-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathindex.html
501 lines (380 loc) · 21.5 KB
/
index.html
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
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<!-- The above 3 meta tags *must* come first in the head; any other head content must come *after* these tags -->
<title>rpy2: Python-R bridge</title>
<script>
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
})(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
ga('create', 'UA-8995033-4', 'auto');
ga('send', 'pageview');
</script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.5.2/css/bootstrap.min.css" integrity="sha384-JcKb8q3iqJ61gNV9KGb8thSsNjpSL0n8PARn9HuZOnIxN0hoP+VmmDGMN5t9UJ0Z" crossorigin="anonymous">
<link rel="stylesheet" href="css/custom.css">
</head>
<body>
<nav class="navbar navbar-expand-lg fixed-top navbar-light bg-light" role="navigation">
<div class="container">
<a class="navbar-brand" href="index.html"><img alt="logo" src="images/rpy2_logo2013.png" style="height: 2em"></a>
<button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
<div id="navbar" class="collapse navbar-collapse">
<ul class="navbar-nav">
<li class="nav-item">
<a class="nav-link" href="doc.html">Documentation </a>
</li>
<li class="nav-item">
<a class="nav-link" href="https://github.com/rpy2/rpy2-docker">Docker </a>
</li>
<li class="nav-item">
<a class="nav-link" href="https://github.com/rpy2/rpy2-mybinder">MyBinder </a>
</li>
<li class="nav-item">
<a class="nav-link" href="extensions.html">Extensions </a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div>
</nav>
<div class="container">
<div class="header">
<h3>rpy2 - R in Python</h3>
</div>
<div class="jumbotron">
<p class="lead">
<img id="imglogo" src="images/rpy2_logo2013.png" alt="rpy2">
<a class="btn btn-lg btn-default" href="https://pypi.python.org/pypi/rpy2" role="button">
<img src="https://img.shields.io/pypi/v/rpy2.svg?style=flat-square"> on Pypi
</a>
</p>
</div>
<div class="row">
<div class="col-lg-6">
<div class="card">
<div class="card-header">About</div>
<div class="card-body">
<p class="card-text">
rpy2 is an interface to <a href="http://www.r-project.org/">R</a>
running embedded in a <a href="http://www.python.org">Python</a> process.
</p>
<p class="card-text">
The project is mature, stable, <a href="https://rpy2.github.io/doc.html">
documented</a>, and widely used.
</p>
</div>
</div>
<div class="card">
<div class="card-header">License</div>
<div class="card-body">
<p class="card-text">The same license as R: GPLv2 or greater.
</p>
</div>
</div>
</div>
<div class="col-lg-6">
<div class="card">
<div class="card-header">Questions and issues</div>
<div class="card-body">
<p class="card-text">
Consider having a look at the documentation.
Otherwise questions should preferably be asked on the
rpy mailing-list on SourceForge,
or on <a href="http://stackoverflow.com/search?q=rpy2">StackOverflow</a>.
Bugs, or wishes, can also go to the
<a href="https://github.com/rpy2/rpy2/issues">Github page</a>
for the project.
</p>
</div>
</div>
<div class="card">
<div class="card-header">Source code</div>
<div class="card-body">
<h4 class="card-title">Repository</h4>
<p class="card-text">
The source code is also in a public repository on
<a href="https://github.com/rpy2/rpy2">Github</a>.
</p>
</div>
</div>
</div>
<div class="row">
<div class="col-lg-12" style="padding-left: 30px; padding-right: 30px;">
<div class="card" style="margin-top: 20px;">
<div class="card-header">rpy2 in the wild</div>
<div class="card-body">
<p class="card-text">
The package is used in a wide range of domains. For example:
</p>
<h4>2020</h4>
<ul class="list-group list-group-flush">
<li class="list-group-item">
Jenjaroenpun, Piroon, et al. "Decoding the epitranscriptional landscape from native RNA sequences." Nucleic Acids Research (2020).
</li>
<li class="list-group-item">
Rotzinger, David C., et al. "CT pulmonary angiography for risk stratification of patients with nonmassive acute pulmonary embolism." Radiology: Cardiothoracic Imaging 2.4 (2020): e190188.
