Open Source S/R Software Development Software for Linux

We developed a systematic algorithmic solution for quantitative drug sensitivity scoring (DSS), based on continuous modeling and integration of multiple dose-response relationships in high-throughput compound testing studies. License: The DSS R-package is made available under the terms of the GNU General Public License, which means that the source code is freely available for use within other software, but if you alter the code and distribute it, you must make the new source code freely available as well. This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY. In case you use the package in your work, we do appreciate a citation to a DSS publication. Citation: Yadav et al. (2014), Quantitative scoring of differential drug sensitivity for individually optimized anticancer therapies. Scientific Reports 4, 5193; DOI:10.1038/srep05193 Please visit the link below for details

Java-based scientific graphics with support for Java, Groovy, MATLAB, Python, the R statistical environment, Scala and SciLab.

ANOSE is a web application (a web site) that allows software engineers to collect information about software projects and perform statistical analysis on the data collected. A key goal in ANOSE is to provide an easy to use user interface and efficient da

The Dataverse Network is a Java EE5 app that enables researchers to share data on-line. It provides data citation standards, facilitates preservation, distribution and replication of data, and includes statistical analysis. More at: http://thedata.org

Django-dataplot enables developers using the Django web framework to seamlessly integrate data-driven graphical plots into their web pages.

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

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

Hoea is a python module for hierarchical ontology enrichment analysis, which facilitated GO (Gene Ontology)/KO (KEGG Orthology) enrichment analysis at any desktop.

A simple tool to help you create an R interface for your Java project. Simply annotate the constructors and methods you want to make available and JAnnotateR will produce a working package, complete with documentation generated from javadocs.

Next generation sequencing has opened new avenues for sequencing prokaryotes which were difficult or either impossible to culture. Now, it is possible to sequence all organisms present in a metagenomic community. However, a critical problem is to determine the host organism for each genomic fragment present in the dataset. This project provides the computational tools for assigning the organismal identity for each genomic scaffold in the given dataset. For more detailed documentation please refer to the link below: https://sourceforge.net/p/ngsscaffolds/wiki/Documentation/

Open Metaheuristic (oMetah) is a library aimed at the conception and the rigourous testing of metaheuristics (i.e. genetic algorithms, simulated annealing, ...). The code design is separated in components : algorithms, problems and a test report generator

IMPORTANT: ========== Our project home page: https://openmpp.org Our latest source code and release available at: https://github.com/openmpp/main/releases/latest Our documentation available at: https://github.com/openmpp/openmpp.github.io/wiki SourceForge files still exist for historical reason. OpenM++ is an open source microsimulation platform inspired by and compatible with Modgen. OpenM++, compared to its closed source predecessor Modgen, has advantages like portability, scalability and open source. It is not a copy of Modgen, but a new, functionally equivalent implementation of the publicly available language specification.

For software developers in domains involving statistical analysis, the "R + Java = Inf" project analyses and enhances the interoperability between the R and Java programming languages. The deliverables are source code, documentation and benchmarks.

R Unit test framework R functions implementing a standard Unit Testing framework, with additional code inspection and report generation tools

TOPS provides the benchtop scientist with a free toolset to analyze, filter and visualize data from functional genomic gene-gene and gene-drug interaction screens with a flexible interface to accommodate various different technologies and analysis algorithms in addition to those already provided here.

An open-source implementation of our network-based target deconvolution approach, named target addiction score (TAS). License: The TAS R-package is made available under the terms of the GNU General Public License, which means that the source code is freely available for use within other software, but if you alter the code and distribute it, you must make the new source code freely available as well. This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY. In case you use the package in your work, we do appreciate a citation to the publications below. Citation: Yadav B, Peddinti G, Pemovska T, Khan SA, Szwajda A, Tang J, Wennerberg K and Aittokallio T. From drug response profiling to target addiction scoring in cancer cell models. (Submitted)

Quick reference for switching between mathematical computation environments for computer algebra, numeric processing and data visualisation. Examples are Matlab, IDL, SPlus, and their open-source counterparts Octave, Scilab, Python+NumPy and R.

The Vyper Dynamic Server framework is a pure-java library for use in the creation of backend / server platforms. VDS is specifically tailored for financial applications, and suited for many high-throughput, asynchronous and distributed environments.

A header file (cexcept.h) that provides Try/Throw/Catch macros similar to those available in C++ for error handling.

An R package implementation of a consensus clustering methodology. This package allows users to perform re-sampling statistics based clustering using multiple clustering algorithms to assess the robustness of both clusters and members of clusters.

RGnome is a gtk based frontend for GNU R, which is a widely used language for statistical computing. It features a fully working R console and an editor with syntax highlighting.

Builds synthetic data applicable across multiple domains. This package also provides flexibility to control data distribution to make it relevant to many industry examples.

This project is goaled a r-language wrap of Artificial Neural Network library libfann. also known as R-binding libfann