Search Results for "processing" - Page 7
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Showing 224 open source projects for "processing"
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iMir
Integrated pipeline for HT miRNA-Seq data analysis
Processing of smallRNA-Seq data to gather biologically relevant information requires application of multiple statistical and bioinformatics tools from different sources, each focusing on a specific step of the analysis pipeline. The analytical workflow can be challenging for the continuous interventions by the operator, a critical factor when large numbers of datasets need to be analyzed at once. -
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PRADA
PRADA : Pipeline for RNA-Sequencing Data Analysis
Massively parallel sequencing of cDNA reverse transcribed from RNA (RNASeq) provides an accurate estimate of the quantity and composition of mRNAs. To characterize the transcriptome through the analysis of RNA-seq data, we developed PRADA. PRADA focuses on the processing and analysis of gene expression estimates, supervised and unsupervised gene fusion identification, and supervised intragenic deletion identification. PRADA currently supports 7 modules to process and identify abnormalities from RNAseq data: preprocess: Generates aligned and recalibrated BAM files. expression: Generates gene expression (RPKM) and quality metrics. ... -
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VisualPerspective
A diagram/modeling tool.
VisualPerspective is a modeling and diagram creation tool. It enables to create free diagrams but also semantic oriented ones (for instance UML diagrams), in order to run automatic processing (transformations, exports, parsing). There is currently no installer, so you should follow this procedure : http://enzweiler.info/visualperspective/002-installation.html You are very welcome to report any issue with VP. -
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Larch: Data Analysis for X-ray Spectra
Data Processing and Analysis for X-ray Spectroscopy and More
Larch is a scientific data processing language that is designed to be easy to use for novices and complete enough for advanced data processing and analysis. Larch provides a wide range of functionality for dealing with arrays of scientific data, and basic tools to make it easy to use and organize complex data. Larch has been primarily developed for dealing with x-ray spectroscopic and scattering data, especially the kind of data collected at modern synchrotrons and x-ray sources. ... -
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Ezys
Ezys 3D medical image registration program
Ezys is a non-linear 3D medical image registration program. Ezys fully exploits the parallel computing power of inexpensive commercial graphics processing units (GPU), resulting in a very fast and accurate program capable of running on desktop PCs and even some laptops. On these systems, non-linear image registrations take less than a minute to complete. Ezys implements a diffeomorphic inverse consistent image registration algorithm with a demons-style regularization based on a non-parametric free form deformation model. ... -
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A collection of code, bundled into a single R package, to perform several aspects of data management, image pre-processing, data analysis and statistical inference related to the quantitative analysis of dynamic contrast-enhanced MRI (DCE-MRI).
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Cascalog
Data processing on Hadoop without the hassle
Cascalog is a powerful Clojure (and Java) data processing and querying library built atop Hadoop (via Cascading), providing a high-level, Datalog-inspired abstraction for both big data processing and local computation. Cascalog is hosted at Clojars, and some of its dependencies are hosted at Conjars. Both Clo/Con-jars are maven repos that's easy to use with maven or leiningen. The Cascalog website contains more information and links to Various articles and tutorials. -
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Graphical Grammar Studio
An user friendly grammar tool for natural language processing tasks
Full documentation with tutorials is included in the download package. Graphical Grammar Studio is a tool for applying grammars which behave as words acceptors/consumers and annotators. GGS grammars can be used to find and annotate sequences of words which respect certain conditions, in a given input. Its purpose is for creating NLP tools like phrase chunkers, named entity finders, pronoun co-reference solvers etc. A grammar is represented by a state machine which can be visualized, edited... -
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iOVFDT
iOVFDT algorithm of incremental decision tree
...Decision tree, which has a high degree of knowledge interpretation, has been favored in many real world applications. However noisy values commonly exist in high-speed data streams, e.g. real-time online data feeds that are prone to interference. When processing big data, it is hard to implement pre-processing and sampling in full batches. To solve this trade-off, we propose a new decision tree so called incrementally optimized very fast decision tree (iOVFDT). Inheriting the use of Hoeffding bound in VFDT algorithm for node-splitting check, it contains four optional strategies of functional tree leaf, which improve the classifying accuracy. ... -
Grafana: The open and composable observability platformGrafana is the open source analytics & monitoring solution for every database.
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Tockit tries to build a framework for Conceptual Knowledge Processing (CKP) and Formal Concept Analysis (FCA) in Java, using a component-based approach, XML formats and a three-tier architecture.
