Open Source S/R Software

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.

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.

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

FishingCNV, a software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data. The inputs are standard coverage files produced by Genome Analysis ToolKit (GATK), and the output is a file containing putative CNVs. The program comes in 2 different releases * GUI version (FishingCNV_X.X.X.zip) * Command line version (FishingCNV_X.X_pipeline) Browse through our files to find the different releases.

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

Use statistical methods to analyze time-course data (gene expression microarray and RNA-seq data in particular, but not limited to). Apply significance tests to filter out only significant genes or time series. Cluster time series into similar groups. Generate network models, including linear or non-linear models. Variable selection and optimization routines included. Written in Scala and R. The application is a cross-platform desktop app with a simple GUI and is fully functional currently. The app was and is developed at the University of Rochester (http://cbim.urmc.rochester.edu) under the GPL 3.0 license. This is a fork of that project.

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

LiDSiM is a tool to estimate the possible influence of error-tolerant database searches and proteogenomic approaches on the amount of unidentified spectra and the ratios of taxonomic relationship of identified spectra in MS/MS studies of microbial proteomes. For more details about LiDSiM and its functioning, please see "Estimating the Computational Limits of Detection of Microbial Non-Model Organisms" Mathias Kuhring and Bernhard Y. Renard (http://onlinelibrary.wiley.com/doi/10.1002/pmic.201400598/abstract) PLEASE NOTE, it is recommended to read the paper and the readme.txt file before using LiDSiM.

Maui is the Maltcms User Interface, a rich client application for Chromatography-Mass Spectrometry and related research areas.

Benchmark instances for multiobjective combinatorial optimization

MoSi - A program for Modeling and Simulation of Indicator Systems. This Java program uses R.

This Java software includes algorithms of combinatorical optimization for the NP-hard offline ship lock scheduling problem. Solutions and performed computations can be displayed graphically. Besides, there is a framework for generating test instances and running these in parallel, as well as R/JGR code for statistical evaluation. Some tools for estimating the quality of calculated solutions will be further improved. Initially the software was developed within a project of TU Berlin regarding the Kiel Canal. See project wiki for conditions that should be met by applications.

A suite of tools for discovering and genotyping genome structural variation from sequencing data, including the Genome STRiP algorithm.

SuRankCo is a machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which have no related reference genome yet. For more details about SuRankCo and its functioning, please see "SuRankCo: Supervised Ranking of Contigs in de novo Assemblies" Mathias Kuhring, Piotr Wojtek Dabrowski, Andreas Nitsche and Bernhard Y. Renard (http://www.biomedcentral.com/1471-2105/16/240/abstract) PLEASE NOTE, it is recommended to read the paper and the readme.txt file before using SuRankCo. Update Jun2015: * Minor changes to enable BAM support. Update Feb2014: * Added support for FASTA/SAM assemblies in addition to ACE/FASTQ(QUAL). NOTE: features of FASTA/SAM assemblies do not include BaseCount, BaseSeqmentCount and ContigQualities yet.

This is the protein similarity network - PSIN. Here, the nodes are human proteins and they are linked only if they share considerable sequence similarity. We found that this network is particularly useful to distinguish approved from problematic drug-targets. Here you also find the complete set of programs and datasets we used for this purpose. Free to help further test and develop this project. Your help and expertise are much appreciated ! If you have any questions, please do not hesitate to contact us in the forum or by email. Please see the original manuscript: Lopes, TJS, et al. (2015) - "Identifying problematic drugs based on the characteristics of their targets" - Frontiers in Pharmacology doi: 10.3389/fphar.2015.00186

YANG (Yet Another Network Generator - Java) enables you to generate social networks given various social rules observed in the real population. Uses: generate realistic networks to be used in individual-centric models, teaching or benchmarking.

Decima is a database that was designed to support time-series data mining. It consists of PostgreSQL custom type definition, implementation of GiST index for that type and snowflake database schema.

dynGraph est un module de FactoMineR qui permet de manipuler des graphiques interactifs.

e-Science Central has moved to BitBucket, please visit: https://bitbucket.org/digitalinstitute/esciencecentral/

This is the new netbeans based RCP release! 0.8.5 beta. This tool provides an intuitive gui for microarray analysis. See here : http://www.pharma.uni-bonn.de/www/mart

vipR is a program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms. Information on this and other projects can be found on: http://www.altmann.eu