Open Source S/R Scientific/Engineering Software

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.

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.

Adverse Drug event Reporting systems miner

DetectiV is an R package for the analysis of pathogen detection microarrays

DuffyRNAseq is an R package that implements an analysis pipeline for processing RNA-seq data from Illumina NextGen sequencers, to measure gene transcription and differential expression.

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.

Ericscript is a computational framework to detect gene fusions from paired end RNA-seq data with high sensitity and specificity.

The current software contains the implementation for the 454 pyrosequencing platform.

GUI for the ISOP R module. The ISOP R module is an implementation of the equal named IRT model by Scheiblechner

A tool to calculate the Pan-Genome of a set of annotated genomes

QRMlib provides a library of methods to investigate Quantitative Risk Management, including Market Risk, Credit Risk and Operational Risk, as developed in the book "Quantitative Risk Management: Concepts, Techniques and Tools".

RMol is an R script with a collection of functions to link information of SD/Molfile structure databases with powerful graph analysis packages in R.

RawGeno Version 2.0-1 is released! RawGeno is an R CRAN library automating the scoring of AFLP electropherograms. The library includes a graphical user interface to simplify its use. Note that the 2.0-1 version is delivered as a source (*.tar.gz for Linux and Mac users) and as a binary file (*.zip, for Windows users). The installation procedure differs slightly according to your system; but this should remain simple. Have a look at the readme file when you download your new copy from https://sourceforge.net/projects/rawgeno/files/rawgeno/RawGeno%202.0-1/ Make also sure to have a look at https://sourceforge.net/projects/rawgeno/files/ where you can find a detailed manual, demo datasets and many demo scripts.

rdv-framework is designed to evaluate and compare ecological conservation reserve selection alogrithms .

Rqt is a library for calling R functions within C++/Qt4 applications. The argument interface uses QVariant for flexible exchange of data to and from R. This allows R calls as if they were part of the local Qt environment.

Syzygy is a toolkit for the analysis of targeted (pooled/individual) resequencing datasets.

Bioinformatics related demos and tutorials using the R programming language for large biological data. Licence: Creative Commons Attribution-NonCommercial 4.0 International License

Microarray analysis database

Image analysis software for quantification of cell density in microbial cultures (e.g. S. cerevisiae) growing on solid agar plates. Specialises in detection of extremely low cell densities. Forms part of the Quantitative Fitness Analysis (QFA) workflow: http://research.ncl.ac.uk/qfa/ Suitable for high-throughput, genome-wide analysis of culture libraries when combined with the following qfa R package: http://qfa.r-forge.r-project.org/ This is the version presented, used and demonstrated in the following manuscripts: Lawless et al. 2010 http://dx.doi.org/10.1186/1471-2105-11-287 Addinall et al. 2011 http://dx.doi.org/10.1371/journal.pgen.1001362 Chang et al. 2011 http://dx.doi.org/10.1534/g3.111.000216 Banks et al. 2012 http://dx.doi.org/10.3791/4018 Development has been moved to github, where Colonyzer has undergone several recent improvements, particuarly making installation easier and analysis faster: https://github.com/CnrLwlss/Colonyzer

m0n0merhunter is a command line program for computing the most frequent delta masses of ultra high mass resolution and accurate mass measurements using mass spectrometer data.

The "molR" is a set of R functions for working with and manipulating (bio)molecular data.

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/