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Scenario Editor And Visualizer
Scenario Editing and Visualization tool for Scientific scenes
...For the inclusive systems this means to make the best use of all interfaces human beings are blessed with taken from visualization, touch, voice, smell and taste. The right blend between visualization, simulation and virtual reality could hold the key to a solution. With reduced costs and processing power available and availability of experimentation platforms could hold the key to an enchanting learning experience. The first step is an editing and visualization tool. Described in paper http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6629931&refinements%3D4278371973%26queryText%3DGlobal+Humanitarian+Technology+Conference%3A+South+Asia+Satellite+.LB.GHTC-SAS.RB.%2C+2013+IEEE#! -
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OpenCMISS-Zinc
A Library for Interactive Modelling and Visualisation
...Models are represented in Zinc as mathematical fields defined over domains, including finite elements with support for high-order basis functions, complex parameter mappings and time variation, and image-based fields. Further fields can be defined by mathematical expressions and algorithms on existing fields, including image processing filters. Zinc model data structures are dynamic, supporting interactive applications which programmatically create, destroy and modify parts of models. -
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Pyphant is a framework for scientific data analysis. It features a flexible plugin architecture allowing for the application in many different fields. For the analysis a graph of processing steps is constructed, that can be applied via the cli as well.
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q pipeline manager
q: integrated platform for pipeline configuration and management
...It expands the value of your existing job scheduler - either Grid Engine or TORQUE PBS - through numerous functions that help you organize, submit, monitor, manage and share your informatics work. Data processing pipelines require high-level organization and parallelization of work to optimize resource utilization and decrease the time to results. q (from queue) allows complex job sequences to be efficiently assembled and managed, including dependency tracking, parallelization, and pipeline-level monitoring, error recovery, and data protection. ... -
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FlowVR is an open source middleware tailored for high performance in situ data processing and analytics running on large parallel machines
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LAVA for AFM
Lloyd's Algorithm-based Volumetric Analysis for AFM Images
This MATLAB-based program enables analysis of AFM images. In particular, it allows the user to measure the volume of all distinguishable features in an image and to isolate and sort those particles. As the name implies, LAVA uses Lloyd's Algorithm, also known as k-means sorting, to identify a small set of volumes representative of the actual distribution of particle in the image. Although developed for determining feature volume, LAVA is also completely compatible with other types of... -
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Malimpa stands for MAtlab Library for IMage Processing and Analysis. It provides functions for 2D/3D grascale/color image creation, filtering, or measurement. It requires, and complements Matlab Image Processing Toolbox. Important notice: the project is now hosted in GitHub, https://github.com/dlegland/matImage
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A production stable Java utility library with convenience methods for string- and stream processing, file handling, XML, XSLTs and XPath, checksums, console formatting, and more. The project is developed by the State and University Library of Denmark
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Pear3DEngine
Pear3DEngine is a modern and modular 3D development framework
Pear3DEngine is a modern and modular 3D development framework that lets you create professional games, simulations and more. You are free to develop your program in C + +, XML or LUA and publish it as open source software or selling it as a commercial program. The rendering engine uses internally OpenGL or DirectX optionally. The planned editor supports software development on Linux, Windows and maybe MacOS X. DirectX 9 and therefore Windows XP are currently not supported and support is not... -
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flNeuronTool
A Fast Light Neuron Tracing and Editor Tool
The flNeuronTool allows users to reconstruct and proofread neuronal morphologies in light microscopy images. The system incorporates automatic tracing and manual editing of neuron reconstruction into a cooperative 3D interactive visualization-assisted environment, which is a powerful tool for analysis of complex neuronal images. -
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ODClean Store
Linked Data management tool
Linked Data management tool with customizable data processing and query capabilities. -
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CirclePack
An application for packing circles into a circle.
It uses two different solutions: - placing of circles closest to the center from the largest to smallest, see brianshaler on github https://github.com/brianshaler/Circle-Packing-in-Processing - simulation "real" world with use of a Java Physics Engine JBox2D, see http://www.jbox2d.org -
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The project has moved to GitHub: https://github.com/pixmeo/osirix
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R Hadoop for Big Data
Download Free Associated R open source script files for big data analy
Download Free Associated R open source script files for big data analysis with Hadoop and R These are R script source file from Ram Venkat from a past Meetup we did at http://www.meetup.com/R-Matlab-Users/events/85160532/ Also, there is a long video and Powerpoint presentation slide PDF with R files at: http://quantlabs.net/blog/2012/11/how-to-use-hadoop-and-r-for-big-data-parallel-processing-free-download-pdf/ Download source files from http://quantlabs.net/blog/2012/11/download-free-associated-r-open-source-script-files-for-big-data-analysis-with-hadoop-and-r-rstats-hadoop/ -
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A MATLAB package for wavelet analysis of circadian rhythms with both discrete (Daubechies) and continuous (Morlet) wavelets, as well as tools for batch processing of multiple time series, all accessible through a graphical user interface.
