Search Results for "markov" - Page 2
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Showing 100 open source projects for "markov"
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Red Hat Ansible Automation Platform on Microsoft AzureDeploy Red Hat Ansible Automation Platform on Microsoft Azure for a strategic automation solution that allows you to orchestrate, govern and operationalize your Azure environment.
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vbTRACK_2D
Bayesian analysis of 2D(x,y) time series particle tracks using Matlab.
Matlab program analyzes 2D (xy) time-series data (tracks) by variaional Bayes, hidden Markov, Gaussian mixture pattern recognition pattern recognition methods. It finds the number of states, the position of each state, and assigns each time-point to its most probable specific state. -
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HMMBase.jl
Hidden Markov Models for Julia
HMMBase is not maintained anymore. It will keep being available as a Julia package but we encourage existing and new users to migrate to HiddenMarkovModels.jl which offers a similar interface. For more information see HiddenMarkovModels.jl: when did HMMs get so fast?. HMMBase provides a lightweight and efficient abstraction for hidden Markov models in Julia. Most HMMs libraries only support discrete (e.g. categorical) or Normal distributions. In contrast HMMBase builds upon Distributions.jl... -
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Carnatic Music Guru / JRaaga
Carnatic Music Guru - JRaaga
VISIT THIS PAGE AS MORE FEATURES ARE BEING ADDED. If you have downloaded 2.03 or above - Use Help>Check Updates to download latest version. If that does not update: Download CMGUpdater from here: update/CMGUpdater.jar Copy it to the update/ folder of your JRaaga installation path. Try again Help>Check for updates. If it does not work. Delete existing installation. Download the latest version and try. Carnatic Music Guru is a tutor/player/lesson generator. YOU NEED Java Runtime... -
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JUMBL
J Usage Model Builder Library
JUMBL is a command line app and Java library that supports automation of model-based statistical testing. It supports creation, management, and application of usage models in the form of finite state Markov chains. -
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Spotlight
Deep recommender models using PyTorch
..., and 20M. It also incorporates utilities for creating synthetic datasets. For example, generate_sequential generates a Markov-chain-derived interaction dataset, where the next item a user chooses is a function of their previous interactions. Recommendations can be seen as a sequence prediction task: given the items a user has interacted with in the past, what will be the next item they will interact with? Spotlight provides a range of models. -
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PhyloMCL
PhyloMCL is a method degined to detect orthologous groups accurately.
PhyloMCL is a Markov clustering based method designed to detect ortholog groups effectively and efficiently. It employs two rounds of clustering aiming to recover the complex nature of gene duplications generated by polyploidization and single gene duplication events. PhyloMCL is implemented in C++ to promote computing speed for ortholog inference in genome scale. -
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hiddenDomains
hiddenDomains: a modern HMM to identify ChIP-seq enrichment
hiddenDomains uses a Hidden Markov Model to identify enriched domains in ChIP-seq data. It accepts BAM files for input and can perform an analysis with or without control data. The output is a BED file, ready for the UCSC genome browser, that contains the domains and is color coded according to their posterior probabilities. -
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GPRED-GC
a Gene PREDiction model accounting for 5'-3' GC gradient
A new hidden Markov model (HMM)-based ab initio gene prediction tool for finding genes with highly variable GC contents such as the genes with negative GC gradients in grass genomes. -
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OMEN
OMEN: Ordered Markov ENumerator - Password Guesser
OMEN is a Markov model-based password guesser written in C. It generates password candidates according to their occurrence probabilities, i.e., it outputs most likely passwords first. OMEN significantly improves guessing speed over existing proposals. If you are interested in the details on how OMEN improves on existing Markov model-based password guessing approaches, please refer to OMEN: Faster Password Guessing Using an Ordered Markov Enumerator. OMEN consists of two separate program modules... -
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The KReator project is a collection of software systems, tools, algorithms and data structures for logic-based knowledge representation. Currently, it includes the software systems KReator and MECore and the library Log4KR: - KReator is an integrated development environment (IDE) for relational probabilistic knowledge representation languages such as Bayesian Logic Programs (BLPs), Markov Logic Networks (MLNs), Relational Maximum Entropy (RME), First-Order Probabilistic...
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Kinetic Model Builder
GUI for building, simulating and optimizing kinetic models.
A 3D graphical interface for building, simulating and optimizing Markov kinetic models in response to user defined time dependent stimuli. Models can be represented as either states and connecting transitions or interacting allosteric elements (see http://dx.doi.org/10.1085/jgp.201411183). Model parameters can be optimized by fitting model responses to user data. Optional user defined constraint equations for model parameters are parsed with EigenLab (https://github.com/marcel-goldschen-ohm... -
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vbSPT
variational Bayes single particle tracking
vbSPT is an acronym for variational Bayes single particle tracking, a software package for hidden Markov Model analysis of single particle tracking data, primarily for biophysical applications. Journal reference: Extracting intracellular diffusive states and transition rates from single-molecule tracking data. Fredrik Persson, Martin Lindén, Cecilia Unoson & Johan Elf. Nature Methods (2013). doi:10.1038/nmeth.2367 http://www.nature.com/nmeth/journal/vaop/ncurrent/abs/nmeth.2367.html -
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This package implements the algorithm bagging markov random field method with c++ together with Java interface. http://nar.oxfordjournals.org/content/41/2/e42.long Cytoscape App: BMRF-Net-CytoscapeV1.0.tar.gz https://sourceforge.net/projects/bmrfcjava/files/BMRF-Net%20Package/BMRF-Net-CytoscapeV1.0.tar.gz/download Source code and standalone version: BMRF-Net-standalone.tar.gz https://sourceforge.net/projects/bmrfcjava/files/BMRF-Net%20Package/BMRF-Net-standaloneV1.1.tar.gz/download...
