Search Results for "algorithm" - Page 3
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Showing 178 open source projects for "algorithm"
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Harmony Data Integration
Fast, sensitive and accurate integration of single-cell data
Harmony is a general-purpose R package with an efficient algorithm for integrating multiple data sets. It is especially useful for large single-cell datasets such as single-cell RNA-seq. Harmony has been tested on R versions =4. Please consult the DESCRIPTION file for more details on required R packages. Harmony has been tested on Linux, OS X, and Windows platforms. -
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Pigale is a graph editor and a C++ algorithm library essentially concerned with planar graphs. This software, particularly intended for graph theoretical research, includes new algorithms based on our recent theoretical researches.
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AutoAni
Compilation-free adaptive swf visualization template
AutoAni is a compilation-free adaptive visualization template designed for creating animated bar chart races and similar time-based visualizations using Flash. It focuses on ease of use for beginners by removing the need to install Flash or compile code—users simply prepare their data and images, place them in the same directory, and open the provided SWF file with any compatible player. The template comes with built-in Source Han Sans fonts, ensuring consistent text rendering without... -
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JBotSim is a multipurpose dynamic network simulator that allows to quickly prototype a distributed algorithm and test its behavior on a set of static or mobile nodes. If mobile, the nodes can be controlled by the mouse or by program.
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JPIV
Particle Image Velocimetry
JPIV is a platform independent, graphical stand-alone application for Particle Image Velocimetry (PIV) written in Java. PIV is an optical technique for measuring fluid flow velocities. JPIV moved to GitHub. Please visit us at: https://eguvep.github.io/jpiv/ -
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AI learning
AiLearning, data analysis plus machine learning practice
We actively respond to the Research Open Source Initiative (DOCX) . Open source today is not just open source, but datasets, models, tutorials, and experimental records. We are also exploring other categories of open source solutions and protocols. I hope you will understand this initiative, combine this initiative with your own interests, and do what you can. Everyone's tiny contributions, together, are the entire open source ecosystem. We are iBooker, a large open-source community,... -
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file digest
A command-line utility for calculating and verifying file checksums.
Digest is a command-line utility which can be used to calculate and verify checksums of any files, similar to md5sum or RHash, but using modern hash algorithms. Supported algorithms: BLAKE, BLAKE2, Grøstl, JH, Kupyna, MD5, SHA-1, SHA-2, SHA-3, Skein, SM3, Streebog, Whirlpool. Usage: digest [-c] <algorithm> <filename(s)> For example, if you want to calculate the checksums using skein512/256 algorithm, use this command: digest skein512/256 * > checksums.skein To verify the checksums: digest -c skein512/256 checksums.skein You can get a full list of supported algorithms and test the performance of different algorithms on your PC using the command: digest test <iterations> <filename> This will calculate hash sum of <filename> multiple times (number of times is specified by <iterations>) and output the results with precise timings. ... -
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EntOpt Layout
Relative entropy optimization network layout plugin
The goal of this project is to implement a graph layout / network visualization algorithm as a Java plugin for Cytoscape (http://cytoscape.org/), using a recently published relative entropy optimization based method, called Unified Data Representation (Kovács IA et al. Sci Rep. 2015). If you are using the plugin, please cite: Ágg B, Császár A, Szalay-Bekő M, Veres DV, Mizsei R, Ferdinandy P, Csermely P and Kovács IA (2019) The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein-protein interaction and signalling networks, Bioinformatics 35(21):4490-4492 https://academic.oup.com/bioinformatics/article/35/21/4490/5475596 Our detailed Tutorial on the use of the plugin: https://suopte.com/entopt_2_1_tutorial_20200518.pdf A video about the version 2.1: http://suopte.com/entopt_2_1_tutorial_video.mp4 Don't hesitate to send any questions, comments or bug reports also to agg.bence {at} med.semmelweis-univ.hu. -
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A spring-based 3D graph layout tool written in Java. Rendering is performed in OpenGL via the JOGL library.
