Search Results for "algorithm" - Page 29
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Showing 2779 open source projects for "algorithm"
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QSdpR
Viral Quasispecies Reconstruction software based on QSdpR algorithm
This is a viral quasispecies reconstruction software for quasispecies assembly problem on mRNA viruses, which is based on a correlation clustering approach and uses semidefinite optimization framework. The software accepts a reference genome, a NGS read set aligned to this reference and set of SNP locations in the form of a vcf file and outputs an optimal set of reconstructed species genomes which describes the underlying viral population. -
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Snappy Driver Installer is an application for installing/updating drivers on PCs running Microsoft Windows using driverpacks or included folders with drivers. It can be used to install drivers on newly assembled PCs at places where Internet isn't available. Users can also use the software to keep their drivers up to date.
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IPAS is a new and practial iterative progressive multiple sequence alignment algorithm, used to align protein sequences, which is a close variant of the MUSCEL algorithm. However, based on the gene sequences length, our algorithm starts either with the "kmer" distance table or with the "Dynamic Programming (DP)" distance table. The other steps of this algorithm include: generating a Guide-tree using UPGMA, multiple sequence alignments, "kimura" distance calculation from aligned sequences...
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IPAS for protein sequences
multiple alignment algorithm for protein sequences
IPAS is a new and practial protein multiple sequence alignment algorithm based on iterative progresive alignment algorithm Assessed on BAliBASE 3.0, PREFAB 4.0, SABMARK 1.65, and OXBENCH, MSAProbs achieves the statistically highest alignment accuracy, compared to ClustalW 2.0.10, MAFFT 6.717( using L-INS-i with --maxiterate = 1000), MUSCLE 3.8.31, ProbCons 1.12, and Probalign 1.3. -
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MCU Media Server
SIP Video Multiconference Media Server with WebRTC support.
REPOSITORY MOVED TO GITHUB!! https://github.com/medooze/media-server Video Multiconference Media Server with WebRTC support. Provide Multiconference and video broadcasting services to any SIP service. Supports VP8, H264, MP4V-ES, H263 and H263P, continuous presence, RTMP flash broadcasting, adhoc conferences, load balancing and administrative WEB interface. JSR309 driver implementation under development. . -
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adapter trimmer
We implement a very simple approach. Each read is searched for the jun
We implement a very simple approach. Each read is searched for the junction adapter (CTGTCTCTTATACACATCT) and its reverse complement (AGATGTGTATAAGAGACAG) based on Hamming distance, the entire junction being CTGTCTCTTATACACATCT+AGATGTGTATAAGAGACAG. If a match to either side of the junction is found then the entire 38bp juncton is clipped. This means the algorithm can tolerate an indel error in one of the sides of the junction, but not both. Optionally Smith-Waterman alignment can be turned... -
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0xyg3n Algorithm
Encrypts Python Source Code with 0xyg3n Algorithm
Python Source Code Encrypter | Author: 0xyg3n This is A Python Source Code Crypter Which Currently Obfuscates Your Python into a obfuscated Code with my algorithm cryptography requries: python 2.7.9 -
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3D Graphics Library for MR (VR & AR)
Experience the Reality !
This is a little Program that I have done recently, made by my Algorithm for showing 3D Objects in 2D & can be implemented on any Programming Language ( No Open Source Packages/APIs are used. ) You can build & animate whatever you want. Final version will be released soon. -
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BISD
Batch incremental SNN-DBSCAN clustering algorithm
Incremental data mining algorithms process frequent up- dates to dynamic datasets efficiently by avoiding redundant computa- tion. Existing incremental extension to shared nearest neighbor density based clustering (SNND) algorithm cannot handle deletions to dataset and handles insertions only one point at a time. We present an incremen- tal algorithm to overcome both these bottlenecks by efficiently identify- ing affected parts of clusters while processing updates to dataset in batch... -
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HGPEC
A tool for gene and phenotype prioritization and evidence collection
Finding gene-disease and disease-disease associations are important issues in the biomedical area and many prioritization methods have been proposed for this goal. Among these, approaches based on heterogeneous network of genes and phenotypes were considered state-of-the-art ones, which can use for diseases with/without known molecular basis. Here, we develop a Cytoscape plugin, namely HGPEC, based on a ran-dom walk with restart algorithm on a heterogeneous network of genes and phenotypes... -
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SUPERmerge
ChIP-seq coverage island analysis algorithm for broad histone marks
SUPERmerge is a ChIP-seq read pileup analysis and annotation algorithm for investigating alignment (BAM) files of diffuse histone modification ChIP-seq datasets with broad chromatin domains at a single base pair resolution level. SUPERmerge allows flexible regulation of a variety of read pileup parameters, thereby revealing how read islands aggregate into areas of coverage across the genome and what annotation features they map to within individual biological replicates. SUPERmerge... -
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GA-tools
general genetic algorithms optimization fortran 95 routines
