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    <title>rpy2: Python-R bridge</title>

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  <h3>rpy2 - R in Python</h3>
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    <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
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    <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>
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    <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>
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  <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>
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    <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>
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	<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>
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