</li>
<li class="list-group-item">
Zhou, Yonghe, et al. "Chromatic, achromatic and bimodal negative patterning discrimination by free-flying bumble bees." Animal Behaviour 169 (2020): 93-101.
</li>
<li class="list-group-item">
Fugere, Tyler, Zhongning Jim Chen, and Issam Makhoul. "Practical Vitamin D Supplementation Using Machine Learning." Journal of bone metabolism 27.2 (2020): 111.
</li>
<li class="list-group-item">
Ulu, K. Narynbek, et al. "On the Use of Cox Regression for Statistical Analysis of Fatigue Life Results." Journal of Testing and Evaluation 48.2 (2020): 1439-1451.
</li>
<li class="list-group-item">
Ponti, Alexandre, et al. "First-Line Selective Internal Radiation Therapy in Patients with Uveal Melanoma Metastatic to the Liver." Journal of Nuclear Medicine 61.3 (2020): 350-356.
</li>
<li class="list-group-item">
Diamantopoulos, Nikos, et al. "Engineering for a science-centric experimentation platform." Proceedings of the ACM/IEEE 42nd International Conference on Software Engineering: Software Engineering in Practice. 2020.
</li>
<li class="list-group-item">
Chopin, Nicolas, and Omiros Papaspiliopoulos. "Linear-Gaussian State-Space Models." An Introduction to Sequential Monte Carlo. Springer, Cham, 2020. 73-80.
</li>
<li class="list-group-item">
Edgcomb, Juliet Beni, et al. "Predicting suicidal behavior and self-harm after general hospitalization of adults with serious mental illness." Journal of psychiatric research (2020).
</li>
</ul>
<h4>2019</h4>
<ul class="list-group list-group-flush">
<li class="list-group-item">
Diamantopoulos, Nikos, et al. "Engineering for a Science-Centric Experimentation Platform." arXiv preprint arXiv:1910.03878 (2019).
</li>
<li class="list-group-item">
Ponti, Alexandre, et al. "First-Line Selective Internal Radiation Therapy in Patient with Uveal Melanoma Liver Metastases." Journal of Nuclear Medicine (2019): jnumed-119.
</li>
<li class="list-group-item">
Levy, Joshua J., et al. "PyMethylProcess—convenient high-throughput preprocessing workflow for DNA methylation data." Bioinformatics (2019).
</li>
<li class="list-group-item">
Gruber, Michaela, et al. "Growth dynamics in naturally progressing chronic lymphocytic leukaemia." Nature (2019): 1.
</li>
<li class="list-group-item">
Dunnmon, Jared, et al. "Cross-Modal Data Programming Enables Rapid Medical Machine Learning." arXiv preprint arXiv:1903.11101 (2019).
</li>
</ul>
<h4>2018</h4>
<ul class="list-group list-group-flush">
<li class="list-group-item">
Christophides, Damianos, et al. "A method for automatic selection of parameters in NTCP modelling." International Journal of Radiation Oncology• Biology• Physics (2018).
</li>
<li class="list-group-item">
Fadda, Giulia, et al. "MRI and laboratory features and the performance of international criteria in the diagnosis of multiple sclerosis in children and adolescents: a prospective cohort study." The Lancet Child & Adolescent Health (2018).
</li>
<li class="list-group-item">
Muschelli, John, et al. "Neuroconductor: an R platform for medical imaging analysis." Biostatistics (2018).
</li>
<li class="list-group-item">
Domingues, Rémi, et al. "A comparative evaluation of outlier detection algorithms: Experiments and analyses." Pattern Recognition 74 (2018): 406-421.
</li>
<li class="list-group-item">
Poirion, Olivier B., and Benedicte Lafay. "Neo-formation of chromosomes in bacteria." bioRxiv (2018): 264945.
</li>
<li class="list-group-item">
de Melo, Vinícius Veloso, and Wolfgang Banzhaf. "Automatic feature engineering for regression models with machine learning: An evolutionary computation and statistics hybrid." Information Sciences 430 (2018): 287-313.
</li>
<li class="list-group-item">
Giuliano, Christopher J., et al. "MELK expression correlates with tumor mitotic activity but is not required for cancer growth." eLife 7 (2018).
