19 papers · ranked by Valyu relevance
Gonzalo Vera, Ritsert C Jansen, Remo L Suppi
Background R is the preferred tool for statistical analysis of many bioinformaticians due in part to the increasing number of freely available analytical methods. Such methods can be quickly reused and adapted to each particular experiment. However, in experiments where large amounts of data are generated, for example…
Nathan J. Evans
Evidence accumulation models (EAMs) have become the dominant models of rapid decision-making. Several variants of these models have been proposed, ranging from the simple linear ballistic accumulator (LBA) to the more complex leaky-competing accumulator (LCA), and further extensions that include time-varying rates of…
Julian Frey, Zoe Schindler, Muhammad Ali, Joshua Braun-Wimmer + 9 more
Background Standardisation, accessibility, and reproducibility remain persistent challenges in data-intensive scientific research. The Galaxy platform addresses these issues by providing a web-based environment for executing, sharing, and publishing computational workflows, yet programmatic access has been largely…
Greg Finak, Bryan T. Mayer, William Fulp, Paul Obrecht + 4 more
A central tenet of reproducible research is that scientific results are published along with the underlying data and software code necessary to reproduce and verify the findings. A host of tools and software have been released that facilitate such work-flows and scientific journals have increasingly demanded that code…
Antonios Makris
Master Thesis Title: Supervisor Konstantinos Tserpes, Lecturer Supervisory Committee Iraklis Varlamis, Assistant Professor Dimitrios Michail, Assistant Professor Antonios Makris(Id.N.: 13108) MSc candidate in Web Engineering BSc in Informatics and Telematics Athens, July 2015 []
Federico M. Giorgi, Carmine Ceraolo, Daniele Mercatelli, Sandeep Kumar Dhanda + 1 more
The R programming language is approaching its 30th birthday, and in the last three decades it has achieved a prominent role in statistics, bioinformatics, and data science in general. It currently ranks among the top 10 most popular languages worldwide, and its community has produced tens of thousands of extensions and…
Jayadev Joshi, Fabio Cumbo, Daniel Blankenberg
R is widely used in statistical computing, data analysis, and bioinformatics. A key contributor to its success in bioinformatics and computational biology is the open-source project Bioconductor. As of its latest release (3.20), the Bioconductor community offers 2,289 software packages for biomedical research…
Althea Hansel-Harris, Andreas Tillack, Diogo Santos-Martins, Matthew Holcomb + 1 more
Virtual screening using molecular docking is now routinely used for the rapid evaluation of very large ligand libraries. As such, it has become an increasingly common approach in early-stage drug discovery. These screenings generate large amounts of data proportional to the size of the compound library used, which must…
Duncan Temple Lang
I describe an approach to compiling common idioms in R code directly to native machine code and illustrate it with several examples. Not only can this yield significant performance gains, but it allows us to use new approaches to computing in R. Importantly, the compilation requires no changes to R itself, but is done…
Maricela Cruz, Marco A. Pinto-Orellana, Daniel L. Gillen, Hernando C. Ombao
'Hernando C. Ombao'] Background Various interacting and interdependent components comprise complex interventions. These components create difficulty in assessing the true impact of interventions designed to improve patient-centered outcomes. Interrupted time series (ITS) designs borrow from case-crossover designs and…
Stefan McKinnon Edwards
The reported R-package provides an easy way for executing and evaluating genotype imputation studies, by providing functions for preparing input files for AlphaImpute and efficiently calculating imputation accuracies. Using the correlation between true and imputed genotypes is used here as it is directly related to the…
Tyler Kolisnik, Faeze Keshavarz-Rahaghi, Rachel Purcell, Adam Smith + 1 more
Random Forest models are widely used in genomic data analysis and can offer insights into complex biological mechanisms, particularly where features influence the target in interactive, non-linear, or non-additive ways. Currently, some of the most efficient random forest methods, in terms of computational speed, are…
Rahim K. Charania
—R is a robust open-source programming language mainly used for statistical computing . Many areas of statistical research are experiencing rapid growth in the size of data sets. Methodological advances drive increased use of simulations. A common approach is to use parallel/concurrent computing. This paper presents an…
Saeid Amiri
R is a programming language and environment that is a central tool in the applied sciences for writing program. Its impact on the development of modern statistics is inevitable. Current research, especially for big data may not be done solely using R and will likely use different programming languages; hence, having a…
Fabian A. Soto, Emily Zheng, Johnny Fonseca, F. Gregory Ashby
Determining whether perceptual properties are processed independently is an important goal in perceptual science, and tools to test independence should be widely available to experimental researchers. The best analytical tools to test for perceptual independence are provided by General Recognition Theory (GRT), a…
Florian Gerber, Kaspar Mösinger, Reinhard Furrer
The R functions .C() and .Fortran() can be used to call compiled C/C++ and Fortran code from R. This so-called foreign function interface is convenient, since it does not require any interactions with the C API of R. However, it does not support long vectors (i. e. , vectors of more than 2 31 elements). To overcome…
Sofia Fregni, Uta Wolfensteller, Hannes Ruge
We used fMRI to investigate the neural changes and representational dynamics associated with different learning modes during initial learning and subsequent implementation of previously acquired stimulus-response (S-R) associations. We compared instruction-based learning (INS) and trial-and-error learning (TE) via a…
Martin Šícho, Xuhan Liu, Daniel Svozil, Gerard van Westen
This manuscript describes the development and architecture of the GenUI software platform for integration of molecular generators. The source code for the components of the platform is available in the following repositories: https://github.com/martin-sicho/genui https://github.com/martin-sicho/genui-gui…
Authors not listed
We developed OpenStats, a user-friendly web application that brings the power of the R language to researchers through a high-level interface and broad support for statistical methods such as t-tests and ANOVA. OpenStats was integrated into our electronic lab notebook Chemotion ELN via its third-party API, enabling…