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The 'surveillance' R Package

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The R-package ’surveillance’ is a framework for the development and the evaluation of outbreak detection algorithms in univariate and multivariate routine collected public health surveillance data. Hence, potential users are biostatisticians, epidemiologists and others working in applied infectious disease epidemiology. However, applications could just as well originate from environmetrics, reliability engineering, econometrics or social sciences.

PyMVPA

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"PyMVPA is a Python module intended to ease pattern classification analyses of large datasets. In the neuroimaging contexts such analysis techniques are also known as decoding or MVPA analysis. PyMVPA provides high-level abstraction of typical processing steps and a number of implementations of some popular algorithms. While it is not limited to the neuroimaging domain, it is eminently suited for such datasets. PyMVPA is truly free software (in every respect) and additionally requires nothing but free-software to run."

PyEEG

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A Python function library to extract EEG feature from EEG time series in standard Python and numpy data structure. Features include classical spectral analysis, entropies, fractal dimensions, DFA, inter-channel synchrony and order, etc.

WEKA

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Weka is a collection of machine learning algorithms for data mining tasks. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization. It is also well-suited for developing new machine learning schemes.

Medical Imaging Interaction Toolkit (MITK)

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The Medical Imaging Interaction Toolkit (MITK) is a free open-source software system for development of interactive medical image processing software. MITK combines the Insight Toolkit (ITK) and the Visualization Toolkit (VTK) with an application framework. As a toolkit, MITK offers those features that are relevant for the development of interactive medical imaging software covered neither by ITK nor VTK.

Core features of the MITK platform:

    Brainstorm

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    Brainstorm is a collaborative open-source Matlab application dedicated to magnetoencephalography (MEG) and electroencephalography(EEG) data visualization, processing and cortical source estimation.
    The intention is to make a comprehensive set of tools available to the scientific community involved in MEG/EEG experimental research.
    For physicians and researchers, the interest of this software package resides in its rich and intuitive graphic interface, which does not require any programming knowledge.

    The 'DiagnosisMed' R Package

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    DiagnosisMed is a package to analyze data from diagnostic test accuracy evaluating health conditions. It is being built to be used by health professionals. This package is able to estimate sensitivity and specificity from categorical and continuous test results including some evaluations of indeterminate results, or compare different categorical tests, and estimate reasonble cut-offs of tests and display it in a way commonly used by health professionals. No graphical interface is avalible yet. Partners are most welcome.

    The 'epi' R Package

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    The Epi package is mainly focused on "classical" chronic disease epidemiology. The package has grown out of the course Statistical Practice in Epidemiology using R.

    ADDIS

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    ADDIS is a software developed within the Dutch Escher-project for managing and analyzing clinical trial information.

    ADDIS is a proof-of-concept system that allows us to simultaneously discover the possibilities of and the requirements on a database of structured clinical trials data. The automated discovery and (meta-)analysis of trial data, as well as benefit-risk assessment is supported.

    ADDIS comes with two built-in examples:

    The 'epibasix' R Package

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    This package contains elementary tools for analysis of common epidemiological problems, ranging from sample size estimation, through 2x2 contingency table analysis and basic measures of agreement (kappa, sensitivity/specificity).

    Appropriate print and summary statements are also written to facilitate interpretation wherever possible.

    This package is a work in progress, so any comments or suggestions would be appreciated. Source code is commented throughout to facilitate modification. The target audience includes graduate students in various epi/biostatistics courses.

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