Open Source S/R Information Analysis Software

IRAMUTEQ : Interface de R pour les Analyses Multidimensionnelles de Textes et de Questionnaires. Logiciel de traitement de données pour des corpus texte ou de type individus/caractères. Permet notamment de réaliser des analyses de type "ALCESTE"

TXM is a free and open-source cross-platform Unicode & XML based text 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.

Xpose - an S/R based population PK/PD model building aid for NONMEM.

An implementation of the Kernel-based Orthogonal Projections to Latent Structures (K-OPLS) method for MATLAB and R. The supplied functionality includes e.g. cross-validation, kernel parameter optimization, model diagnostics and plot tools.

a R package. 'Qair' gives access to data bases used by air quality monitoring associations in France. It also contains functions to manipualte air quality datas.

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.

AWclust is easy to use non-parametric population structure analysis software written for R with a GUI interface. Just point and click and you will be on your way to discovering the important cluster information in your SNP data sets.

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

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

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.

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.

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

Development codes for hierarchical stochastic block models

This program takes a .txt input file containing the raw output from a Lotek SRX800 receiver and removes false detections based on a user-provided .csv of tagging data.

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.

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

This is a variant of k-means algorithm which allows datas to belong to several clusters instead of just one.

PROMPT is a system for retrieval, analysis, mapping and comparison of proteins. It allows easy mapping of different types of sequence IDs, data retrieval and integration, a multitude of analysis and comparison algorithms and a full-blown easy to use GUI.

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).

R-gregmisc is a set of extension package for the open-source statistical environment/language "R''. It includes functions for plotting (gplots), data manupulation (gdata), modeling (gmodels), and programming tools (gtools), creation and management of sub-processes (fork), determing sample sizes for -omics experiments (ssize), and a variety of other packages.

The R package to be built aims at implementing what I did in a few scripts for the preparation of the papers I published in CaGEO and TGIS (see below). Basically this is related to the computation of the distribution of k co-occurrences of spatial events (generalising the contiguity distributions - 2 co-occurrences at distance 0) to derive spatial clustering statistics (mainly using the Shannon entropy, then called the k-spatial entropy) and methods linked to this: SOOk, SelSOOk (see caGEO paper) and scankOO (see TGIS). Another method (CAkOO) performing a k-Correspondence Analysis (i.e. on a multiway table with k entries) on the contingencies of co-occurrenceshas been already "published in my JSS paper about another R package: PTAk. At the moment the basic scripts I have are based on points and use the R package spatstat, but I would like also to extend to any geometry type. So from all this "a plan" has first to be drawn! ... (see Homepage website for references)

R based genetic algorithm for optimization, variable selection and other machine learning and statistical analysis approaches.

R2HTML is a package for R, which includes HTML function and methods to output R objects to HTML. Allow for redirection on the fly. A driver for Sweave allows to parse HTML flat files containing R code and to automatically write the corresponding outputs.

Implematation of robust depth-based inference tools for microarray data (a scale curve, to measure the dispersion of a set of curves, a rank test to decide if two groups of curves come from the same population, and classification techniques).

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.