scholarly journals digeR: a graphical user interface R package for analyzing 2D-DIGE data

2009 ◽  
Vol 25 (22) ◽  
pp. 3033-3034 ◽  
Author(s):  
Yue Fan ◽  
T. Brendan Murphy ◽  
R. William G. Watson
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
R Package ◽  
2D Dige

scholarly journals LexOPS: An R package and user interface for the controlled generation of word stimuli

2020 ◽  
Vol 52 (6) ◽  
pp. 2372-2382
Author(s):  
Jack E. Taylor ◽  
Alistair Beith ◽  
Sara C. Sereno
Keyword(s):  
User Interface ◽  
Factorial Design ◽  
Graphical User Interface ◽  
R Package ◽  
Psycholinguistic Research ◽  
Link Type ◽  
Control Current ◽  
Word Lists ◽  
And Control ◽  
Manipulation And Control

AbstractLexOPS is an R package and user interface designed to facilitate the generation of word stimuli for use in research. Notably, the tool permits the generation of suitably controlled word lists for any user-specified factorial design and can be adapted for use with any language. It features an intuitive graphical user interface, including the visualization of both the distributions within and relationships among variables of interest. An inbuilt database of English words is also provided, including a range of lexical variables commonly used in psycholinguistic research. This article introduces LexOPS, outlining the features of the package and detailing the sources of the inbuilt dataset. We also report a validation analysis, showing that, in comparison to stimuli of existing studies, stimuli optimized with LexOPS generally demonstrate greater constraint and consistency in variable manipulation and control. Current instructions for installing and using LexOPS are available at https://JackEdTaylor.github.io/LexOPSdocs/.

scholarly journals ntbox : An r package with graphical user interface for modelling and evaluating multidimensional ecological niches

2020 ◽  
Vol 11 (10) ◽  
pp. 1199-1206 ◽  
Author(s):  
Luis Osorio‐Olvera ◽  
Andrés Lira‐Noriega ◽  
Jorge Soberón ◽  
Andrew Townsend Peterson ◽  
Manuel Falconi ◽  
...  
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
R Package ◽  
Ecological Niches

scholarly journals genBaRcode: a comprehensive R-package for genetic barcode analysis

2019 ◽  
Vol 36 (7) ◽  
pp. 2189-2194 ◽  
Author(s):  
Lars Thielecke ◽  
Kerstin Cornils ◽  
Ingmar Glauche
Keyword(s):  
User Interface ◽  
Next Generation Sequencing ◽  
Error Correction ◽  
Graphical User Interface ◽  
R Package ◽  
Next Generation ◽  
Analysis Strategies ◽  
Genetic Sequences ◽  
Reproducible Analysis ◽  
Generation Sequencing

Abstract Motivation Genetic barcodes have been established as an efficient method to trace clonal progeny of uniquely labeled cells by introducing artificial genetic sequences into the corresponding genomes. The assessment of those sequences relies on next generation sequencing and the subsequent analysis aiming to identify sequences of interest and correctly quantifying their abundance. Results We developed the genBaRcode package as a toolbox combining the flexibility of digesting next generation sequencing reads with or without a sophisticated barcode structure, with a variety of error-correction approaches and the availability of several types of visualization routines. Furthermore, a graphical user interface was incorporated to allow also less experienced R users package-based analyses. Finally, the provided tool is intended to bridge the gap between generating and analyzing barcode data and thereby supporting the establishment of standardized and reproducible analysis strategies. Availability and implementation The genBaRcode package is available at CRAN (https://cran.r-project.org/package=genBaRcode).

scholarly journals rawDiag - an R package supporting rational LC-MS method optimization for bottom-up proteomics

2018 ◽  
Author(s):  
Christian Trachsel ◽  
Christian Panse ◽  
Tobias Kockmann ◽  
Witold E. Wolski ◽  
Jonas Grossmann ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
User Interface ◽  
Graphical User Interface ◽  
Real World ◽  
Software Tool ◽  
R Package ◽  
Command Line ◽  
Diagnostic Plots ◽  
Method Optimization

AbstractOptimizing methods for liquid chromatography coupled to mass spectrometry (LC-MS) is a non-trivial task. Here we present rawDiag, a software tool supporting rational method optimization by providing MS operator-tailored diagnostic plots of scan level metadata. rawDiag is implemented as R package and can be executed on the command line, or through a graphical user interface (GUI) for less experienced users. The code runs platform independent and can process a hundred raw files in less than three minutes on current consumer hardware as we show by our benchmark. In order to demonstrate the functionality of our package, we included a real-world example taken from our daily core facility business.

