Search Results for "probability" - Page 5
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Showing 160 open source projects for "probability"
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Statcato is a Java software application for elementary statistics. Its features include data and graph generation, probability distributions, descriptive statistics, confidence intervals, hypothesis tests, correlation, regression, and analysis of var
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SIMtoEXP
For comparison of simulation and experimental scattering data
SIMulation to EXPeriment is software that allows the direct comparison of simulation density information with that obtained from X-ray and neutron scattering experiments, by converting the simulation data to form factors. It also calculates volume probability distributions according to a space filling volumetric model. Written in C++ and Qt, SIMtoEXP has a very simple and easy to use GUI with interactive plotting. The software was originally developed by Norbert Kucerka. The code has been tested on OpenSUSE and Ubuntu (both binary and compilation); Windows and Mac are not officially supported, see the 'Notes' in the tar. ... -
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PythonStatsLab
A collection of useful statistical functions written in Python
There are functions for numerical integration of the standard normal probability distribution. They can be used to find probabilities, find z-alpha values, calculate confidence interval, etc. New functionality I wish to add are hypothesis testing and calculation of p-value, type I & II errors, etc. These functions would come in handy to anyone taking introductory or intermediate-level courses in probability, statistics and data analysis. -
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K-Surfer
A KNIME extension for the management and analysis of FreeSurfer Data
...K-Surfer consists of a suite of KNIME nodes that perform several tasks, such as importing diffusion data generated from TRACULA, importing morphological measures obtained from the segmentation and reconstruction of neuroimages and visualising the probability distribution of white matter pathways. For installation guide read the pdf inside the zip. References: Sarica Alessia, Giuseppe Di Fatta, and Mario Cannataro. "K-Surfer: A KNIME Extension for the Management and Analysis of Human Brain MRI FreeSurfer/FSL Data." Brain Informatics and Health. Springer International Publishing, 2014. 481-492. ... -
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Net Responsibility
Free Accountability Software
Net Responsibility is intended to be a good open source accountability software for all major platforms. It's purpose is to prevent people from certain surfing habits by holding them accountable to others. This is done by logging all internet traffic and generating clear reports that are emailed regularly to one or more accountability partners by choice. Most users will probably want to go to our website, http://www.netresponsibility.com, where all needed information is found. This... -
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ProteinLP
A linear programming model for protein inference problem
In this paper, we present a linear programming model (ProteinLP) for protein inference, which is built on two simple probability equations. ProteinLP is implemented in Java and can run on any Java Virtual Machine (JVM) regardless of computer architecture. Since ProteinLP introduces linear programming to solve protein inference problem, the software uses a standard LP software package, Glpk for Java (v4.47). -
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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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Myrtle
A simple programmable spreadsheet for learning statistics.
...It provides the standard spreadsheet functionality one would expect like multiple tabbed sheets, relative and absolute row and column referencing in formulas, and a large catalog of built-in functions. Functions specific to logic and computer science, mathematics, probability, and statistics are available. Student's can easily create, customize, and update plots and graphical summaries of their analyses. Myrtle offers a unique bookmarking facility which allows students to create and reuse named references to their favorite cell ranges. This can help students focus attention on the important relationships among particular rows or columns of data. ... -
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Non-Gaussian Realisations
Generate non-Gaussian fields with a specified spectral index
This code provides a module based on a spectral distortion/quantile transformation that generates a realisation of a field on a cubic grid that has a specified probability distribution function and a specified power spectrum. A preprint based on this code is available at http://arxiv.org/abs/1305.2345 -
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RNA-Seq-Simulator
Realistic simulation of RNA-Seq short reads
...The starting positions of the reads and the distributions of read errors and quality codes are all empirically derived from real RNA-Seq datasets. The suite includes Python scripts to prepare the empirical read creation probability and read error distribution tables, and to generate and postprocess the simulated reads. -
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Bayesian Network tools in Java (BNJ) is an open-source suite of software tools for research and development using graphical models of probability. It is published by the Kansas State University Laboratory for Knowledge Discovery in Databases (KDD).
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...The package is designed to solve any of the following reactions by either one of the two approaches mentioned: Synthesis-Decompostion Reaction Chain Reaction Nuclear Chemical Reaction Lodka Model Brusselator Model Furthermore, the Stochastic approach can be computed by several stochastic simulation algorithms. The DetStoch package offers four stochastic algorithms that use probability functions simulated via Monte Carlo methods: Gillespie's Direct Method, Gillespie's First Reaction Method, Bruck and Gibson Next Reaction Method and Tau-Leaping Method.
