Open Source S/R Software
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S/R Software
Browse free open source S/R Software and projects below. Use the toggles on the left to filter open source S/R Software by OS, license, language, programming language, and project status.
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IRAMUTEQ : Interface de R pour les Analyses Multidimensionnelles de Textes et de Questionnaires. Logiciel de traitement de données pour des corpus texte ou de type individus/caractères. Permet notamment de réaliser des analyses de type "ALCESTE"
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NppToR: R in Notepad++
NppToR provides R auto-completion and code passing between Notepad++ a
Similar to the windows R gui built in editor, NppToR aims to extend the functionality of code passing to the Notepad++ code editor. In addition to passing to the R gui, NppToR provides optional passing to a PuTTY window for passing to an R instance a remote machine. Easy shortcuts are also provided for easy batch execution, with a monitor for longer running scripts. -
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PS Matching in SPSS
Propensity score matching in SPSS
Propensity score matching in SPSS Provides SPSS custom dialog to perform propensity score matching. Using the SPSS-R plugin, the software calls several R packages, mainly MatchIt and optmatch. Proper citations of these R packages is provided in the program. -
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gVirtualXRay
Virtual X-Ray Imaging Library on GPU
gVirtualXRay is a C++ library to simulate X-ray imaging. It is based on the Beer-Lambert law to compute the absorption of light (i.e. photons) by 3D objects (here polygon meshes). It is implemented on the graphics processing unit (GPU) using the OpenGL Shading Language (GLSL). SimpleGVXR is a smaller library build on the top of gVirtualXRay. It provides wrappers to Python, R, Ruby, Tcl, C#, Java, and GNU Octave. -
Go From AI Idea to AI App FastAccess Gemini 3 and 200+ models. Build chatbots, agents, or custom models with built-in monitoring and scaling.
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bootf2BCA
computing f2 bootstrap CI BCA
Computing similarity factor (f2) bootstrap bias corrected and accelerated confidence interval -
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HeatmapGenerator is a graphical user interface software program written in C++, R, and OpenGL to create customized gene expression heatmaps from RNA-seq and microarray data in medical research. HeatmapGenerator can also be used to make heatmaps in a variety of other non-medical fields. HeatmapGenerator is peer-reviewed published software (http://www.scfbm.org/content/9/1/30). Please cite: [Khomtchouk et al.: "HeatmapGenerator: High performance RNAseq and microarray visualization software suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline." Source Code for Biology and Medicine, 2014 9:30] HeatmapGenerator source code is available at: https://github.com/Bohdan-Khomtchouk/HeatmapGenerator Bohdan Khomtchouk wishes to acknowledge the support of the Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program. HeatmapGenerator is released under the GNU GPL.
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R packages (maintained by YJLEE)
R packages for PK/PD modeling , BE/BA, drug stability, ivivc, etc.
These R packages are developed for data analysis of PK/PD modeling & simulation, bioequivalence/bioavailability (BE/BA), drug stability, in-vitro and in-vivo correlation (ivivc), as well as therapeutic drug monitoring (TDM). -
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CanReg5 (moved to Github)
Canreg5 is a software package for population based cancer registries
Cancer registries need a tool to input, store, check and analyse their data. If these data are also coded and verified in a standard way, it facilitates the production of comparable analyses across registry populations. The main goal of the CanReg5 project is to provide a flexible and easy to use tool to accomplish these objectives. CanReg5 is a multi user, multi platform, open source tool to input, store, check and analyse cancer registry data. It has modules to do: data entry, quality control, consistency checks and basic analysis of the data It was designed with an emphasis on user friendliness, it has a modern user interface and is easy to navigate. Is available in several languages. (English, French, Spanish, Portuguese, Russian, Turkish, Georgian, and Chinese.) -
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TXM
Unicode XML TEI text analysis platform
TXM is a free and open-source cross-platform Unicode & XML based text analysis environment and graphical client, supporting Windows, Linux and Mac OS X. It can also be used online as a J2EE standard compliant web portal (GWT based) with access control built in. DOWNLOAD LATEST VERSION OF TXM : http://textometrie.ens-lyon.fr/spip.php?rubrique61&lang=en TXM offers a comprehensive range of analysis tools (concordances, collocate search, frequency lists, etc.) based on the powerfull CQP full text search engine (http://cwb.sourceforge.net) and a range of statistical functions (factorial analysis, classification, cooccurrency analysis, etc.) based on R packages (http://www.r-project.org). Read the scientific background at the Textométrie project web site http://textometrie.ens-lyon.fr/?lang=en. Read a full description at the TEI Tools wiki http://wiki.tei-c.org/index.php/TXM. -
Enterprise-grade ITSM, for every businessFreshservice is an intuitive, AI-powered platform that helps IT, operations, and business teams deliver exceptional service without the usual complexity. Automate repetitive tasks, resolve issues faster, and provide seamless support across the organization. From managing incidents and assets to driving smarter decisions, Freshservice makes it easy to stay efficient and scale with confidence.
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Computer programs for application in Sports science, Physical Culture, among others. By Enrique R.P. Buendía Lozada. buendiaenr@gmail.com , Benemérita Universidad Autónoma de Puebla (BUAP), México. (Software without any warranty).
