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Tools to analyse and use passport data for biological collections.

...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

Development of a common “open source” tool for assessing the accuracy of parameter estimates collected within the framework of the DCR (EU Regulation 1639/2001 and 1581/2004)

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

You may also like some newer work: http://createdatasol.com/ Project imDEV is an application of RExcel, which seamlessly integrates Excel and R for tasks focused on multivariate data visualization, exploration, and analysis. Interactive modules for dimensional reduction (imPCA), prediction (imPLS), feature selection, analysis of correlation (imCorrelations) and generation of networked structures (imGraph) provide an integrated environment for systems level analysis of multivariate data.

A R based universal workflow for analysising miRNA sequencing data

An R package that performs forward-backward fragment assembling segmentation. Reference: BMC Bioinformatics. 2007 May 3;8:145.

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.

Software of decision support

MICROSATELIGHT is a Perl/Tk graphical user interface (GUI) that facilitates several tasks when scoring microsatellites.

CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV). Learn about CNV Workshop in our associated BMC Bioinformatics manuscript: http://www.biomedcentral.com/1471-2105/11/74

Peakplot is a Perl implemented freely available software application which labels peptide tandem mass spectra retrospectively after a Mascot database search. Availability: http://fgcz-peakplot.uzh.ch/

BigBang/Horizon is a proteomics data analysis pipeline with focus on the shotgun LC/MSMS workflow.

r-ggorjan is a collection of addon packages for R (http://www.r-project.org)

Acanthocephalan Proboscis Profiler is a tool for detecting acanthocephalan morphotypes.

...For NGS data Chipster contains a built-in genome browser, which highlights SNPs and automatically indexes BAM files and calculates coverage. Chipster’s ability to provide a biologist-friendly access to a powerful analysis platform is technically based on a desktop application user interface, a flexible distributed architecture, and the ability to integrate many types of analysis tools (command line, R/Bioconductor, Java, Web Services etc). The platform is generic and easily extendable to other areas, even beyond bioinformatics. For more information, please see http://chipster.csc.fi and http://genomebiology.com/1471-2164/12/

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.

GenCart: Genome Cartology in the R Statistical Programming Language

Neural Network for physicists. A flexible code in which the user has high control of the network parameters. The code provides a chi^2 cost function. The code accepts user-defined cost function and neuron activation functions.

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 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.

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.

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

CAStoolsBazaar is a collection of software tools for actuaries around the world who are looking for a little more fun while doing their work.

MGARCH is a software library for R-Project to simulate and estimate various MGARCH processes. This project also provides convenience tools for preparing data, summarizing and visualizing results, prediction and documentation.