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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La version gratuite d'Auth0 s'enrichit !Vous l'avez demandé, nous l'avons fait ! Les versions gratuite et payante d'Auth0 incluent des options qui vous permettent de développer, déployer et faire évoluer vos applications en toute sécurité. Utilisez Auth0 dès maintenant pour découvrir tous ses avantages.
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MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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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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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.">
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SimpleITK: a simplified layer build on top of the Insight Toolkit (ITK), intended to facilitate its use in rapid prototyping, education and interpreted languages.
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Virtual Laboratory Environment
A multi-modeling and simulation environment to study complex systems
VLE is a multi-modeling and simulation environment to study complex dynamic systems. VLE is based on the discrete event specification DEVS. and it implements the DSDE formalism (A merge of Dynamic Structure DEVS, DSDEVS, with Parallel DEVS, PDEVS). VLE provides a complete set of C++ libraries, called VFL (VLE Foundation Libraries), to develop DEVS models, to gets results of simulations, to launch simulation on cluster. The models can be developed with the DEVS formalism or with the classical mathematical formalism: Ordinary Differential Equation with Euler, Range-Kutta or QSS integrator, Finite state automaton (FDDEVS, UML State chart, Hybrid Petri net). The VLE environment provides an IDE to develop C++ models, DEVS coupled models. VLE have also three ports to use the VFL with Python, Java and R programming languages. -
Monitoring, Securing, Optimizing 3rd party scriptsc/side is crawling many sites to get ahead of new attacks. c/side is the only fully autonomous detection tool for assessing 3rd party scripts. We do not rely purely on threat feed intel or easy to circumvent detections. We also use historical context and AI to review the payload and behavior of scripts.
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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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The application Bio7 is an integrated development environment for ecological modelling and contains powerful tools for model creation, scientific image analysis and statistical analysis. The application itself is based on an RCP-Eclipse-Environment (Rich-Client-Platform) which offers a huge flexibility in configuration and extensibility because of its plug-in structure and the possibility of customization.
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PyRate
Bayesian Estimation of Speciation and Extinction from Fossil Data
PyRate is a Python program to estimate speciation, extinction, and preservation rates from fossil occurrence data using a Bayesian framework. The method was described by D Silvestro, J Schnitzler, LH Liow, A Antonelli, and N Salamin in Systematic Biology (http://sysbio.oxfordjournals.org/content/early/2014/02/08/sysbio.syu006.abstract). *Please download the most up-to-date code from the "PyRate code" tab on this page or from: https://github.com/dsilvestro/PyRate * *An updated manual can be found here: https://github.com/dsilvestro/PyRate/tree/master/tutorials * -
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The igraph library
Library for creating and manipulating graphs
This is a library for creating and manipulating graphs with focus on speedy operations for large, sparse graphs. -
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Waterloo
Java-based scientific graphics
Java-based scientific graphics with support for Java, Groovy, MATLAB, Python, the R statistical environment, Scala and SciLab. -
ManageEngine Endpoint Central for IT ProfessionalsManageEngine's Endpoint Central is a Unified Endpoint Management Solution, that takes care of enterprise mobility management (including all features of mobile application management and mobile device management), as well as client management for a diversified range of endpoints - mobile devices, laptops, computers, tablets, server machines etc. With ManageEngine Endpoint Central, users can automate their regular desktop management routines like distributing software, installing patches, managing IT assets, imaging and deploying OS, and more.
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TEACUP
TCP Experiment Automation Controlled Using Python
TEACUP automates many aspects of running TCP performance experiments in a specially-constructed physical testbed. TEACUP enables repeatable testing of different TCP algorithms over a range of emulated network path conditions, bottleneck rate limits and bottleneck queuing disciplines. TEACUP utilises a text-based configuration file to define experiments as combinations of parameters specifying desired network path and end host conditions. When multiple values are provided (e.g. for TCP congestion control algorithm), an experiment is made up of multiple tests. For each experiment and test, TEACUP collects a range of data, such as tcpdump files of traffic seen or TCP stack information (e.g. using Web10G). TEACUP also collects a variety of metadata from the end hosts and bottleneck router, such as the actual OS/kernel version(s) used. TEACUP also provides some simple tools for analysing the results of experiments, such as plotting a flow's experienced RTT over time. -
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ncPRO-seq
Non-Coding RNA PROfiling from sRNA-seq
ncPRO-seq is a tool for annotation and profiling of ncRNAs from smallRNA sequencing data. It aims to interrogate and perform detailed analysis on small RNAs derived from annotated non-coding regions in miRBase, piRBase, Rfam and repeatMasker, and regions defined by users. The ncPRO pipeline also has a module to identify regions significantly enriched with short reads that can not be classified as known ncRNA families. ############# Docker version : download and run Dockerfile (go in "Files" section) ############# GitHub : https://github.com/jbrayet/ncpro-seq -
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ADTEx
Aberration detection in tumour exome
Aberration Detection in Tumour Exome (ADTEx) is a tool for copy number variation (CNV) detection for whole-exome data from paired tumour/matched normal samples. -
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A collection of bioinformatics-related software created by members of Cancer Research UK (possibly among others).
