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.
R packages for PK/PD modeling, BE/BA, drug stability, ivivc, etc.
These R packages are developed for data analysis of PK/PD modeling, bioequivalence/bioavailability (BE/BA), drug stability, in-vitro and in-vivo correlation (ivivc), as well as therapeutic drug monitoring (TDM). They include bear, ivivc, PKfit, stab and tdm.
Tools for multivariate data visualization, exploration and analysis.
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.
Suite of community detection algorithms based on Modularity
- MixtureModel_v1r1: overlapping community algorithm , which includes novel partition density and fuzzy modularity metrics. - OpenMP versions of algorithms in  are available to download. - Main suite containing three community detection algorithms based on the Modularity measure containing: Geodesic and Random Walk edge Betweenness  and Spectral Modularity . Collaborator: Theologos Kotsos.  M. Newman & M. Girvan, Physical Review, E 69 (026113), 2004.  M. Newman, Physical Review E, 74(3):036104, 2006.  B. Ball et al, An efficient and principled method for detecting communities in networks, 2011. The suite is based upon the fast community algorithm implemented by Aaron Clauset <firstname.lastname@example.org>, Chris Moore, Mark Newman, and the R IGraph library Copyright (C) 2007 Gabor Csardi <email@example.com>. It also makes of the classes available from Numerical Recipies 3rd Edition W. Press, S. Teukolsky, W. Vetterling, B. Flanne
computing f2 bootstrap CI BCA
Computing similarity factor (f2) bootstrap bias corrected and accelerated confidence interval
OpenM++: open source microsimulation platform
OpenM++ is an open source microsimulation platform inspired by and compatible with Modgen. OpenM++, compared to its closed source predecessor Modgen, has advantages like portability, scalability and open source. It is not a copy of Modgen, but a new, functionally equivalent implementation of the publicly available language specification.
The 'runjags' R package and standalone JAGS extension module
This package provides high-level interface utilities for MCMC models via Just Another Gibbs Sampler (JAGS), facilitating the use of parallel (or distributed) processors for multiple chains, automated control of convergence and sample length diagnostics, and evaluation of the performance of a model using drop-k validation or against simulated data. Template model specifications can be generated using a standard lme4-style formula interface to assist users less familiar with the BUGS syntax. A JAGS extension module provides additional distributions including the Pareto family of distributions, the DuMouchel prior and the half-Cauchy prior.
Excel's Interface to R
Excelsi-R is an Excel add-in that allows Excel spreadsheets to harness the power of the R statistical language by connecting to a running R process. R does not need to be installed on the computer running Excel, but it does require access to an R instance running Rserve (which can be on a remote computer). It supports incorporating R plots and graphs in an Excel workbook.
R package for modelling anthropogenic deforestation
phcfM is an R package for modelling anthropogenic deforestation. It was named after the REDD+ pilot-project 'programme holistique de conservation des forêts à Madagascar'. phcfM includes two main functions: (i) demography(), to model the population growth with time in a hierarchical Bayesian framework using population census data and Gaussian linear mixed models and (ii) deforestation(), to model the deforestation process in a hierarchical Bayesian framework using land-cover change data and Binomial logistic regression models with variable time-intervals between land-cover observations. The two functions use embedded Gibbs samplers written in C++ with the Scythe statistical library to reduce computational time.
BigBang/Horizon is a proteomics data analysis pipeline with focus on the shotgun LC/MSMS workflow.
CORe microBiome Analysis Tools
Corbata is a set of statistical tools that can be used to analyze the core microbiome across a set of samples.
Event studies in several statistical packages
Software to perform event studies in several statistical packages, such as SAS, Stata and R.
R packages supporting parallel computing.
Qt-based C++ GUI programming interface to R
VisualR is a (currently) Windows only C++ GUI programming interface to R. It allows creating full featured applications that complelely control R and serves as a GUI programming toolkit that can be controlled from inside R code.
Sistema Estadístico basado en R
Priotelus (Sistema Estadístico basado en R) es un software libre para realizar análisis estadísticos utilizando R. Su interfaz limpia y sus potentes funcionalidades tienen como objetivo facilitarle su trabajo, enfocándose cada vez más en estudios completos y evitar la realización de muchos cálculos parciales para poder completar un estudio. Los análisis estadísticos se realizan utilizando el lenguaje y entorno de programación para análisis estadístico y gráfico, R, con más de 6000 paquetes desarrollados y avalados por su amplia comunidad científica. Funcionalidades: -Carga de datos desde los formatos XLS, CSV y TXT. -Exportación de datos hacia los formatos XLS, CSV, TXT y PDF. -Construcción y edición de tablas de datos. -Salva de un proyecto con el estado actual de nuestro trabajo. -Cifrado de un proyecto utilizando el método AES con una clave de 256 bits. -Graficado de datos, utilizando diferentes tipos de gráficas.
RIPE (Regulatory network Inference from joint Perturbation and Expression data) is a novel three-step method that integrates both perturbation data and steady state gene expression data in order to estimate a regulatory network. The ripe package is written in R, with additional functionality provided by a MATLAB executable file. The executable file uses a runtime engine called the MATLAB Compiler Runtime (MCR). The executable for different architectures is distributed on this site together with the R package itself.
User Friendly Data Analysis Tool for Interaction Data
TOPS provides the benchtop scientist with a free toolset to analyze, filter and visualize data from functional genomic gene-gene and gene-drug interaction screens with a flexible interface to accommodate various different technologies and analysis algorithms in addition to those already provided here.
R package for hierarchical species distribution models
hSDM is an R package for hierarchical species distribution models. Such models allows interpreting the observations (occurrence and abundance of a species) as a result of several hierarchical processes including ecological processes (habitat suitability, spatial dependence and anthropogenic disturbance) and observation processes (species detectability). Hierarchical species distribution models are essential for accurately characterizing the environmental response of species, predicting their probability of occurrence, and assessing uncertainty in the model results.
The project liquiditymeter is for measuring liquidity in various financial markets.
Tools to analyse and use passport data for biological collections.