Search Results for "mixture" - Page 4
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Showing 148 open source projects for "mixture"
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Accord.NET Framework
Scientific computing, machine learning and computer vision for .NET
The Accord.NET Framework provides machine learning, mathematics, statistics, computer vision, computer audition, and several scientific computing related methods and techniques to .NET. The project is compatible with the .NET Framework. NET Standard, .NET Core, and Mono. -
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mixture fraction
Calculate mixture fraction field in OpenFOAM
A small flexible library plugin to calculate mixture fraction from species fields in OpenFOAM. -
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EBprotV2
Bayesian Analysis of labeling-based Quantitative Proteomics Data
EBprotV2 is an extension to the existing EBprot (version 1) which adopts a more flexible non-parametric mixture model. It serves as an differential expression analysis tool which takes into account the direct peptide to protein hierarchy which differs from the usual analysis which occurs at the protein-summary level. The tool is implemented in C++ which minimize computational time and also, incorporates an additional module which help users to generate comparison ratios between groups with multiple samples. -
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EBprot
Bayesian Analysis of labeling-based Quantitative Proteomics Data
EBprot implements a hierarchical mixture model directly representing the peptide-protein map. The model fit is used to score differential expression of proteins in a (signed) probability scale based on reproducible quantification over multiple peptides. The package takes as input a data matrix with each row containing the data for one peptide, including protein and peptide identifier and peptide ratio(s), and returns the protein-level score table with PPscore, BFDR, Posterior Odds score, and flag for each comparison. -
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Pathoscope
Predicts strains of genomes in Nextgen seq alignment file (sam/bl8)
This page is here for archival purpose. Please visit github for the latest version of the software: https://github.com/pathoscope PathoScope takes next-generation sequencing reads from a mixture sample and predicts which genomes are present. We use a Bayesian framework combined with an initial reference-based alignment to assign reads to the correct genome of origin. Pathoscope 2.0: Wiki: http://sourceforge.net/p/pathoscope/wiki/Home/ Tutorial: http://sourceforge.net/projects/pathoscope/files/pathoscope2.0_v0.02_tutorial.pdf Clinical Pathoscope version: http://sourceforge.net/p/pathoscope/wiki/clinical_pathoscope/ PathoQC download: http://sourceforge.net/projects/pathoscope/files/pathoqc_v0.1.4.tar.gz/download Publications: http://www.microbiomejournal.com/content/2/1/33 http://www.biomedcentral.com/1471-2105/15/262 http://genome.cshlp.org/content/23/10/1721 Support: PS: Please send an email to mani2012 at bu dot edu if you have any questions. -
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BNP-Homology
Alignment data for Protein Remote Homology Search
Alignment data from the application of a Bayesian mixture model to protein remote homology detection. -
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jLDADMM
A Java package for the LDA and DMM topic models
The Java package jLDADMM is released to provide alternative choices for topic modeling on normal or short texts. It provides implementations of the Latent Dirichlet Allocation topic model and the one-topic-per-document Dirichlet Multinomial Mixture model (i.e. mixture of unigrams), using collapsed Gibbs sampling. In addition, jLDADMM supplies a document clustering evaluation to compare topic models. See the usage of jLDADMM in its website at http://jldadmm.sourceforge.net/ -
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fitGCP
Fitting genome coverage distributions with mixture models
...fitGCP is a framework for fitting mixtures of probability distributions to genome coverage profiles. Besides commonly used distributions, fitGCP uses distributions tailored to account for common artifacts. The mixture models are iteratively fitted based on the Expectation-Maximization algorithm. Please find the accompanying paper here: http://dx.doi.org/10.1093/bioinformatics/btt147 -
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AMD_HealthSocialCareSim
Multi-paradigm simulation of health and social care for AMD sufferers
...This is an AnyLogic-based simulation of age-related macular degeneration (AMD), which tries to capture both the detailed operation of an eye clinic and the broader social care of AMD sufferers. It uses a mixture of agent-based modelling (ABM), discrete-event simulation (DES) and system dynamics (SD). It also serves as a demonstration simulation model for the Java Simulation Infrastructure Toolkit (JSIT), using its AnyLogic helper library, and an example of other software-engineering-best-practice ways to structure simulation models (which are covered in the journal paper "Simulation Design: Trans-Paradigm Best-Practice from Software Engineering" which introduces JSIT). ... -
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BiomeNet
BAYESIAN INFERENCE OF METABOLIC DIVERGENCE AMONG MICROBIAL COMMUNITIES
...To infer the structure of community-level metabolic interactions, BiomeNet applies a mixed-membership modelling framework to enzyme abundance information. The basic idea is that the mixture components of the model (metabolic reactions, subnetworks, and networks) are shared across all groups (microbiome samples), but the mixture proportions vary from group to group. Through this framework, the model can capture nested structures within the data. BiomeNet is unique in modeling each metagenome sample as a mixture of complex metabolic systems (metabosystems). -
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PopR
Analysis of population structure in R with finite and infinite mixture
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Programmed in Java, this game is a mixture between FreeCell and normal Solitaire. The current version is Beta v.76.
