Search Results for "toolbox"
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Showing 31 open source projects for "toolbox"
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ReViMS
ReViMS, a 3D volume rendering tool for light-sheet/confocal microscopy
...ReViMS is written in MATLAB (The MathWorks, Inc., Massachusetts, USA). It is an open-source tool and the source code is freely available at: http://sourceforge.net/p/revims Requirements: MATLAB R2017b and Image Processing Toolbox 10.1 or later versions. -
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MarsBaR is a Matlab toolbox for analyzing image data within Regions of Interest (ROIs). Its current home is on Github: see http://marsbar-toolbox.github.io/marsbar
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ANDTool
Analysis Nuclei DAB (AND) Tool
...ANDTool is written in MATLAB (The MathWorks, Inc., Massachusetts, USA) and the source code and standalone versions are here available for download. USER MANUAL: see the specific PDF available in the Files section. REQUIREMENTS: MATLAB R2017b and Image Processing Toolbox 10.1 or later versions. MAIN CONTACT: Filippo Piccinini (E-mail: filippo.piccinini85@gmail.com) -
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gogadget
A toolbox for interpretation and visualization of RNA-seq GO analysis
gogadget is an R package, and can help with the visualization and interpretation of GO enrichment analysis of RNA-seq data. It is developed especially for the use in combination with goseq. The functions that are available in this package are extensively described in the user's guide. To install the package download the "gogadget_2.1.tar.gz" file, open R and install with the following line: install.packages( "C:/your/directory/gogadget_2.1.tar.gz", repos = NULL,... -
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AKtoolbox
Matlab Toolbox for coevolution analysis of multiple sequence alignment
AK Toolbox is a Matlab Toolbox for co-evolution analysis for protein Multiple Sequence Alignment (MSA) distributed under Simplified BSD License. The aim of AK toolbox is to provide a set of Matlab functions, which are independent of Matlab Bioinforamtics Toolbox, for coevolution anaylsis for MSA. At present, co-evolution methods available in this package are Statistical Coupling Analysis (SCA), Explicit Likelihood of Subset Covariance (ELSC), Mutual Information (MI), Observed Minus Expected Square method (OMES), McLanhlan Based Substitution Correlation (MCBASC), Direct-coupling analysis (DCA) and logR. ... -
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All future developments will be implemented in the new MATLAB toolbox SciXMiner, please visit https://sourceforge.net/projects/scixminer/ to download the newest version. The former Matlab toolbox Gait-CAD was designed for the visualization and analysis of time series and features with a special focus to data mining problems including classification, regression, and clustering.
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F-Tracker3D
A software tool for tracking fluorescent cells in 3D
...F-Tracker3D is written in MATLAB (©, The MathWorks, Inc., Massachusetts, USA) and the source code is freely provided. Requirements: MATLAB 2015a and Image Processing Toolbox 9.2 or later versions. -
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NGS-TOOLBOX
Handy tools to process/analyze next generation sequencing (NGS) data
...If you use the NGS TOOLBOX you for publication purposes you can cite the following methods paper: Rosenkranz D, Han CT, Roovers EF, Zischler H, Ketting RF. Piwi proteins and piRNAs in mammalian oocytes and early embryos: From sample to sequence. Genomics Data 2015 5:309-313. -
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FieldTrip
The MATLAB software toolbox for MEG and EEG analysis
FieldTrip is the Matlab toolbox for EEG and MEG data. It includes algorithms for simple and advanced analysis, such as importing, preprocessing, time-frequency analysis, source reconstruction, statistical testing and connectivity analysis. -
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NBT is an open source Matlab toolbox for the computation and integration of neurophysiological biomarkers. NBT allows for easy implementation of new biomarkers, and incorporates an online wiki with extensive help and tutorials.
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SysGenSIM is a bioinformatics toolbox to create artificial gene expression datasets by simulating Systems Genetics experiments.
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AbMining ToolBox
python scripts to analyze antibody libraries
02-14-2014. Hamming distance calculation has been updated. These are python scripts to analyze antibody libraries sequenced by next generation sequencing methods (454, Ion Torrent, MiSeq) as described in D'Angelo et al MAbs. 2014 Jan 1;6(1):160-72. -
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FluxModules
Module Computation for Metabolic Networks
Genome Scale Metabolic Networks are complex systems, Modules help to break them down and hence ease understanding and algorithmic complexity. FluxModules is a toolbox with code for module detection and module visualization. -
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WM Hyperintensities Segmentation Toolbox
Open Source White Matter Hyperintensities Segmentation Toolbox
...Our toolbox provides a self-sufficient set of tools for segmenting these WMHs reliably and further quantifying their burden for down-processing studies. -
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Systems Glycobiology
Glycosylation Network Analysis Toolbox (GNAT)
...For information about GNAT installation and usage, please see the GettingStarted.pdf file enclosed in the package. To cite GNAT: [1] Gang Liu, Apurv Puri and Sriram Neelamegham, Glycosylation Network Analysis Toolbox (GNAT): a MATLAB based environment for systems glycobiology, Bioinformatics 2013 29: 404-406 -
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SBEToolbox
Systems Biology and Evolution Toolbox (SBEToolbox).
...SBEToolbox: a Matlab toolbox for biological network analysis. Evolutionary Bioinformatics, 8:1-15 -
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abc-sde
approximate Bayesian computation for stochastic differential equations
A MATLAB toolbox for approximate Bayesian computation (ABC) in stochastic differential equation models. It performs approximate Bayesian computation for stochastic models having latent dynamics defined by stochastic differential equations (SDEs) and not limited to the "state-space" modelling framework. Both one- and multi-dimensional SDE systems are supported and partially observed systems are easily accommodated. -
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DyMMM
Dynamic Multispecies Metabolic Modeling framework
The Dynamic Multispecies Metabolic Modeling (DyMMM [dĭm]) framework is a mathematical modeling tool that integrates multiple constraint-based metabolic models into a single dynamic community metabolic model. The DyMMM framework was formerly known as the DMMM framework. Please use the following citation for bibliographical purposes: Zhuang, K., Izallalen, M., Mouser, P., Richter, H., Risso, C., Mahadevan, R., & Lovley, D. R. (2011). Genome-scale dynamic modeling of the competition... -
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SemaRule Navigator is an Integrated Suite of Open-Source and Free-License Software, placing Semantic and Text Analysis Technologies in the toolbox of Researchers, Students, and Enterprises.
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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.
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Structlab is a machine learning C++ framework for structured domains, which provides a toolbox of learning methods and tools for preprocessing and visualization. It also provides a GUI to setup elaborate experiments in a visual and intuitive way.
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SPKtool is a toolbox developed on MATLAB which enables a user to perform spike (action potential of neurons) detection, spike sorting (manually or automatically) and spike train analysis.
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The Swiss Protein Identification Toolbox (swissPIT) is a project at the Swiss Institute for Bioinformatics (SIB) in Geneva which aims at the development of an automated analysis system to identify proteins using MS and MS/MS based data.
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JGenAlg is a java toolbox for working with metaheuristic procedures (Genetic Algorithms, Island model, Particle Swarm, Ant Swarm). JGenAlg have a GUI, a Client/Server architecture, work with threads and can be use under distributed enviroments.