scholarly journals glmGUI v1.0: an R-based graphical user interface and toolbox for GLM (General Lake Model) simulations

2020 ◽  
Vol 13 (2) ◽  
pp. 565-580 ◽  
Author(s):  
Thomas Bueche ◽  
Marko Wenk ◽  
Benjamin Poschlod ◽  
Filippo Giadrossich ◽  
Mario Pirastru ◽  
...  
Keyword(s):  
User Interface ◽  
Water Temperature ◽  
Graphical User Interface ◽  
Lake Level ◽  
R Package ◽  
Climatic Conditions ◽  
Model Parameters ◽  
Lake Model ◽  
Code Language ◽  
The One

Abstract. Numerical modeling provides an opportunity to quantify the reaction of lakes to alterations in their environment, such as changes in climate or hydrological conditions. The one-dimensional hydrodynamic General Lake Model (GLM) is an open-source software and widely used within the limnological research community. Nevertheless, no interface to process the input data and run the model and no tools for an automatic parameter calibration yet exist. Hence, we developed glmGUI, a graphical user interface (GUI) including a toolbox for an autocalibration, parameter sensitivity analysis, and several plot options. The tool is provided as a package for the freely available scientific code language R. The model parameters can be analyzed and calibrated for the simulation output variables water temperature and lake level. The glmGUI package is tested for two sites (lake Ammersee, Germany, and lake Baratz, Italy), distinguishing size, mixing regime, hydrology of the catchment area (i.e., the number of inflows and their runoff seasonality), and climatic conditions. A robust simulation of water temperature for both lakes (Ammersee: RMSE =1.17 ∘C; Baratz: RMSE =1.30 ∘C) is achieved by a quick automatic calibration. The quality of a water temperature simulation can be assessed immediately by means of a difference plot provided by glmGUI, which displays the distribution of the spatial (vertical) and temporal deviations. The calibration of the lake-level simulations of lake Ammersee for multiple hydrological inputs including also unknown inflows yielded a satisfactory model fit (RMSE =0.20 m). This shows that GLM can also be used to estimate the water balance of lakes correctly. The tools provided by glmGUI enable a less time-consuming and simplified parameter optimization within the calibration process. Due to this, i.e., the free availability and the implementation in a GUI, the presented R package expands the application of GLM to a broader field of lake modeling research and even beyond limnological experts.

scholarly journals LexOPS: An R Package and User Interface for the Controlled Generation of Word Stimuli

2019 ◽  
Author(s):  
Jack Edward Taylor ◽  
Alistair Beith ◽  
Sara C. Sereno
Keyword(s):  
User Interface ◽  
Factorial Design ◽  
Graphical User Interface ◽  
R Package ◽  
Psycholinguistic Research ◽  
Control Current ◽  
Word Lists ◽  
And Control ◽  
Manipulation And Control

LexOPS is an R package and user interface designed to facilitate the generation of word stimuli for use in research. Notably, the tool permits the generation of suitably controlled word lists for any user-specified factorial design and can be adapted for use with any language. It features an intuitive graphical user interface, including the visualization of both the distributions within and relationships among variables of interest. An inbuilt database of English words is also provided, including a range of lexical variables commonly used in psycholinguistic research. This article introduces LexOPS, outlining the features of the package and detailing the sources of the inbuilt dataset. We also report a validation analysis, showing that, in comparison to stimuli of existing studies, stimuli optimised with LexOPS generally demonstrate greater constraint and consistency in variable manipulation and control. Current instructions for installing and using LexOPS are available at https://JackEdTaylor.github.io/LexOPSdocs/.

scholarly journals beanz: An R Package for Bayesian Analysis of Heterogeneous Treatment Effects with a Graphical User Interface

2018 ◽  
Vol 85 (7) ◽  
Author(s):  
Chenguang Wang ◽  
Thomas A. Louis ◽  
Nicholas C. Henderson ◽  
Carlos O. Weiss ◽  
Ravi Varadhan
Keyword(s):  
User Interface ◽  
Bayesian Analysis ◽  
Graphical User Interface ◽  
Treatment Effects ◽  
R Package ◽  
Heterogeneous Treatment Effects
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