</li>
<li class="list-group-item">
De Vries, Stefan PW, et al. "Phylogenetic analyses and antimicrobial resistance profiles of Campylobacter spp. from diarrhoeal patients and chickens in Botswana." PloS one 13.3 (2018): e0194481.
</li>
</ul>
<h4>2017</h4>
<ul class="list-group list-group-flush">
<li class="list-group-item">
Cherifi, Nadir, et al. "Automatic Inference of Energy Models for Peripheral Components in Embedded Systems." FiCloud 2017: The 5th International Conference on Future Internet of Things and Cloud. 2017.
</li>
<li class="list-group-item">
Lowe, Andrew John. "Language-agnostic data analysis workflows and reproducible research." (2017).
</li>
<li class="list-group-item">
Alexander, William M., et al. "multiplierz v2. 0: a Python‐based ecosystem for shared access and analysis of native mass spectrometry data." Proteomics (2017).
</li>
<li class="list-group-item">
Liu, Lingjie, et al. "An approach of identifying differential nucleosome regions in multiple samples." BMC genomics 18.1 (2017): 135.
</li>
<li class="list-group-item">
Olesen, Scott W., Claire Duvallet, and Eric J. Alm. "dbOTU3: A new implementation of distribution-based OTU calling." PloS one 12.5 (2017): e0176335.
</li>
<li class="list-group-item">
Peacock, Jacob, and Harish Sethu. "Which Leaflet is More Effective: A Reanalysis." (2017).
</li>
<li class="list-group-item">
Sharker, Yushuf, and Eben Kenah. "Estimation of the Household Secondary Attack Rate: Binomial Considered Harmful." arXiv preprint arXiv:1705.01135 (2017).
</li>
<li class="list-group-item">
Domingues, Rémi, et al. "A comparative evaluation of outlier detection algorithms: experiments and analyses." Pattern Recognition (2017).
</li>
<li class="list-group-item">
Zhao, Xuefang, Alexandra M. Weber, and Ryan E. Mills. "A recurrence based approach for validating structural variation using long-read sequencing technology." bioRxiv (2017): 105817.
</li>
<li class="list-group-item">
Laycock, Silas GT. "From blackbirds to black holes: Investigating capture-recapture methods for time domain astronomy." New Astronomy 54 (2017): 91-102.
</li>
<li class="list-group-item">
Chiera, Belinda A., and Małgorzata W. Korolkiewicz. "Visualizing Big Data: Everything Old Is New Again." Big Data Management. Springer International Publishing, 2017. 1-27.
</li>
<li class="list-group-item">
Amarante, Linda M., Marcelo S. Caetano, and Mark Laubach. "Medial frontal theta is entrained to rewarded actions." Journal of Neuroscience (2017): 1965-17.
</li>
</ul>
<h4>2016</h4>
<ul class="list-group list-group-flush">
<li class="list-group-item">
Freer, Rosie, et al. "A protein homeostasis signature in healthy brains recapitulates tissue vulnerability to Alzheimer’s disease." Science Advances 2.8 (2016): e1600947.
</li>
<li class="list-group-item">
Haslwanter, Thomas. An Introduction to Statistics with Python. Springer, 2016.
</li>
<li class="list-group-item">
Ekmekci, Berk, Charles E. McAnany, and Cameron Mura. "An Introduction to Programming for Bioscientists: A Python-Based Primer." PLoS Comput Biol 12.6 (2016): e1004867.
</li>
<li class="list-group-item">
<a href="https://aws.amazon.com/blogs/compute/analyzing-genomics-data-at-scale-using-r-aws-lambda-and-amazon-api-gateway/">Analyzing genomics data at scale with R, AWS Lambda and Amazon API gateway</a> (AWS Compute Blog)
</li>
<li class="list-group-item">
Anaya, Jordan. "OncoLnc: Linking TCGA survival data to mRNAs, miRNAs, and lncRNAs." PeerJ PrePrints 4 (2016): e1780v1.
</li>
<li class="list-group-item">
Cleland, Edward John, et al. "The bacterial microbiome in chronic rhinosinusitis: Richness, diversity, postoperative changes, and patient outcomes." American journal of rhinology & allergy 30.1 (2016): 37-43.