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PANDA
A comprehensive and flexible quantification tool for proteomics data
PANDA is a comprehensive and flexib tool for quantitative proteomics data analysis, which is developed based on our solid foundations in quantitative proteomics for years. Several novelties have been implemented in it. First, we implement the advantage algorithms of LFQuant (Proteomics 2012, 12, (23-24), 3475-84) and SILVER (Bioinformatics 2014, 30, (4), 586-7) into PANDA. Second, we consider the state-of-art concept of quantification reliability in this quantitative workflow. On the levels of spectra, peptides and proteins, PANDA works out a few quantitative filters and new scores for quantification confidence. Third, PANDA is designed for processing proteomics big data in parallel. -
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SPINA
Structure parameter inference approach for endocrine feedback control
SPINA is software for the rapid, reliable and accurate determination of constant structure parameters of endocrine feedback control systems. It is a class of static function tests that require nothing more than steady-state concentrations of hormones or metabolites obtained in vivo. The first version of this cybernetic approach had been developed for the evaluation of the functional status of the thyroid gland, i.e. thyroid's secretory capacity (gain of thyroid, GT or SPINA-GT) and sum activity of peripheral deiodinases (GD or SPINA-GD). A second version has been established for insulin-glucose homeostasis. It delivers the secretory capacity of pancreatic beta cells (SPINA-GBeta), an estimate for the insulin receptor amplification (SPINA-GR) and a static disposition index as a measure for the loop gain of the feedback loop (SPINA-DI). Both implementations of SPINA have been validated in more than 50 clinical studies based on large cohorts. -
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The Life Cycle Assessment Spreadsheet allows you to calculate carbon footprints and other environmental impacts for given product systems. Use requires basic skills in LCA and matrix algebra, but rewards effort with professional analytical tools.
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PAMGuide
An analysis tool in MATLAB and R for acoustic habitat characterisation
PAMGuide is acoustic analysis software for the characterisation of the acoustic environment from sound recordings. PAMGuide can be used to produce calibrated spectrograms and statistical analyses of sound levels, and is provided in both MATLAB and R. A Tutorial on getting started with PAMGuide can be downloaded here: http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12330/suppinfo PAMGuide was published as supplementary material to the following Open Access journal article: Merchant, N.D., Fristrup, K.M., Johnson, M.P., Tyack, P.L., Witt, M.J., Blondel, P., Parks, S.E. (2015). Measuring acoustic habitats. Methods in Ecology and Evolution. http://dx.doi.org/10.1111/2041-210X.12330 -
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Splicing Prediction Pipeline
Splicing Prediction Pipeline or SPiP
SPiP is a tool to predict the splice alteration of variant by integrate several prediction tool in a global pipeline. You can also download SPiP in zip format: https://sourceforge.net/projects/splicing-prediction-pipeline/files/SPiP_alone_v2_1.zip For Linux (GitHub): https://github.com/LBGC-CFB/SPiP If you have questions, please contact me to: r.leman@baclesse.unicancer.fr or raphael.leman@orange.fr v2.1 corrected (07/2021) : correction of score calculation v2.1 (06/2021): Most strigent on "Alter by complex event" v2.0 (04/2021): New SPiP with random forest modelization old change detailled in https://sourceforge.net/projects/splicing-prediction-pipeline/files/changeLogBeforev2.0.txt -
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cpR Chemical Pathology interface for R
A graphical user interface to R for use in Clinical Chemistry
This project is a graphical user interface to the R statistical programming language designed for use in Clinical Chemistry. It allows the user to perform Passing Bablok, Deming and Linear Regression and to produce high quality images in any file format for publication. The front end is written in Python 3.3 and PyQt4 and the form was designed using Qt4 Designer. The statistical analysis is written in R. The compiled binary was made with cx_freeze. This software is free and open-source. It is released under the GNU Public license and comes with absolutely no warranty. -
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mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.
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R Tools for Biologists (RT4Bio) is a multi-functional package writen in R language developed in the Laboratory of Behavioral and Computational Ecology at State University of Montes Claros - MG - Brazil. Formerly known as RRJ.
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'geoconv' is a package to use with R (r-cran). This package is made of functions to convert geographic coordinates and to project geographic coordinates.
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IQuant
A pipeline for quantitative proteomics based upon isobaric tags
IQuant is an automated pipeline for quantitative proteomics based upon isobaric tags. It integrates post-processing tool of protein identification and advanced statistical algorithms to process the MS/MS signals generated from the peptides labeled by isobaric tags for quantification. IQuant can run from a graphical user interface (GUI) as well as a command-line interface and work with both Windows and Linux system. This website contains the IQuant software, an example data labeled by iTRAQ-8plex for testing and a user's manual. If you have any question about IQuant, please contact me: wenbo@genomics.cn. The source code of IQuant can be found here "https://sourceforge.net/p/iquant/code/". -
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An implementation of the Kernel-based Orthogonal Projections to Latent Structures (K-OPLS) method for MATLAB and R. The supplied functionality includes e.g. cross-validation, kernel parameter optimization, model diagnostics and plot tools.
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We are developing data standards and software tools that implement these standards to develop a systemic approach to modeling, capturing, analyzing and disseminating flow cytometry data.
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Copy Number Analysis for Targeted Resequencing (CONTRA) is a tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data.
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Mass-Up
MALDI-TOF data analysis tool
Mass-Up is an Open-Source mass spectrometry utility for proteomics designed to support the preprocessing and analysis of MALDI-TOF mass spectrometry data. Mass-Up includes several tools and operations to load, preprocess and analyze MALDI-TOF data. -
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MoPAC
The Modular Pipeline for the Analysis of CRISPR screens
To facilitate the comparison of gene essentialities in two or more cell samples, we propose MoPAC (Modular Pipeline for Analysis of CRISPR screens), a Shiny-driven interactive tool for differential essentiality analysis in CRISPR/Cas9 screens. For installation and usage instructions please refer to the wiki page.