High level optimization routines in Fortran 95 for optimization problems using a genetic algorithm with elitism, steady-state-reproduction, dynamic operator scoring by merit, no-duplicates-in-population. Chromosome representation may be integer-array, real-array, permutation-array, character-array. Single objective and multi-objective maximization routines are present. Possible to incorporate own crossover and mutation operators exclusively or in addition to standard operators... -
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syngen
R package for inferring drug synergy interactions
The syngen package infer drug synergistic interactions by comparing each drug MOA, as inferred by the VIPER algorithm, with the Master Regulators of a defined phenotype -
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Satsuma .NET Graph Library
a delicious .NET graph library
Satsuma is a graph library for .NET, written in C#. Satsuma is an easy-to-use and flexible library, which implements all the necessary graph structures, and the fastest possible graph algorithms. DOCUMENTATION: http://satsumagraph.sourceforge.net/ Satsuma is not a charting library. 'Graph' is used in the mathematical sense here (e.g. nodes connected with arcs). Satsuma is released under the zlib license. This license is very permissive and allows you to use Satsuma for both personal... -
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iLib
The most comprehensive library of Javascript i18n classes available
Note: development has been moved over to github! Please see https://github.com/iLib-js/iLib "I18N" means way more than just translation. Other libraries claim to be an i18n solution when translation and string formatting is really all they offer. Yes, iLib has classes that do translation too, but there is also much, much more. From date formatting to name parsing to phone number handling to collation, iLib has classes that do it. And, it has the ability to support thousands of possible... -
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MSU's Sparse Fourier Repository
The Home of DMSFT, AAFFT, GFFT, and MSFFT.
... efficiently. It is much slower than it should be. 3.) GFFT, implemented by Ben Segal and Mark Iwen. This code is less easy to use, and also not terribly efficient. But, the *algorithm* itself is significantly simpler and has "essentially no parameters". 4.) MSFFT, implemented by David Lawlor and Bosu Choi. This code is fast, but is not terribly easy to use. The algorithm is robust to some noise, but requires a lot of parameter tuning. Enjoy at your own risk :), Mark Iwen -
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GAKNN is a data mining software for gene annotation data. GAKNN is built with k- Nearest Neighbour algorithm optimized by the genetic algorithm. Gene annotation datasets saved under .csv or .arff formats with Gene Ontology or FunCat categorization can use GAKNN to predict gene functions.
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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. In conclusion, RBF is a novel framework that performs strongly especially on data... -
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mailcheck.js
Reduce misspelled email addresses in your web apps
The Javascript library and jQuery plugin that suggests a right domain when your users misspell it in an email address. Mailcheck will offer up suggestions for second and top level domains too. For instant use, download the minified library mailcheck.min.js into your javascripts directory. mailcheck.js is also available unminimised if you want to hack on it, or have your own minimizer. Mailcheck takes in two callbacks, suggested and empty. We recommend you supply both. Mailcheck does not want... -
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passgen
Passgen - easy to use, simple password generator
Passgen is easy to use, simple based on hexal and octal digits system password generator. -
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AGA-8
Natural gas and related hydrocarbon compressibility factor calculation
The software can be used to calculate compressibility factor (z factor), molecular weight, density at standard and flowing conditions. It requires pressure, temperature and mole fraction composition of the gas. The algorithm utilized is as per AGA Report Number 8. -
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karkinos
Tumor genotyper for Exome sequence that detects SNV,CNV, aTumor purity
karkinos is tumor genotyper which detects single nucleotide variation (SNV), integer copy number variation (CNV) and calculates tumor cellularity from tumor-normal paired sequencing data. Accurate CNV calling is achieved using continuous wavelet analysis and multi-state HMM, while SNV call is adjusted by tumor cellularity and filtered by heuristic filtering algorithm and Fisher Test. Also, Noise calls in low depth region are removed using EM algorithm. -
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mergepbx
script for merging XCode project files in git
Tracking a Xcode project in a version control system is annoying. Simply adding files can lead to merge conflicts that have to be solved manually, although it would be possible to resolve the conflict automatically if the merge algorithm would be aware of the structure of Xcode's project file. After long and annoying merge sessions in one of my projects, I came to the conclusion, that writing a merge driver for git which understands the structure of the project file would be a worthwhile... -
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RAtom
solves nonlinear Kohn-Sham equation for the neutral atom.
RAtom solves nonlinear Kohn-Sham equation for the neutral atom. The adaptive algorithm based on finite element method (FEM) is implemented. Discretization of the differential eigenvalue problem is done by finite element method with Lobatto polynomials as a basis functions. High order Gauss quadratures are applied in order to obtain the total energy of atom with absolut accuracy of 1E-6 hartree. Disctretization leads to generalized eigenvalue problem, which is solved by procedures from...
