Scientific/Engineering Software
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Cell-ID
Toolchain for quantification of fluorescence intensity and morphological parameters in single cells using microscope based cytometry.
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TXM
Unicode-XML-TEI text/corpus analysis platform
TXM is a free and open-source cross-platform Unicode & XML based text/corpus analysis environment and graphical client, supporting Windows, Linux and Mac OS X. It can also be used online as a J2EE standard compliant web portal (GWT based) with access control built in. DOWNLOAD LATEST VERSION OF TXM : http://textometrie.ens-lyon.fr/spip.php?rubrique61&lang=en TXM offers a comprehensive range of analysis tools (concordances, collocate search, frequency lists, etc.) based on the powerfull CQP full text search engine (http://cwb.sourceforge.net) and a range of statistical functions (factorial analysis, classification, cooccurrency analysis, etc.) based on R packages (http://www.r-project.org). Read the scientific background at the Textométrie project web site http://textometrie.ens-lyon.fr/?lang=en. Read a full description at the TEI Tools wiki http://wiki.tei-c.org/index.php/TXM.
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mzmatch
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.
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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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libirt
The new site is at http://psychometricon.net/libirt/
The new site is at http://psychometricon.net/libirt/ Library of functions to estimate the items and abilities from the responses of subjects to a questionnaire. The IRT models supported are the logistic model, the multivariate logistic model, the graded model and smoothing by penalization and kernel.
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Hyperspectral data analysis in R
Handling and basic analysis of hyperspectral data in R
The hsdar package contains classes and functions to manage, analyse and simulate hyperspectral data. These might be either spectrometer measurements or hyperspectral images through the interface of rgdal.
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YANG J. (Yet Another Network Generator)
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.
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KMWin
Kaplan-Meier for Windows
KMWin (Kaplan-Meier for Windows) is a convenient tool for graphical presentation of results from Kaplan-Meier survival time analysis. The programme is based on the statistical software environment R and provides an easy to use graphical interface. As an introduction, see http://dx.plos.org/10.1371/journal.pone.0038960#s2.
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AutoShim
Tools to build molecular-docking activity prediction models by PLS regression with iterative training and pose-selection. Descriptors include (i) docking score(s), (ii) pharmacophore features, (iii) multi-feature descriptors learned by decision trees.
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CMDS - Cohort DNA Copy Number Analysis
A population-based method for DNA copy number analysis: recurrent copy number aberration indentification in multiple samples (with no need of single-sample calling). Developed for a quick analysis of high resolution and large population data.
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cexcept: exception handling in C
A header file (cexcept.h) that provides Try/Throw/Catch macros similar to those available in C++ for error handling.
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BODE: Bioinformatics ODds and Ends
A collection of bioinformatics-related software created by members of Cancer Research UK (possibly among others).
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Basketball Simulation Engine
Built with R, this code allows the user to simulate the game of basketball. While the main focus is on simulating the NBA, the code provides a framework for simulating other leagues by modifying the default set of rules.
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Celsius
Celsius is a data warehouse that provides web services for upload, archival, download, annotation, quantification, and normalization of all Affymetrix microarray platforms.
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GADA
GADA - Genome Alteration Detection Algorithm
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GNUexp
GNUexp is a GNUstep/Cocoa framework and a collection of tools helping you to plan, develop, and administer applications associated with visual psychophysics, experimental psychology and statistical data analysis.
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Generalized Splines
A set of tools in R to facilitate the use of parametric and semi-parametric splines in multilevel models.
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Hackathon for Outbreak Analysis in R
A hackathon for the analysis of disease outbreaks in R
This is the sourceforge project supporting "Hackout: A hackathon for the analysis of disease outbreaks in R". It includes a repository for the collective development of the project's R package.
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MetaBoFlux
Metaboflux is a generic approach for predicting flux distribution in metabolic networks under multiple and various constraints deducted from the experiments, to increase the biological relevance of the model.
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MoCObench
Benchmark instances for multiobjective combinatorial optimization
Benchmark instances for multiobjective combinatorial optimization
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MyNook
A machine learning system for supervised document classification
An open source system for supervised document classification based on statistical machine learning techniques. On the contrary of the state of art classification techniques, MyNook just requires the title of the document, not the content itself.
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QUASI
QUASI is a toolkit to rapidly assess the quality of shRNA-Seq based data and call differential abundance using common statistical inference methods (DESeq, edgeR, baySeq).
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R Packages for proteomics
We use R (www.r-project.org) in order to generate a greater specificity and sensitivity of protein identification by Mass Spectrometry. These functions are implemented as add-on packages to the open source GPL software R.
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Sage Bionetworks
Opensource software projects for genetics and genomics from Sage Bionetworks.
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comparaExecucao
Program that compares the time of execution between a Neural Network and the formula of distance.
