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An empirical study of identical function clones in CRAN

Maelick Claes, Tom Mens, Narjisse Tabout, Philippe Grosjean
2015 2015 IEEE 9th International Workshop on Software Clones (IWSC)  
This article presents an empirical study of identical function clones in the CRAN package archive network, in order to understand the extent of this practice in the R community.  ...  We study how the characteristics of cloned functions in CRAN snapshots evolve over time, and classify these clones depending on what has prevented package developers to rely on dependencies instead.  ...  ACKNOWLEDGEMENTS This research was carried out in the context of ARC research project AUWB-12/17-UMONS-3.  ... 
doi:10.1109/iwsc.2015.7069885 dblp:conf/iwsc/ClaesMTG15 fatcat:3ozlcrbwwndnnomw6djliwlwja

Estimating Clonality [article]

Yi Liu, Andrew Z. Fire, Scott Boyd, Richard A. Olshen
2014 arXiv   pre-print
Our work has led to software, which we call lymphclon; it has been deposited in the CRAN library.  ...  A principal takeaway message is that knowing a functional of p well may not depend on knowing p itself very well.  ...  Funding was supported in part by grant 5U19AI090019 from the National Institute of Allergy and Infectious Diseases, and also by grant 4R37EB002784 from the National Institute of Biomedical Imaging and  ... 
arXiv:1408.1149v1 fatcat:atzuyqztu5al5l4wqtao5kjusu

SimilaR: R Code Clone and Plagiarism Detection

Maciej Bartoszuk, Marek Gagolewski
2020 The R Journal  
We demonstrate its accuracy and efficiency in a real-world case study. • Syntactic -an approach based on abstract syntax trees (ASTs).  ...  They may be useful in gaining a better understanding of the component interdependencies, avoiding cloned code as well as detecting plagiarism in programming classes.  ...  Structure and Interpretation of Computer Programs. MIT Press, 1996. [p368]  ... 
doi:10.32614/rj-2020-017 fatcat:cwbngpbwijew5oxus5ve3kolqq

Model for comparative analysis of antigen receptor repertoires

Grzegorz A. Rempala, MichaŁ Seweryn, Leszek Ignatowicz
2011 Journal of Theoretical Biology  
In modern molecular biology one of the standard ways of analyzing a vertebrate immune system is to sequence and compare the counts of specific antigen receptor clones (either immunoglobulins or T-cell  ...  ecological studies.  ...  The authors would like to acknowledge the insightful comments of the Associate Editor and the Reviewers, which helped them improve the original manuscript.  ... 
doi:10.1016/j.jtbi.2010.10.001 pmid:20955715 pmcid:PMC3006491 fatcat:nxmbudm2qvah3niohjo2ntoatq

Expression Profile of microRNAs Regulating Proliferation and Differentiation in Mouse Adult Cardiac Stem Cells

Luis Brás-Rosário, Alex Matsuda, Ana Isabel Pinheiro, Rui Gardner, Telma Lopes, Andreia Amaral, Margarida Gama-Carvalho, Piero Anversa
2013 PLoS ONE  
To obtain insights into the regulatory networks active in cardiac stem cells, we characterized the expression profile of 95 microRNAs with reported functions in stem cell and tissue differentiation in  ...  The most highly expressed microRNAs identified in cardiac stem cells are known to target key genes involved in the control of cell proliferation and adhesion, vascular function and cardiomyocyte differentiation  ...  Future studies will help address this question and explore the role of specific miRs identified in this work in the control of CSC function.  ... 
doi:10.1371/journal.pone.0063041 pmid:23690977 pmcid:PMC3656880 fatcat:th4gkjqahrduzfr2s75vg4e74a

Joint single cell DNA-Seq and RNA-Seq of gastric cancer reveals subclonal signatures of genomic instability and gene expression [article]

Noemi Andor, Billy T Lau, Claudia Catalanotti, Vijay Kumar, Anuja Sathe, Kamila Belhocine, Tobias D Wheeler, Andrew D Price, Maengseok Song, David Stafford, Zachary Bent, Laura DeMare (+21 others)
2018 bioRxiv   pre-print
This joint study, covering thousands of single cell genomes and transcriptomes, revealed extensive cellular diversity based on distinct copy number changes, numerous subclonal populations and in the case  ...  We found genomic evidence of positive selection where the percentage of replicating cells per clone is higher than expected indicating ongoing tumor evolution.  ...  The barcoded GB was similar to those used in previous studies for phasing genomes 19 and single cell transcriptome profiling 20 - an individual GB was functionalized with millions of copies of identical  ... 
doi:10.1101/445932 fatcat:rfk67xvlmrfi7epcxhfhdmfxym

Cluster Analysis of Genomic Data [chapter]

K. S. Pollard, M. J. van der Laan
2005 Bioinformatics and Computational Biology Solutions Using R and Bioconductor  
We provide an overview of existing partitioning and hierarchical clustering algorithms in R.  ...  We discuss statistical issues and methods in choosing the number of clusters, the choice of clustering algorithm, and the choice of dissimilarity matrix.  ...  These I independent and identically distributed (i.i.d.) observations can be stored in an observed J × I data matrix X.  ... 
doi:10.1007/0-387-29362-0_13 fatcat:4hgk6snaevhhxjysdbihr37tci