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CGI-HMM
Find CpG island by HMM
Find CpG island for whole genome/chromosome by Hidden-Markov Mode -
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PercolaLand
PercolaLand 1.0 A tool to calculate landscapes percolation probability
PercolaLand software is a result implementing of new structural metric used to calculate percolation probability in binary landscapes. Much of the progress in spatial patterns and structure changes understanding have supported in percolation theory. Percolation theory aims to evaluate how connectivity is broken into spatially structured systems or quantifies the connectivity structure. Connectivity in this case refers spatial continuity of arrangements habitat areas. -
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Altrans
Quantification of Splicing Events
...When there are overlapping exons, these are grouped into “exon groups” and unique portions of each exon in an exon group are identified which are used when assigning reads to an exon. The link counts ascertained from unique regions are normalized with the probability of observing such a link given the insert size distribution which is referred to as link coverage. Finally the quantitative metric produced is the fraction of one link’s coverage over the sum of the coverages of all the links that the initial first exon makes. -
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Monopoly clone written in Java for 2-8 players (including computer players) that was designed to make quite a lot of things customisable from the user's point of view. Four board files are included. Two are based on regional variations of Monopoly but with places named after colours instead, the other two are there more to demonstrate what can be done. Hopefully there are no major bugs in the game - I cannot guarantee that there are none, but I've done some testing on Linux and Windows...
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Bayesloc
Bayesian Hierarchical Seismic Event Locator
Given a set of seismic arrivals for one or more events, Bayesloc estimates the joint probability of event locations, corrections to travel time predictions, precision of arrival time measurements, and phase labels for the arrival times. Bayesloc also accepts probabilistic prior constraints on any of the input parameters, which can significantly tighten the distribution of all parameters. -
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Averaged N-Dependence Estimators - AnDE
AnDE implements A1DE and A2DE
...Not So Naive Bayes: Aggregating One-Dependence Estimators. Machine Learning. 58(1):5-24 and G.I. Webb, J. Boughton, F. Zheng, K.M. Ting and H. Salem (2012). Learning by extrapolation from marginal to full-multivariate probability distributions: decreasingly naive {Bayesian} classification. Machine Learning. 86(2):233-272. -
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MEPCM Package
This is a package for multi-element probabilistic collocation method.
The Multi-Element Probabilistic Collocation Method Package (MEPCMP) is a C++ package which can generate high dimensional, multi-element collocation points based on arbitrary probability density function for the application of Multi-Element Probabilistic Collocation Method (MEPCM). This package can generate high-dimensional stochastic collocation points based on tensor product rule, non-nested sparse grids method or anchored-ANOVA method. It can also be used for the multi-element probabilistic polynomial chaos method. -
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...Not So Naive Bayes: Aggregating One-Dependence Estimators. Machine Learning. 58(1):5-24 and G.I. Webb, J. Boughton, F. Zheng, K.M. Ting and H. Salem (2012). Learning by extrapolation from marginal to full-multivariate probability distributions: decreasingly naive {Bayesian} classification. Machine Learning. 86(2):233-272.
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CRUMp
A probabilistic prediction system of protein phosphorylation sites
CRUMp is based on a kernel-based learning method called Classification Relevance Units Machine (CRUM). Given an input set of protein sequences in FASTA format, the system outputs the position, residue type (S, T, or Y), and the estimated probability of each tested site being phosphorylatable. Latest downloadable files: - crump-0.2.0.tar.gz: CRUMp GNU Octave package - crump-0.2.0.zip: CRUMp MATLAB script - crumptestset.fasta: A testing dataset in FASTA format. The sequence headers list the accession number of the protein sequence and the position numbers of known phosphorylation sites. ... -
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MIDA
Mitochondiral Infectious Damage Adaptation (MIDA) model of aging
...A probabilistic modeling approach is applied by solving the master equation in mitochondrial quality state space in the presence of fusion-fission events, decay of functional quality, mitophagy and mitochondrial biogenesis, as well as molecular damage originating from a random source or from infectious events during fusion and fission. The provided source code is written in C and performs the time integration of the master equation for the time-evolution of the probability to find mitochondria in states of quality q at time t. Output is generated in terms of data files and the graphical visualization of readout parameters is automatically performed using the Graphical Layout Engine (GLE; see: http://glx.sourceforge.net/). Please, send email to thilo.figge<at>hki-jena.de to request a copy of the source code. -
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Iris
Iris is a web based bayes data classifier.
Iris is a web based classification system. The system is a bayes classifier and calculates (and compare) the decision based upon conditional probability of the decision options. This system currently classify 3 groups of flowers from the iris dataset depending upon a few selected features. The concept which makes Iris stand out is the use of a 'window'. A window is incorporated along with the threshold while sampling. The window helps using a small dataset and emulate more samples. ... -
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Noisy Channel Simulator
Demonstrate errors in transmission of a file over a noisy channel.
This program was written to dimonstrate errors in transmission for a presentation on Claude Shannon's Noisy Channel Coding Theorem. It takes an input file, the probability of a bit being flipped, and, if specified, the size of the header of the file. The program was intended to take monochrome bitmap files as input, so that each bit refers to a pixel in the image and thus, it would be easy to see errors in the output file, as some of the pixels would be flipped; however, it will work on any input file. -
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giPlayer-ext
Extended version of giPlayer
...I have now been able to contact the original author and so it's likely that this will be merged back to the original project in the future (sometime in the New Year 2012 in all probability). See the wiki page for more information
