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R is a programming language for statistical computing and data visualization. It has been adopted in the fields of data mining, bioinformatics and data analysis. [9] The core R language is augmented by a large number of extension packages, containing reusable code, documentation, and sample data. R software is open-source and free software.
R Pipeline based on CGR method for accurate classification and tracking of rapidly evolving viruses [39] ETE: Python ETE (Environment for Tree Exploration) is a toolkit that assists in the automated manipulation, analysis and visualization of trees. [40] ggtree: R An R package for tree visualization and annotation with grammar of graphics ...
RStudio IDE (or RStudio) is an integrated development environment for R, a programming language for statistical computing and graphics. It is available in two formats: RStudio Desktop is a regular desktop application while RStudio Server runs on a remote server and allows accessing RStudio using a web browser.
Shogun, an open-source large-scale machine-learning toolbox that provides several SVM implementations (like libSVM, SVMlight) under a common framework and interfaces to Octave, MATLAB, Python, R; Waffles is a free-software collection of command-line tools designed for scripting machine-learning operations in automated experiments and processes.
This is a list of software to create any kind of information graphics: either includes the ability to create one or more infographics from a provided data set; either it is provided specifically for information visualization
pathway based data integration and visualization, easy to use and integrate into pathway analysis multiplatform (R/Bioconductor) GPL: SBMLDiagrams [2] Python API to display and edit SBML layout/render extension: multiplatform: MIT: Systrip: analysis of time-series data in the context of biological networks Windows, Linux: LGPL, GPL
Python tool for modeling and analyzing SBML models [21] [22] [23] multiplatform (Python) BSD-3: Yes pySB: Python-based [24] platform with specialization in rule-based models. multiplatform (Python) BSD-3: Partial ReaDDy: Particle-based spatial simulator with intermolecular potentials [25] Linux and Mac: Custom: Not applicable SBSCL
VMD visualization of a 1-billion atom aerosolized SARS-CoV-2 virion, rendered with Tachyon on a workstation with 1TB RAM. Visual Molecular Dynamics (VMD) is a molecular modelling and visualization computer program. [2] VMD is developed mainly as a tool to view and analyze the results of molecular dynamics simulations.