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Ordered Bijective Interpolated Warping (OBI-Warp) aligns matrices using Dynamic Time Warping with a one-to-one (bijective) smooth warp-function. It is ideal for the chromatographic alignment of complex mass spectrometry proteomics data.
SARSE is a scientific data editor that uses the extendable column format, allows interactive overview, tracks editing history, and has a user extendable tool box.
A comparative map and trait visualization framework enabling visual integration of genomic data from disparate data sources and allowing rich client-side interactivity and manipulation. Extensible through plugins for new datasources and algorithms.
JFlux is a java library and graphical user interface to work with flow cytometry data. In particular, it is adapted to the COPAS biosorter and can analyze expression profiles.
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DuffyRNAseq is an R package that implements an analysis pipeline for processing RNA-seq data from Illumina NextGen sequencers, to measure gene transcription and differential expression.
Protein Data Bank transformed into an SQL database with a very powerful search engine and a rich web interface. The engine combines chemical, sequence and 3D structure searches. The interface provides statistics, sequence and 3D structure alignments.
An open source MAGE-TAB database and import/export tools to read and write MAGE-TAB formatted data. MOLGENIS is being used to autogenerate it. Import/export tools creation is in progress.
Basic Electronical Medical Management (BEMM) is an application to control medical data of a set of patients. It is built on top of open source technologies, to provide an integration skeleton of mvn, Datanucleus, Spring, Vaadin, Acceleo technologies.
BigRedBin is a web-based tool designed to pre-process metabolomics data generated by a mass spectrometer in an attempt to increase the signal-to-noise ratio. This is accomplished by using information from multiple technical replicates.
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The DNA Sequence Read Toolkit is a set of programs to convert data from DNA sequencing instruments into formats suitable for archiving, viewing or for onward processing (for example alignment or assembly).
Molecular Graphics and Dynamics. Molecular model builder. Part of the Ascalaph Designer http://sourceforge.net/projects/asc-designer/ project. Windows & Linux.
Peakplot is a Perl implemented freely available software application which labels peptide tandem mass spectra retrospectively after a Mascot database search.
Availability: http://fgcz-peakplot.uzh.ch/
CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV). Learn about CNV Workshop in our associated BMC Bioinformatics manuscript: http://www.biomedcentral.com/1471-2105/11/74
MGFp is open parser implementation for the Mascot Generic Format (MGF). It uses bison/flex to define a formal grammar and provides the necessary C++ adapter classes. The software is provided under a BSD license.
Development on SF.net has ceased. You can find the project at http://kirchnerlab.github.com/libmgf/
DIVAT (Diagnostic Immunohistochemistry Visualization and Analysis Tool) is designed to graphically analyse comprehensive data sets of immunohistochemical results as those used in clinical diagnostic pathology.
Phylogenetic Representativeness is a method for estimating adequacy of taxon sampling for phylogenetic studies. Through a series of statistics generated by PhyRe, it is possible to evaluate taxon coverage within a given group.
--UPDATE-- New Version is now integrated in the official PyMOL plugin repository! --UPDATE--
The BNI (Beyond Normal Interaction)- Tools is a plug in for the PyMOL molecular visualization system which adds additional functionalities and presets to the PyMOL GUI and also adds useful extended commands.
An R package for detailed inspection and analysis of LCMS data. An R package developed by Sukhdeep Singh at Department of Surgery and Cancer, Imperial College London,UK.