Search Results for "estimates" - Page 5
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Showing 151 open source projects for "estimates"
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LFSpro
Estimating TP53 Mutation Carrier Probability in Families with LFS
Identifying TP53 mutation carrier is critical to people with Li-Fraumeni syndrome for cancer prevention and survival improvement. A new method is needed for clinical counselors because of the limitations of current clinical criteria. LFSpro is built on a Mendelian model and estimates the TP53 mutation probability through Elston-Stewart algorithm with accuracy. Unlike previously used models, our model incorporates de novo mutation rate, which greatly improved estimation accuracy. -
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MRI-PDQ:Phase Detection & Quantification
Detect sphere-shaped paramagnetic deposits in MRI datasets
Moved to http://parkermills.github.io/MRI-PDQ/ -
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bagemass
Bayesian age and mass estimates for transiting planet host stars
Source code, makefile and README for installation of software used for the analysis in Maxted, Serenelli & Southworth, "Bayesian mass and age estimates for transiting exoplanet host stars", A&A 575, 36, 2015. -
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SLOCCount is an easy-to-use tool that counts Source Lines of Code (SLOC). It auto-determines the language(s) (inc. C, C++, Ada, Assembly, shell, COBOL, C#, Fortran, Haskell, Java, LISP/Scheme, Perl, PHP, Python, Ruby, SQL). It also estimates cost & time.
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luciphor
Calculates phospho-site localizations
Luciphor is a program that performs phospho-site localization on MS/MS data processed by the Trans-Proteomic Pipeline (TPP). It is the first phospho-site prediction program to provide estimates for the false localization rate (FLR). The program is multithreaded and written in C++ for linux. -
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kernel_smoother
Binned Kernel Density Estimate via FFTW
The library implements multivariate kernel density estimates via fast fourier transform from http://www.fftw.org/ The main code is used for constructing jet templates for computing data-driven jet substructure estimate for QCD backgrounds. -
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TAMrS
Transcriptome assembly made (really) simple
TAMrS aims to make transcriptome assembly 'really easy'. In short, the software will allow the user to --USING A SINGLE COMMAND-- input paired end or single end Illumina data, and get out an assembly and estimates of gene expression. The program only operates on Linux. executing 'make' downloads the required software (using curl and wget) and ensures that the everything is in the right place. -
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SVG_plot
Plot data in SVG format using C++ library
...It has been maintained and enhanced since then in Boost Sandbox, but is judged unsuitable for a Boost Library, so now being made more widely available here. Version 2 adds representation of uncertainty estimates as numbers and zones. -
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FreDec
Parallelized FREquency DEComposer algorithm
...The algorithm analyses all suspicious frequencies, including the ones that look like an alias at a glance, but may become preferable later. After selection of the initial frequency candidates, the algorithm passes through all their possible combinations and estimates their multi-frequency statistical significance. In the end, it prints out the set of largest frequency tuples that were still found significant. The GPU computing is implemented through CUDA and brings a significant performance increase. It is still possible to run FreDec solely on CPU, if no suitable GPU device is available in the system. ... -
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Yahtzee
A simple Yahtzee game coded in java.
A simple Yahtzee game coded in java. This is the working source code for the final project for the course CIS 256 that my partner and I turned in. (2007). This is posted here as a portfolio project. -
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incometax-AU
A simple program to handle Australian tax estimates.
This program is able to handle Australian tax brackets and output a simple tax estimate. Version 0.1.4 is now in Beta and includes all of the recent improvements. -
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QuasiRecomb
Probabilistic inference of viral Quasispecies
...We present a jumping hidden Markov model that describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data. We offer an implementation of the EM algorithm to find maximum a posteriori estimates of the model parameters and a method to estimate the distribution of viral strains in the quasispecies. The model is validated on simulated data, showing the advantage of explicitly taking the recombination process into account, and tested by applying to reads obtained from experimental HIV samples. -
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ARDEN
Specificity Control for Read Alignments Using an Artificial Reference
We introduce ARDEN (Artificial Reference Driven Estimation of false positives in NGS data), a novel benchmark that estimates error rates based on real experimental reads and an additionally generated artificial reference genome. It allows the computation of error rates specifically for a dataset and the construction of a ROC-curve. Thereby, it can be used to optimize parameters for read mappers, to select read mappers for a specific problem or also to filter alignments based on quality estimation. -
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Gradesystem
Gradesystem
C programmed text-based software. Inputs : -Name of a course -Number of students -The 100% value of a mark -All the marks Then it estimates the Standard Deviation and grades, then assigns the marks to the grades inside a text. -
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Development of a common open source tool for assessing the accuracy of parameter estimates collected within the framework of the DCR (EU Regulation 1639/2001 and 1581/2004)
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passphrase-generator
Generate a set of random passphrases for you to choose from.