</li>
<li class="list-group-item">
Vandenbulcke, Hélène, et al. "Alcohol intake increases the risk of hepatocellular carcinoma in patients with hepatitis C virus-related compensated cirrhosis: a prospective study." Journal of hepatology (2016).
</li>
<li class="list-group-item">
Jeong, Seongwoon, et al. "A NoSQL Data Management Infrastructure for Bridge Monitoring." (2016).
</li>
<li class="list-group-item">
Kenah, Eben, et al. "Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees." PLoS Comput Biol 12.4 (2016): e1004869.
</li>
<li class="list-group-item">
Kittas, Aristotelis, et al. "Organizational principles of the Reactome human BioPAX model using graph theory methods." Journal of Complex Networks (2016): cnw003.
</li>
</ul>
<h4>2015</h4>
<ul class="list-group list-group-flush">
<li class="list-group-item">
Zhang, Zhi-Min, et al. "Multiscale peak detection in wavelet space." Analyst 140.23 (2015): 7955-7964.
</li>
<li class="list-group-item">
Woon, Wei Lee, et al. "Changes in Occupational Skills-A Case Study Using Non-negative Matrix Factorization." Neural Information Processing. Springer International Publishing, 2015.
</li>
<li class="list-group-item">
Antao, Tiago. Bioinformatics with Python cookbook. Packt Publishing Ltd, 2015.
</li>
<li class="list-group-item">
Terna, Pietro. "Introducing the Swarm-Like Agent Protocol in Python (SLAPP)." Agent-based Models of the Economy. Palgrave Macmillan UK, 2015. 31-54.
</li>
</ul>
<h4>2014</h4>
<ul class="list-group list-group-flush">
<li class="list-group-item">
Nakamura, Kunio, et al. "Correlation between brain volume change and T2 relaxation time induced by dehydration and rehydration: implications for monitoring atrophy in clinical studies." NeuroImage: Clinical 6 (2014): 166-170.
</li>
<li class="list-group-item">
Filosi, Michele, et al. "ReNette: a web-infrastructure for reproducible network analysis." bioRxiv (2014): 008433.
</li>
<li class="list-group-item">
Angeli, Nicole F., et al. A process to support species conservation planning and climate change readiness in protected areas. No. e492v2. PeerJ PrePrints, 2014.
</li>
<li class="list-group-item">
Röst, Hannes L., et al. "pyOpenMS: A Python‐based interface to the OpenMS mass‐spectrometry algorithm library." Proteomics 14.1 (2014): 74-77.
</li>
<li class="list-group-item">
Heavey, Cathal, et al. "Development of an open-source discrete event simulation cloud enabled platform." Proceedings of the 2014 Winter Simulation Conference. IEEE Press, 2014.
</li>
<li class="list-group-item">
De Melo, Vinícius Veloso. "Kaizen programming." Proceedings of the 2014 conference on Genetic and evolutionary computation. ACM, 2014.
</li>
<li class="list-group-item">
Onggo, B. S., et al. "TOWARDS AUTOMATED SIMULATION INPUT DATA." 8TH SIMULATION WORKSHOP. 2014.
</li>
<li class="list-group-item">
Via, Allegra, Kristian Rother, and Anna Tramontano. Managing Your Biological Data with Python. CRC Press, 2014.
</li>
<li class="list-group-item">
Brown, Robert A., Sridar Narayanan, and Douglas L. Arnold. "Imaging of repeated episodes of demyelination and remyelination in multiple sclerosis." NeuroImage: Clinical 6 (2014): 20-25.
</li>
</ul>
<h4>2013</h4>
<ul class="list-group list-group-flush">
<li class="list-group-item">
Krishnan, Hari, et al. "Exploring Collaborative HPC Visualization Workflows using VisIt and Python." Proceedings of the 12th Python in Science Conference (SciPy 2013). 2013.
</li>
<li class="list-group-item">
Parks, Donovan H., et al. "GenGIS 2: Geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework." PloS one 8.7 (2013): e69885.