Is hybridization driving the evolution of climatic niche in Alyssum montanum

Nils Arrigo, Marylaure de La Harpe, Glenn Litsios, Judita Zozomová-Lihová, Stanislav Španiel, Karol Marhold, Michael S. Barker, Nadir Alvarez
2016 American Journal of Botany  
ITS cloning.  ...  Th is research is funded by an SNSF Ambizione research grant (PZ00P3_148224) to N.Ar., an SNSF professor ship (PP00P3_144870)  ...  We then used nonlinear least-squares (using the nls function in R CRAN (R Core Team, 2014) included in the stats package) to estimate the respective model parameters of allo-and autopolyploids.  ... 
doi:10.3732/ajb.1500368 pmid:27206461 fatcat:2cdw2frczfhozdxpgvdz6m3ora

Model for Diversity Analysis of Antigen Receptor Repertoires [article]

Grzegorz A. Rempala, Michal Seweryn, Leszek Ignatowicz
2010 arXiv   pre-print
studies.  ...  The parametric model is based on a flexible multivariate Poisson-lognormal distribution and is seen to be a natural generalization of the univariate Poisson-lognormal models used in ecological studies  ...  The frequency of individual T-cell clones in normal individuals is very low.  ... 
arXiv:1003.1066v1 fatcat:kcvoc3zujzb3hbv7362wgup7wm

A Fuzzy R Code Similarity Detection Algorithm [chapter]

Maciej Bartoszuk, Marek Gagolewski
2014 Communications in Computer and Information Science  
of code recycling or code cloning in R's open source packages repositories.  ...  Its analysis on empirical data indicates that the system may in future be successfully applied in practice in order e.g. to detect plagiarism among students' homework submissions or to perform an analysis  ...  .04.01.01-00-051/10-00 via the Interdisciplinary PhD Studies Program.  ... 
doi:10.1007/978-3-319-08852-5_3 fatcat:f5mlwr3eorg5jcldlrp2syrlpa

Wavelet-Based Clustering for Mixed-Effects Functional Models in High Dimension

M. Giacofci, S. Lambert-Lacroix, G. Marot, F. Picard
2013 Biometrics  
The properties of the overall procedure are validated by an extensive simulation study.  ...  on the CRAN).  ...  Acknowledgements Part of this work was supported by the Interuniversity Attraction Pole (IAP) research network in Statistics P5/24 and by the MSTIC project of the Joseph-Fourier University.  ... 
doi:10.1111/j.1541-0420.2012.01828.x pmid:23379722 fatcat:u3yb4d46bzgqjezfp7lhqielny

The microRNAs of Caenorhabditis elegans

L. P. Lim
2003 Genes & Development  
MicroRNAs (miRNAs) are an abundant class of tiny RNAs thought to regulate the expression of protein-coding genes in plants and animals.  ...  Our census of the worm miRNAs and their expression patterns helps define this class of noncoding RNAs, lays the groundwork for functional studies, and provides the tools for more comprehensive analyses  ...  The publication costs of this article were defrayed in part by payment of page charges.  ... 
doi:10.1101/gad.1074403 pmid:12672692 pmcid:PMC196042 fatcat:yryy43gjnnbz3h3nubpe6kbwcm

distr6: R6 Object-Oriented Probability Distributions Interface in R [article]

Raphael Sonabend, Franz Kiraly
2021 arXiv   pre-print
distr6 is an object-oriented (OO) probability distributions interface leveraging the extensibility and scalability of R6, and the speed and efficiency of Rcpp.  ...  This paper presents the core functionality of the package and demonstrates examples for key use-cases.  ...  Matthias Kohl for their work on the distr package and for extensive discussions, planning, and design decisions that were utilised in the development of distr6.  ... 
arXiv:2009.02993v3 fatcat:3b7vo7ma6zguzdk4tbmhbufxk4

Gene synthesis allows biologists to source genes from farther away in the tree of life

Aditya M. Kunjapur, Philipp Pfingstag, Neil C. Thompson
2018 Nature Communications  
Gene synthesis enables creation and modification of genetic sequences at an unprecedented pace, offering enormous potential for new biological functionality but also increasing the need for biosurveillance  ...  We provide empirical evidence that gene synthesis is leading biologists to sample more broadly across the diversity of life, and we provide a foundational tool for the biosurveillance community.  ...  Machine readable versions of the data presented in the Supplementary Information are available at https://github.com/AKunjapur/Synthetic-geneclassification.  ... 
doi:10.1038/s41467-018-06798-7 fatcat:33qlvbzpszaercup33wv3ppmti

World of Code: Enabling a Research Workflow for Mining and Analyzing the Universe of Open Source VCS data [article]

Yuxing Ma, Tapajit Dey, Chris Bogart, Sadika Amreen, Marat Valiev, Adam Tutko, David Kennard, Russell Zaretzki, Audris Mockus
2020 arXiv   pre-print
In particular, we find that it is capable of supporting trend evaluation, ecosystem measurement, and the determination of package usage.  ...  For example, how are the tens of millions of projects in the periphery interconnected through. technical dependencies, code sharing, or knowledge flow?  ...  Specifically, it provides capabilities a) for stratified sampling in order to improve external generalizability of empirical studies; b) to measure critical properties of code, dependencies, and developer  ... 
arXiv:2010.16196v1 fatcat:wonvbkuqtncttja2us5uiidvdy
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