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vizceral
WebGL visualization for displaying animated traffic graphs
vizceral is a component for displaying traffic data on a webgl canvas. If a graph of nodes and edges with data about traffic volume is provided, it will render a traffic graph animating the connection volume between nodes. This component can take multiple traffic graphs and will generate a 'global' graph showing all incoming traffic into each of the 'regions', with support for cross-region traffic. There are three levels of information, global, regional, and service-level, with clicking or... -
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ipytracer
Algorithm Visualizer for IPython/Jupyter Notebook
Algorithm Visualizer for IPython/Jupyter Notebook. If you use the display(TracerObject) code from where you want to see, you can use it without any special modification. -
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Illustrated Algorithms
Interactive algorithm visualizations
...Visual representations of variables and operations augment the control flow, alongside actual source code. You can fast forward and rewind the execution to closely observe how an algorithm works. The same code that is displayed next to the illustration is also decorated using babel-plugin-trace-execution and executed to record the context at every step. Literally the same source file. Going back and forth between function execution (and call stack when algorithm uses recursion) is effortless. So is pausing and resuming. ... -
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TESTIMAGES
Testing images for scientific purposes
...The archive includes more than 2 million images originally acquired and divided in three different categories: SAMPLING and SAMPLING_PATTERNS (aimed at testing resampling algorithms), COLOR (aimed at testing color rendering on different displays) and PATTERNS (aimed at testing the rendering of standard geometrical patterns). Please cite the following papers when using any image in this archive: * ASUNI N, GIACHETTI A, "TESTIMAGES: A Large Data Archive For Display and Algorithm Testing", Journal of Graphics Tools, Volume 17, Issue 4, 2015, pages 113-125, DOI:10.1080/2165347X.2015.1024298 * ASUNI N, GIACHETTI A, "TESTIMAGES: a large-scale archive for testing visual devices and basic image processing algorithms", STAG - Smart Tools & Apps for Graphics Conference, 2014. -
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Random Bits Forest
RBF: a Strong Classifier/Regressor for Big Data
We present a classification and regression algorithm called Random Bits Forest (RBF). RBF integrates neural network (for depth), boosting (for wideness) and random forest (for accuracy). It first generates and selects ~10,000 small three-layer threshold random neural networks as basis by gradient boosting scheme. These binary basis are then feed into a modified random forest algorithm to obtain predictions. -
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SmartRoot
Semi-automated root image analysis software
SmartRoot is a semi-automated image analysis software which streamlines the quantification of root growth and architecture for complex root systems. The software combines a vectorial representation of root objects with a powerful tracing algorithm which accommodates to a wide range of image source and quality. The software supports a sampling-based analysis of root system images, in which detailed information is collected on a limited number of roots selected by the user according to specific research requirements. SmartRoot is an operating system independent freeware based on ImageJ and uses cross-platform standards (XML, SQL, Java) for communication with data analysis softwares. ... -
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Mortgage-Calculator
A console command based application for calculating mortgage paybacks
This command-line program written in C++ is a highly accurate calculator used to calculate monthly, yearly and full term mortgage repayments at a fixed interest rate. The program rounds up to the nearest whole pound and uses the same precise algorithm as other mortgage calculators. The program is fast, efficient and you can know your exact mortgage repayments in just 30 seconds!* *Additional fees not calculated - Harry Groom -
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MS-ML Studio
Free and Open-Source Tool for Mass Feature Extraction
Mass spectrometer is a useful tool for biochemistry research field analysis. It is used to identify microorganisms, protein, chemical compounds and complex diseases by blood analysis. There is many tools and libraries to handle different steps of mass spectrometry (MS) data analysis. However, the integration of all these tools lacks user friendly approaches. We developed a machine learning solution capable to handle all steps of MS data analysis. The ML-MS Tool is an free software that... -
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Visualization of Protein-Ligand Graphs
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
...The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/ -
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Sched-SPM
A C++ schedule generator based on Genetic Algorithm and Hill Climbing
Sched-SPM is a C++ schedule generator for software project staffing and rescheduling based on Genetic Algorithm (GA) and Hill Climbing (HC). This preliminary tool is mainly for academic purpose. It is implemented with GALib (http://lancet.mit.edu/ga/), an open-source toolkit of Genetic Algorithms in various platforms including Unix and Windows. The input and output files of the software are required as XML format. The input file includes tasks' and employees' information according to predefined file format. ... -
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Primes
Calculate primes by using extremely fast sorting
This project considers the problem of calculating primes as a sorting problem. It includes the most efficient tree-based sorting algorithm that is possible and shows that finding a new prime can be done by sorting the differences between the previous primes in the right way. Unfortunately it has turned out that going this way is even more slowly than trying to find primes by brute force. So it can only be used as a test with heavy load for the sorting algorithm, which can be used for sorting any kind of data. ... -
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ChEnMTD
Calculate the number of theoretical trays with McCabe-Thiele method
Use the McCabe-Thiele method to calculate the number of theoretical trays in a distillation column operated under the conditions specified. It has tools for data analysis to obtain empirical or semi-empirical equilibrium models. You can even use cubic splines. This project uses icons of "Open Icon Library" https://sourceforge.net/projects/openiconlibrary/ -
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PortOpt
A portfolio-optimizer using Markowitz(1952) mean-variance model
...It returns the vector of assets' shares that composes the optimal portfolio. In order to minimise the variance it internally uses QuadProg++, a library that implement the algorithm of Goldfarb and Idnani for the solution of a (convex) Quadratic Programming problem by means of an active-set dual method. This solution is very efficient as it allows to solve hundred of thousand of portfolio problems in seconds. PortOpt runs as a text/console tool so it can be easily used in your own scripts. -
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LaNet-vi provides images of large scale networks on a two-dimensional layout. The algorithm is based on the k-core and k-dense (m-core) decomposition. For more details see http://lanet-vi.fi.uba.ar.
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New Terrain and 3D Map System
a very lightweight advanced terrain-rendering and 3D map rendering sys
...(multitread vesion not released yet) 3. Seme as point 2.. Multithread terrain-rendering, roads on it, and vehicles to go around. The most important part is terrain-rendering. The Algorithm at the heart of it features my first and second theorem abut polygonal surface approximation. It took something like 2 years to develop it. It's technically a view-dependent, continuous dynamic level-of-detail rendering algorithm. Main features are simplicity and documentation. Does easily a 4k x 4k terrain, but also much more. -
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Open Simplex Project
A Simple GUI Implementation of the Simplex Algorithm