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BayesRate
Bayesian estimation of diversification rates
BayesRate is a program to estimate speciation and extinction rates from dated phylogenies in a Bayesian framework. The methods are described in: Silvestro, D., Schnitzler, J. and Zizka, G. (2011) A Bayesian framework to estimate diversification rates and their variation through time and space. BMC Evolutionary Biology, 11, 311 Silvestro D., Zizka G. & Schulte K. (2014) Disentangling the effects of key innovations on the diversification of Bromelioideae (Bromeliaceae). Evolution, 68, 163-175. -
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CoLabR
A simple user interface to the R software environment.
A simple user interface to the R software environment. It is designed for people new to R and provides the user with easy access to their variables and data along with pointers to the most basic commands. It also allows for multiple people to share data across different sessions on different machines. In this way it also offers a collaborative environment for people to work together in remote locations. -
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ConDEnSE (Confidential Data Enabled Statistical Exploration) will be a web-based environment for statistical analysis of confidential data from various database sources, based on Plone and R, and using the Jackknife method of confidentiality protection.
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Cygwin Ports
Repository of desktops and programs for the Cygwin platform
A large repository of open-source programs built for Cygwin, including X11 desktops, language interpreters, multimedia frameworks, cross-compiler toolchains, and much more. Also hosted here is the cygport tool for building Cygwin packages. cygport releases and the Ports Git repositories are hosted here; Ports packages are available from the website. -
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DEAPathways
Differential Expression Analysis for Pathways
This project contains the source code associated with the PLoS Computational Biology publication: "Differential Expression Analysis for Pathways". The paper text can be found here: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002967 -
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Django-dataplot enables developers using the Django web framework to seamlessly integrate data-driven graphical plots into their web pages.
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A Python library bringing together utilities I've written over the years for work in bioinformatics and biostatistics, which should be generally applicable outside these fields as well. Focuses on string processing, DBI, and math.
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Electrophysiology & circular stats tools
Data analysis and circular statistics with OpenElectrophy and R
Set of tools for basic analysis of electrophysiological data. The Python classes show how to call OpenElectrophy functions and save data. The R library applies circular statistics to spike phase data and saves the best von Mises fit and the Rayleigh statistics on the disk. The wavelet coherence analysis is done in R by the package "sowas". Check the module R_coherence to see how we solved that problem. This packages may be useful for people who start using OpenElectrophy and circular statistics in R. If you find errors, please report them. The project is still in development, so in the future you'll get updates. -
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GEPETTO - Gene Prioritization in Java
GEPETTO (GEne Prioritization ExTended TOol)
GEPETTO (GEne PrioriTization ExTended TOol) is an original open-source framework, distributed under the LGPL license, for gene selection and prioritization on a desktop computer that ensures confidentiality of personal data. It takes advantage of the data integration capabilities in the SM2PH-Central Framework(KD4v,MSV3d,BIRD,..), combined with in-house developed gene prioritization methods. It currently incorporates six prioritization modules, based on gene sequence, protein-protein interactions, gene expression, disease-causing probabilities, genomic context). GEPETTO is written in Java/Python and supported by an advanced modular architecture, which means that it can easily be modified and extended by the user, in order to include alternative scoring methods and new data sources. We intend to extend the system from gene-level to variant-level prioritization, by exploiting the variant data in the MSV3D database. Contact: bmhoan@gmail.com or walter.vincent.fr@gmail.com -
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GISBox by Citiviz
Ready-to-use appliance for GIS, Data Mining and Analysis, Modelling...
GISBox by Citiviz is a ready-to-use virtual appliance containing an assortment of powerful, free and open source GIS, Data Mining and Analysis, Modelling and Programming software and packages. The pre-configured and tested GISBox allows you to try and use in few minutes a variety of software used by data scientists, engineers, physicists, mathematicians, geomatics engineers, and geographers from around the globe, without installing anything more than once the Oracle VirtualBox™ software (https://www.virtualbox.org/) on your Linux, Windows or Mac computer. The GISBox is free and open, allowing it to be freely distributed, duplicated and passed around, even with your own datasets and in-house applications. If you read this and are related to the Ecole polytechnique de Lausanne - EPFL (http://www.epfl.ch) in Switzerland, please use this link for downloading or support information: http://gisbox.epfl.ch. Happy (geo)Data Hacking! Brought to you by Citiviz' Builders -
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Hoea is a python module for hierarchical ontology enrichment analysis, which facilitated GO (Gene Ontology)/KO (KEGG Orthology) enrichment analysis at any desktop.
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Hierarchical Stochastic Block Model
just a bunch of PhD projects
Development codes for hierarchical stochastic block models