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Fast Matrix for Java
General purpose matrix utilities for Java in Parallel Computing
Fast Matrix for Java (fm4j) is a general-purpose matrix utility library for computing with dense matrices. fm4j encapsulated different underlying implementations and select the optimal one in run-time depending on the size of the input matrix. Moreover, fm4j employs Java (Tm) Concurrency to take advantage of the computation power of multi-cor processors. -
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MRHMMs
multivariate regression hidden Markov models
It includes a various hidden Markov models: regression, logistic regression, hidden Markov models, and emission probability density of a mixture of multivariate Normal distributions. Also available at https://github.com/yonoklee/MRHMMs Work in progress (Jun 20, 2021 - ) -
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OrthoRBH
Rapidly identify orthologous cDNA sequences in related species
...It can search through databases of full-length cDNAs, ESTs or mRNA-seq data. Optional assembly of candidate sequences allows assembly of contigs. It is suited to handling a mixture of EST and mRNA-seq sequence data. It performs batch blast searches, so it is ideal for large multi-gene families. After collecting candidate sequences, it performs sequence alignment and deposits sequences into a fasta sequence file for downstream molecular evolutionary analysis. -
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MCTIMME
Microbial Counts Trajectories Infinite Mixture Model Engine
MCTIMME is a nonparametric Bayesian computational framework for analyzing microbial time-series data.The current implementation is in Matlab. -
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DNAcompact
Genome compression algorithm with/without reference (Linux/Windows)
As the technique of acquiring genome sequences advances, the storage and data transferring of large genome data are becoming important concerns for biomedical researchers. We propose a two pass genome compression algorithm, which highlights the synthesis of complementary contextual models and the introduction of logistic regression mixture method, to improve the compression performance. The proposed framework handles genome compression with and without reference seque- nces, and demonstrated performance advantage over the best existing algorithms. The proposed method without a reference led to bit rates of 1.720 and 1.838 bits per base for bacteria and yeast, which are approximately 3.7% and 2.6% better than the state-of-the-art algorithm. ... -
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GalGen Trader
A 2D Elite-style game written in Python 3.2.
...This functionality is supported by the game being written in Python 3, with its powerful support for including external code at run-time. The graphics will be a simple mixture of 2D raster and vector imagery with text-based menus, and the music will be highly reminiscent of the 80's 'chiptunes' that made up the soundtracks for games on the Amiga and Commodore 64. -
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GenoTan identifies inherited variation of microsatellite loci from short sequence reads using a discretized Gaussian mixture model combined with a rules-based approach.
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The AK toolkit is another kit for building and use Hidden Markov Models (HMMs). Originally developed for handwritten text recognition (HTR) using Bernoulli HMMs, it also implements diagonal Gaussians and can be used for any other purpose.
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KlustaKwik is an open-source C++ and Java program for automatic clustering of continuous data into a mixture of Gaussians. The program was originally developed for sorting of neuronal action potentials, but can be applied to any sort of data. NOTE (25/04/12): For those interested in trying the new masked version of KlustaKwik designed for large dense electrode array, download KlustaKwik3.0.1 in the maskedKlustaKwik folder. UPDATE (04/07/12): Bugs have been fixed in the new masked version of KlustaKwik. ...
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Mixture3D
A simple tool to create a 3D mixture
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MercuryBoard is a powerful message board system dedicated to raw speed with a mixture of features, ease of use, and ease of customization coupled with expandability, and diverse language services.
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The SNOMP Library
SNOMP (SNOMP is Not OpenMP) is a library for semi-shared memory parall
SNOMP (SNOMP is Not OpenMP) is a library for semi-shared memory parallelization. -
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...I was a pretty bad programmer back then, so the code is sloppy. The next version will be better. Similar to a stream cipher, but rather than performing an exclusive OR on the input bytes and cipher, it performs a mixture of 'rolling' (see x86 instruction ROR) and bit NOT operations according to the key.
