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An analysis pipeline for mining exome-Seq and RNA-Seq data, focusing on quality control, SNP identification and annotation, RNA quantification, differentially expressed genes analysis, eqtl, and pathway analysis. http://seqgene.sourceforge.net
This is an add-on visualization package for the Weka datamining tool.
Parallel coordinates is a common way of visualizing high-dimensional geometry and analyzing multivariate data. To show a set of points in an n-dimensional space, a backdrop is dr
C2Mat is a simple wrapper library that allows OpenCV data structures to be transferred between C++ and Matlab. It lets a program combine the speed of OpenCV with the power of Matlab.
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MSA2SNP is a tool for mining SNP sites in multiple sequence alignment (MSA). This tool inherits the easy-to-use interface from MEGA4 Explorer with advance data presentation. MSA2SNP lets you visualize alignments and import from CLUSTAL program directly.
A unified collection of algorithms for Artificial Life. It includes evolutionary algorithms, neural networks, datamining tools, compilers, among others.
Knime (http://www.knime.org) nodes for sequence bioinformatics. Sequime is an eclipse plug-in for the KNIME datamining platform, providing additional nodes for reading, processing and visualizing sequence information.
This is a MATLAB toolbox for the quality control and scoring of EMAP and SGA genetic interaction data. It includes a graphical user interface and some automatic plot-generating tools.
MVPaa has merged into the automatic analysis project on gihub:
https://github.com/rhodricusack/automaticanalysis
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MVPaa is a MVPA (Multi-Voxel Pattern Analysis) package made for the automatic analysis (http://www.cambridgeneuroimaging.com/aawiki) package.
Ferda is a user friendly datamining tool. It is a modular distributed multiplatform framework based on Internet Communications Engine. Ferda is very powerful in working with association rules.
Windows application for datamining with self-organizing neural networks. It works with text data files and has convenient user interface. Is solves datamining tasks of class Recognition, continuous value Prediction, and time series Forecast.
A Matlab GUI for reviewing, processing, and annotating electrocardiogram (ECG) data files. ECG Viewer offers an annotation database, ECG filtering, beat detection using template matching, and inter-beat interval (IBI or RR) filtering.
Cougar Squared is a new Java library for machine learning and datamining research, supporting research needs of the community. It is written by researchers for researchers. It extends the WEKA and YALE machine learning frameworks.
Gepoclu - Gene Positional Clustering is a suite of Matlab functions for performing positional clustering on genes with optional use of expression data such as what can be obtained from Microarray, EST and qRT-PCR, and PCR.
Open Source Particle Image Velocimetry and PIV Analysis
OpenPIV is an initiative of scientists to develop a software, algorithms and methods for the state-of-the-art experimental tool of Particle Image Velocimetry (PIV) which are free, open source, and easy to operate.
Leark is a DataMining library developed in C#.NET. It contains several methods for ranking web documents described with a set of normalized features, and a feature selection algorithm. The methods are based on perceptron and clustering.
The NJ toolbox (njTBX) is a matlab object API, built on top of Unidata's Netcdf-Java API to facilitate netCDF model data manipulation. Development of njTBX is a part of 'An Open-Source Community Model for Coastal Sediment Transport' project.