</li>
</ul>
<h4>2012</h4>
<ul class="list-group list-group-flush">
<li class="list-group-item">
Harper, Marc, and Christopher J. Lee. "Genome-wide analysis of mutagenesis bias and context sensitivity of N-methyl-N′-nitro-N-nitrosoguanidine (NTG)." Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 731.1 (2012): 64-67.
</li>
<li class="list-group-item">
Strickland, C. M., et al. "PyMCMC: A Python Package for Bayesian Estimation Using Markov Chain Monte Carlo." (2012).
</li>
<li class="list-group-item">
Vitolo, Claudia, W. O. U. T. E. R. Buytaert, and D. Reusser. "Hydrological Models as Web Services: An Implementation Using OGC Standards." Proceedings of the 10th International Conference on Hydroinformatics, HIC, Hamburg, Germany. 2012.
</li>
<li class="list-group-item">
Talevich, Eric, et al. "Bio. Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython." BMC bioinformatics 13.1 (2012): 1.
</li>
<li class="list-group-item">
Bagger, Frederik Otzen, et al. "HemaExplorer: a database of mRNA expression profiles in normal and malignant haematopoiesis." Nucleic acids research (2012): gks1021.
</li>
</ul>
<h4>2011</h4>
<ul class="list-group list-group-flush">
<li class="list-group-item">
Buske, Orion J., et al. "Exploratory analysis of genomic segmentations with Segtools." BMC bioinformatics 12.1 (2011): 1.
</li>
<li class="list-group-item">
Tolk, A., et al. "TOWARDS AUTOMATED SIMULATION INPUT DATA: AN OPEN SOURCE TOOL TO ENHANCE THE INPUT DATA PHASE IN DISCRETE EVENT SIMULATION."
</li>
<li class="list-group-item">
Patton, Evan W., et al. "SemNExT: A Framework for Semantically Integrating and Exploring Numeric Analyses."
</li>
<li class="list-group-item">
Connolly, Daniel W., et al. "Integrating R efficiently to allow secure, interactive analysis within a clinical data warehouse." The 8th International R User Conference. Vanderbilt University.
</li>
<li class="list-group-item">
Masica, David L., and Rachel Karchin. "Correlation of somatic mutation and expression identifies genes important in human glioblastoma progression and survival." Cancer research 71.13 (2011): 4550-4561.
</li>
<li class="list-group-item">
Simone, James. "PoS (Lattice 2011) 048 Data analysis using the Gnu R system for statistical computation." (2011).
</li>
<li class="list-group-item">
Liu, Sanmin, et al. "HDX-analyzer: a novel package for statistical analysis of protein structure dynamics." BMC bioinformatics 12.1 (2011): 1.
</li>
</ul>
<h4>2009</h4>
<ul class="list-group list-group-flush">
<li class="list-group-item">
Roseline, Bilina, and Steve Lawford. "Python for Unified Research in Econometrics and Statistics." Available at SSRN 1429822 (2009).
</li>
<li class="list-group-item">
Wijffels, Jan. "Prediction and Fuzzy Logic at ThomasCook to automate price settings of last minute offers." (2009).
</li>
<li class="list-group-item">
McBeth, Rafe. "Computational investigation of biological dose-volume outcome predictors in 29 canine nasal tumor patients treated with stereotactic radiation therapy." (2007).
</li>
</ul>
</div>
</div>
</div>
</div>
</div>
</div><!-- /.container -->
<script src="https://code.jquery.com/jquery-3.5.1.slim.min.js" integrity="sha384-DfXdz2htPH0lsSSs5nCTpuj/zy4C+OGpamoFVy38MVBnE+IbbVYUew+OrCXaRkfj" crossorigin="anonymous"></script>
<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/umd/popper.min.js" integrity="sha384-9/reFTGAW83EW2RDu2S0VKaIzap3H66lZH81PoYlFhbGU+6BZp6G7niu735Sk7lN" crossorigin="anonymous"></script>
<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.5.2/js/bootstrap.min.js" integrity="sha384-B4gt1jrGC7Jh4AgTPSdUtOBvfO8shuf57BaghqFfPlYxofvL8/KUEfYiJOMMV+rV" crossorigin="anonymous"></script>
</body>
</html>