Search Results for "hidden markov java" - Page 2
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Showing 133 open source projects for "hidden markov java"
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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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MetaErg
Metagenome Annotation Pipeline
MetaErg is a stand-alone and fully automated metagenome and metaproteome annotation pipeline published at: https://www.frontiersin.org/articles/10.3389/fgene.2019.00999/full. If you are using this pipeline for your work, please cite: Dong X and Strous M (2019) An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. Front. Genet. 10:999. doi: 10.3389/fgene.2019.00999 The instructions on configuring and running the MetaErg pipeline is available at GitHub... -
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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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Eta
The Eta Programming Language, a dialect of Haskell on the JVM
...Eta's concurrency support helps you to build highly scalable systems. Eta has a strongly-typed Foreign Function Interface (FFI) that allows you to safely interoperate with Java. Eta has global type inference, giving you a dynamic language experience, but with a strong typing hidden underneath. Eta offers a wide range of strategies for handling concurrency including Software Transaction Memory (STM), MVars, and Fibers. Using the powerful and type-safe Servant web framework, we define our API as a type and the handler types for each endpoint are automatically generated and conversions happen automatically. -
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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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Whonix
Whonix is an Anonymous Operating System.
THIS IS NOT WHONIX'S HOMEPAGE. Please go to: https://www.whonix.org/ (This is only Whonix's sourceforge must-have project page.) Whonix is an operating system focused on anonymity, privacy and security. It's based on the Tor anonymity network, Debian GNU/Linux and security by isolation. DNS leaks are impossible, and not even malware with root privileges can find out the user's real IP. Whonix consists of two parts: One solely runs Tor and acts as a gateway, which we call... -
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Lihang
Statistical learning methods (2nd edition) [Li Hang]
...The repository aims to help readers understand the theoretical foundations of machine learning algorithms through practical implementations and detailed explanations. It includes notebooks and scripts that demonstrate how key algorithms such as perceptrons, decision trees, logistic regression, support vector machines, and hidden Markov models work in practice. In addition to code examples, the project contains supplementary materials such as formula references, glossaries of technical terms, and documentation explaining mathematical notation used throughout the algorithms. The repository also provides links to related research papers and references that expand on the theoretical background presented in the book. -
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CrococryptFile
An encryption tool for creating file archives
CrococryptFile is a file encryption tool which creates encrypted archives of files and folders. The encryption features of CrococryptFile can be compared to a ZIP utility that uses ZIP's AES encryption. However, there are significant differences. CrococryptFile... - encrypts all file and folder information including filenames, time/date and filesize information, - disguises any information of the archive's content, because all data and meta-data is simply integrated into a... -
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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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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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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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SnowyOwl
RNA-Seq based gene prediction pipeline for fungal genomes
SnowyOwl is a gene prediction pipeline that uses RNA-Seq data to train and provide hints for the generation of Hidden Markov Model (HMM)-based gene predictions, and to evaluate the resulting models. The pipeline has been validated and streamlined by comparing its predictions to manually curated gene models in three fungal genomes, and its results show substantial increases in sensitivity and selectivity over previous gene predictions. Sensitivity is gained by repeatedly running the HMM gene predictor Augustus with varied input parameters, and selectivity by choosing the models with best homology to known proteins and best agreement to the RNA-Seq data. ... -
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Hi anybody, This 7z allow you hiding many files using LSB Steganographic method in many pics, also let you the possibility to cipher the hidden files using private and public key with ECC(Elliptic curve cryptography), using BouncyCastle Java library or AES-256 bits. HOW TO USE: Its software needs JRE 1.7 or Higher!! Just unzip the dist.7z file and open Faster-Hiding.jar file, you can download the sources. Please open tickets if you found a problem or copyright trouble. ...
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Hamstr
A tool for directed ortholog search in ESTs and proteins
HaMStR has moved to https://github.com/bionf/hamstr where it is now part of the HaMStR-OneSeq package. HaMStR is a profile hidden Markov model based tool for a directed ortholog search in EST or protein sequence data. The program takes a pre-defined core group of orthologous sequences (core orthologs) and a set of sequences from a search taxon as input. HaMStR then combines in a two-step strategy a pHMM based search and a reverse search via BLAST to extend the core ortholog group with novel sequences from the search taxon. -
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Abandoned Mansion
Classic text-based treasure hunt
This game is an original game based loosely (very loosely) on classic text-based adventure games such as Zork and Adventure. The object of the game is to use simple one and two-word commands to navigate an abandoned mansion and find all the treasures hidden within. -
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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 BMRF-Net-standalone V1.1: fix issues in analyzing large scale network
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...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 the architecture (primer dimers, contaminants etc.) are automatically discarded
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ML Manager 1.X
A modern, easy and customizable app manager for Android with Material
A modern, easy and customizable APK extractor & app manager for Android that allows you to extract any installed and system app, mark them as favorite, share .apk files easily and much more. -
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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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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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mCarts
A hidden Markov model to predict clustered RNA motif sites
Many RBPs recognize very short and degenerate sequences, with targeting specificity achieved by mechanisms such as synergistic binding to multiple clustered sites and modulation of site accessibility through different RNA-secondary structures. mCarts integrates the number and spacing of individual motif sites, their accessibility and conservation, which substantially improves signal to noise ratio. This algorithm learns and quantifies rules of these features, taking advantage of a large... -
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Grand Theft Auto Collectibles Guide
Find hidden items and track your progress.
Use GTA Collectibles Guide to help you find hidden items in earlier Grand Theft Auto games. -
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TransGeneScan
TransGeneScan is a gene finding tool for metatranscriptomic sequences
...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/), and can predict a sense transcript containing one or multiple genes (in an operon) or an antisense transcript. -
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Ether Buzz
Easy remote Java methods calls with streaming
EtherBuzz is a java library optimized to perform remote Java methods calls between a client and a server. All the inner network details are hidden as well as all the parameters serialization and exception management. Each remote method call just works as if it was executed locally. Your server side application can setup one or more servers, each one serving on a different network port. -
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High-order HMM in Matlab
Implementation of duration high-order hidden Markov model in Matlab.
Implementation of duration high-order hidden Markov model (DHO-HMM) in Matlab with application in speech recognition.