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Raw sequences produced by next generation sequencing (NGS) machines may contain adapter, linker, barcode and fingerprint sequences. TagDust2 is a program to extract and correctly label the sequences to be mapped in downstream pipelines. TagDust allows users to specify the expected architecture of a read and converts it into a hidden Markov model. The latter can assign sequences to a particular barcode (or index) even in the presence of sequencing errors. Sequences not matching...
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The General Hidden Markov Model Library (GHMM) is a C library with additional Python bindings implementing a wide range of types of Hidden Markov Models and algorithms: discrete, continous emissions, basic training, HMM clustering, HMM mixtures.
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Logi (Local Observations to Global Integration) transforms several local coordinate systems (composed of polar measurements) into a global spatial uniform network with respect to the Guide to the Expression of Uncertainty in Measurement (GUM).
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TransGeneScan
TransGeneScan is a gene finding tool for metatranscriptomic sequences
NOTE: TransGeneScan is migrated to Github (https://github.com/COL-IU/TransGeneScan). TransGeneScan is no longer maintained in SourceForge. Please find the latest version in Github. TransGeneScan is a gene finding tool for Metatranscriptomic sequences. TransGeneScan incorporates strand-speci c hidden states, representing coding sequences in sense and anti-sense strands on transcripts in a Hidden Markov Model similar to the one used in FragGeneScan (http://fraggenescan.sourceforge.net... -
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libpondyparser
A multi-core C++ parser library using chaotic systems (GPL and LGPL 2)
Markov and L-systems can be used to thread a parser library albeit a simple example parser which can be extended to a full blown one. L-systems classes are fitted with stack and deque structures for propagation. Markov systems can be extended from the codebase which uses operators for a decision process. The library can be used to make bigger systems such as neural nets and so on. -
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StatAlign
An extendable statistical multiple alignment tool.
StatAlign is an extendable software package for Bayesian analysis of Protein, DNA and RNA sequences. Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable measurement of the accuracy of the results. This approach eliminates common artifacts that traditional methods suffer from, at the cost of increased computational time. These artifacts include the dependency of the constructed phylogeny... -
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FamSeq
Variant calling on the basis of pedigree information
... implementations of the Mendelian genetic model: the Bayesian network algorithm, Elston-Stewart algorithm and Markov chain Monte Carlo algorithm. To make the software efficient and applicable to large families, we parallelized the Bayesian network algorithm that copes with pedigrees with inbreeding loops without losing calculation precision on an NVIDIA® graphics processing unit. -
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HMM-FRAME
Frameshift detection and correction for next-generation sequences
HMM-FRAME is designed to accurately locate and correct frameshift errors in next-generation sequencing (NGS) data using an augmented Viterbi algorithm on profile hidden Markov models (profile HMMs). By correcting the frameshift errors, it can classify more NGS sequences into their native protein domain families. -
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vbTPM
Variational Bayes for tethered particle motion
vbTPM is an analysis package aimed at analyzing time series from a single molecule technique called tethered particle motion, which are common for in vitro investigations of protein-nucleic acid interactions. vbTPM uses a variational approach to hidden Markov models, and resembles recent methods for single molecule FRET (http://vbfret.sourcefore.net/) and single particle tracking (http://vbspt.sourceforge.net/) data. 2014-08-12: NAR manuscript in print! http://dx.doi.org/10.1093/nar... -
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Protdraw
Create portable, flexible domain drawings of protein sequences
... of hidden Markov models and formats results for ProtDraw. Highest-scoring domains are selected in cases of overlap. Domain drawings may be organized by sequence classification. -
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diCal
Demographic Inference using Composite Approximate Likelihood
diCal is a scalable demographic inference method based on the sequentially Markov conditional sampling distribution framework. At present, diCal can infer a piecewise-constant population size history from the genomes of multiple individuals sampled from a single population. We are currently working on extending the method to handle more complex demography, incorporating multiple populations, population splits, migration, admixture, etc. Version 1.3 released on Jan 10, 2014. See "Files... -
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GLProbs
GLProbs: Aligning multiple sequences adaptively
GLProbs is a simple and effective approach to improve the accuracy of multiple sequence alignment. We use a natural measure to estimate the similarity of the input sequences, and based on this measure, we align the input sequences differently. To test the effectiveness of this approach, we have implemented a multiple sequence alignment tool called GLProbs and compared its performance with a dozen leading alignment tools on three benchmark alignment databases, and GLProbs’s alignments has the...