Repository of desktops and programs for the Cygwin platform
A large repository of open-source programs built for Cygwin, including X11 desktops, language interpreters, multimedia frameworks, cross-compiler toolchains, and much more. Also hosted here is the cygport tool for building Cygwin packages. cygport releases and the Ports Git repositories are hosted here; Ports packages are available from the website.
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.
SimpleITK: a simplified layer build on top of the Insight Toolkit (ITK), intended to facilitate its use in rapid prototyping, education and interpreted languages.
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 application Bio7 is an integrated development environment for ecological modelling and contains powerful tools for model creation, scientific image analysis and statistical analysis. The application itself is based on an RCP-Eclipse-Environment (Rich-Client-Platform) which offers a huge flexibility in configuration and extensibility because of its plug-in structure and the possibility of customization.
Scheduling lockages at ship locks with several parallel lock chambers
This Java software includes algorithms of combinatorical optimization for the NP-hard offline ship lock scheduling problem. Solutions and performed computations can be displayed graphically. Besides, there is a framework for generating test instances and running these in parallel, as well as R/JGR code for statistical evaluation. Some tools for estimating the quality of calculated solutions will be further improved. Initially the software was developed within a project of TU Berlin regarding the Kiel Canal. See project wiki for conditions that should be met by applications.
Java-based scientific graphics
Java-based scientific graphics with support for Java, Groovy, MATLAB, Python, the R statistical environment, Scala and SciLab.
Computer programs for application in Sports science, Physical Culture, among others. By Enrique R.P. Buendía Lozada. email@example.com , Benemérita Universidad Autónoma de Puebla (BUAP), México. (Software without any warranty).
Bayesian estimation of diversification rates
BayesRate is a program to estimate speciation and extinction rates from dated phylogenies in a Bayesian framework. The methods are described in: Silvestro, D., Schnitzler, J. and Zizka, G. (2011) A Bayesian framework to estimate diversification rates and their variation through time and space. BMC Evolutionary Biology, 11, 311 Silvestro D., Zizka G. & Schulte K. (2014) Disentangling the effects of key innovations on the diversification of Bromelioideae (Bromeliaceae). Evolution, 68, 163-175.
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.
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.
Analyze 4C-seq data.
fourSig is a suite of programs for analyzing and visualizing 4C-seq data.
MALDI-TOF data analysis tool
Mass-Up is an Open-Source mass spectrometry utility for proteomics designed to support the preprocessing and analysis of MALDI-TOF mass spectrometry data. Mass-Up includes several tools and operations to load, preprocess and analyze MALDI-TOF data.
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.
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.
Maui is the Maltcms User Interface
Maui is the Maltcms User Interface, a rich client application for Chromatography-Mass Spectrometry and related research areas.
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.
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
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.
Benchmark instances for multiobjective combinatorial optimization
Benchmark instances for multiobjective combinatorial optimization
City of Hope CpG Island Analysis Pipeline
COHCAP (City of Hope CpG Island Analysis Pipeline) is an algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values. Please note: 1) The standalone version of COHCAP is no longer being updated. Please see the Bioconductor version: http://bioconductor.org/packages/release/bioc/html/COHCAP.html 2) In addition to the original NAR paper, please see the following links: Benchmarks: http://www.nature.com/protocolexchange/protocols/2965#/introduction Protocol Exchange Files: http://sourceforge.net/projects/cohcap/files/Protocol_Exchange_Example.zip 3) Bioconductor Custom Annotation Files (including EPIC Array): https://sourceforge.net/projects/cohcap/files/additional_Bioconductor_annotations.zip/download
Bidirectional Functional Enrichment of Gene Expression Data
BD-Func is an algorithm to predict activation or inhibition of pathways based upon gene expression patterns. If you use BD-Func, please cite: Warden C, Kanaya N, Chen S, and Yuan Y-C. (2013) BD-Func: A Streamlined Algorithm for Predicting Activation and Inhibition of Pathways. peerJ, 1:e159
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"
An R package for metrology. metRology provides classes and calculation and plotting functions for metrology applications, including measurement uncertainty estimation and (eventually) inter-laboratory metrology comparison studies.