lahti and Anne Salonen and Riina A. Kekkonen and
Jarkko Salojarvi and Jonna Jalanka-Tuovinen and Airi
Palva and Matej Orešič and Willem M. de Vos},
title = {{Associations between the human intestinal
microbiota, {\it Lactobacillus rhamnosus} GG and
serum lipids indicated by integrated analysis of
high-throughput profiling data}},
journal = {PeerJ},
year = 2013,
volume = 1,
pages = {e32},
url = {http://dx.doi.org/10.7717/peerj.32},
pmid = 23638368
}
@Article{Lahti_2013,
title = {A fully scalable online-preprocessing algorithm for short oligonucleotide microarray atlases},
author = {Leo Lahti and Aurora Torrente and Laura L. Elo and Alvis Brazma and Johan Rung},
journal = {Nucleic Acids Research},
year = {2013},
volume = {41},
issue = {10},
pages = {e110},
note = {R/BioC: http://bioconductor.org/packages/release/bioc/html/RPA.html},
url = {http://nar.oxfordjournals.org/content/41/10/e110},
}
@Article{Langfelder_2008,
author = {Peter Langfelder and Steve Horvath},
title = {WGCNA: an R package for weighted correlation network analysis},
journal = {BMC Bioinformatics},
year = {2008},
number = {1},
pages = {559},
pubmedid = {19114008},
}
@Article{Langfelder_2012,
title = {Fast {R} Functions for Robust Correlations and Hierarchical Clustering},
author = {Peter Langfelder and Steve Horvath},
journal = {Journal of Statistical Software},
year = {2012},
volume = {46},
number = {11},
pages = {1--17},
url = {http://www.jstatsoft.org/v46/i11/},
}
@Article{McMurdie_2013,
author = {Paul J. McMurdie and Susan Holmes},
journal = {PLoS ONE},
pages = {e61217},
title = {phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data},
volume = {8},
number = {4},
year = {2013},
url = {http://dx.plos.org/10.1371/journal.pone.0061217},
}
@Article{Meyer_2008,
title = {MINET: An open source R/Bioconductor Package for Mutual Information based Network Inference},
author = {Patrick E. Meyer and Frederic Lafitte and Gianluca Bontempi},
journal = {BMC Bioinformatics},
year = {2008},
volume = {9},
url = {http://www.biomedcentral.com/1471-2105/9/461},
}
@Article{Mullner_2013,
title = {{fastcluster}: Fast Hierarchical, Agglomerative Clustering Routines for {R} and {Python}},
author = {Daniel M\"ullner},
journal = {Journal of Statistical Software},
year = {2013},
volume = {53},
number = {9},
pages = {1--18},
url = {http://www.jstatsoft.org/v53/i09/},
}
@Manual{Oksanen_2015,
title = {vegan: Community Ecology Package},
author = {Jari Oksanen and F. Guillaume Blanchet and Roeland Kindt and Pierre Legendre and Peter R. Minchin and R. B. O'Hara and Gavin L. Simpson and Peter Solymos and M. Henry H. Stevens and Helene Wagner},
year = {2015},
note = {R package version 2.2-1},
url = {http://CRAN.R-project.org/package=vegan},
}
@Manual{Oksanen_2017,
title = {vegan: Community Ecology Package},
author = {Jari Oksanen and F. Guillaume Blanchet and Michael Friendly and Roeland Kindt and Pierre Legendre and Dan McGlinn and Peter R. Minchin and R. B. O'Hara and Gavin L. Simpson and Peter Solymos and M. Henry H. Stevens and Eduard Szoecs and Helene Wagner},
year = {2017},
note = {R package version 2.4-3},
url = {https://CRAN.R-project.org/package=vegan},
}
@Manual{R_Core_Team_2017,
title = {R: A Language and Environment for Statistical Computing},
author = {{R Core Team}},
organization = {R Foundation for Statistical Computing},
address = {Vienna, Austria},
year = {2017},
url = {https://www.R-project.org/},
}
@Manual{Temple_Lang_2014,
title = {RCurl: General network (HTTP/FTP/...) client interface for R},
author = {Duncan {Temple Lang}},
year = {2014},
note = {R package version 1.95-4.3},
url = {http://CRAN.R-project.org/package=RCurl},
}
@Article{Wickham_2007,
author = {{Wickham} and {Hadley}},
journal = {Journal of Statistical Software},
number = {12},
title = {Reshaping data with the reshape package},
url = {http://www.jstatsoft.org/v21/i12/paper},
volume = {21},
year = {2007},
}
@Book{Wickham_2009,
author = {Hadley Wickham},
title = {ggplot2: Elegant Graphics for Data Analysis},
publisher = {Springer-Verlag New York},
year = {2009},
isbn = {978-0-387-98140-6},
url = {http://ggplot2.org},
}
@Article{Wickham_2011,
title = {The Split-Apply-Combine Strategy for Data Analysis},
author = {Hadley Wickham},
journal = {Journal of Statistical Software},
year = {2011},
volume = {40},
number = {1},
pages = {1--29},
url = {http://www.jstatsoft.org/v40/i01/},
}
@Manual{Wickham_2017,
title = {dplyr: A Grammar of Data Manipulation},
author = {Hadley Wickham and Romain Francois and Lionel Henry and Kirill M{\"u}ller},
year = {2017},
note = {R package version 0.7.1},
url = {https://CRAN.R-project.org/package=dplyr},
}
@Manual{Wickham_2017a,
title = {tidyr: Easily Tidy Data with 'spread()' and 'gather()' Functions},
author = {Hadley Wickham},
year = {2017},
note = {R package version 0.6.3},
url = {https://CRAN.R-project.org/package=tidyr},
}
@Article{lahti14natcomm,
author = {Leo Lahti and Jarkko Salojarvi and Anne Salonen and
Marten Scheffer and Willem M. de Vos},
title = {Tipping elements in the human intestinal ecosystem},
journal = {Nature Communications},
year = 2014,
volume = 5,
pages = 4344,
month = {July},
doi = {10.1038/ncomms5344}
}
@Book{rcore13,
author = {{R Core Team}},
title = {R: A language and environment for statistical
computing},
publisher = {R Foundation for Statistical Computing},
year = {2013},
isbn = {ISBN 3-900051-07-0},
address = {Vienna, Austria},
url = {http://www.R-project.org/},
}
@Book{venables02,
author = {W. N. Venables and B. D. Ripley},
title = {Modern Applied Statistics with S},
publisher = {Springer},
year = {2002},
isbn = {ISBN },
address = {New York},
edition = {fourth},
isbn = {ISBN },
}