...The passphrase-generator defaults to only 3 words instead of the 4 suggested by XKCD, but uses a larger dictionary found in many unix like systems at /usr/share/dict/words. It also provides estimates for the entropy of the generated passphrases. The randomization is based on /dev/urandom and SHA1. See http://xkcd.com/936/ for an entertaining take on passwords vs. passphrases. See my post in stackoverflow for links to other solutions and discussions on passphrases vs passwords: http://stackoverflow.com/a/12646320/1148030 -
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Nagios TCP Degradation Detection Plugin
Nagios TCP traffic degradation detection plugin from link utilization
This Nagios plugin estimates the TCP traffic performance degradation from coarse link utilization traces, such as those obtainable by SNMP. TCP adapts its transmission rate to the available bandwidth and the performance is degraded before achieving the 100% link occupancy. This plugin is based on the method described in [1] and M/G/R processor sharing model to estimate TCP performance degradation from the analysis of the link utilization variance (it normally increases as the mean link-utilization increases but starts to decrease when the link performance is degraded). ... -
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Growth Curve is a simple software which allows to build microorganism growth curves in the logarithmic scale. It estimates medium doubling time and it's standard deviation. All curves are proposed to be the duplications of one experiment.
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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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SPSens
Stochastic parameter sensitivity analysis for chemical networks
SPSens is a complete software package written in C that estimates parameter sensitivities for stochastic models of chemical and biochemical reaction networks using Monte Carlo (MC) stochastic simulations. It is possible to estimate sensitivities with respect to system parameters using the following algorithms: finite difference methods (crude monte carlo, common reaction path, coupled finite differences); likelihood ratio methods; and regularized pathwise derivatives. -
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R-SAP
RNA-Seq analysis pipeline
R-SAP is a user-friendly and fully automated bioinformatics pipeline that analyzes and quantitates high-throughput RNA-Seq datasets. R-SAP accurately characterizes various classes of transcripts resulted from aberrant splicing and chimeric transcripts. Expression level estimates are reported as RPKM (reads per kilobase of exon model per million mapped reads) values. -
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Dema-Bai
Program to create demographic estimates based on multiple sources.
This program implements the "Best Available Information" method of demographic estimation developed by Katherine Nesse and Andrew M. Isserman. This version assumes the sources are from the Census Bureau's Population Estimates Program and the American Community Survey. -
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MICROMECHANICS
A collection of lecture notes and accompanying code on micromechanics
...Instructions on using the codes are given in the README file of each exercise. Further instructions can be found in the file microcode.tar.bz2. The MATLAB codes are used for visualization, evaluating analytical bounds and estimates as well as in the generation of digital and particulate microstructures. The Fortran codes are based on the finite element method in linear and nonlinear settings, the latter capable of finite deformations with damage. The underlying theory is outlined in the lecture notes. -- İlker Temizer Assistant Professor Department of Mechanical Engineering Bilkent University 06800 Bilkent, Ankara Turkey -
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KonSol
Integrated Architectural Design Program! Intend for BIM!
"Konsol" 3.0 is a 3D AutoCAD software which supports architectural designs covering from 3D modeling to technical plan-drawing for buildings. As the software oriented towards BIM used on a worldwide scale in architectural design and construction area, it estimates a building on a spatial, functional and elemental basis, designs its 3D architectural model in the way of assembling architectural elements such as walls, windows, door, columns, beams and slabs, and then automatically generates technical plans for ground, sectional and elevational views, thus shortening design time and increasing the precision of plans. ... -
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PHACCS is a bioinformatic tool designed for a scientific public. It gives estimates of the structure and diversity of uncultured viral communities using metagenomic information.
