Search Results for "reference" - Page 44
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Showing 2124 open source projects for "reference"
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SPANDx
Comparative analysis of haploid next-generation genome sequence data
SPANDx is your one-stop tool for identifying SNP and indel variants in haploid genomes using NGS data. SPANDx performs alignment of raw NGS reads against your chosen reference genome or pan-genome, followed by accurate variant calling and annotation, and locus presence/absence determination. SPANDx produces SNP and indel matrices for downstream phylogenetic analyses. Annotated, genome-wide SNPs and indels can also be identified if specified, and are output in human readable format. A presence/absence matrix is also generated to allow you to identify the core/accessory genome content across all your genomes. ... -
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Colibri - The ENVI / IDL Code Library
A collection of well documented ENVI / IDL algorithms and applications
...The complete set of code and documentation are available to the remote sensing community. ENVI/IDL code developers and remote sensing researchers are requested to actively contribute to this ENVI/IDL Code Library in order to obtain a solid reference of user developed applications for the remote sensing community. -
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Pop Framework
Use Java bean as model of web page, reference beans in hyperlinks
Pop Framework (or Pop), http://www.popframework.net, is a bean-based MVC framework for Java/J2EE web applications. Pop implements IoC, Dependency Injection, and AOP. Pop provides annotations for users to define and reference a bean. Pop can help users to customize a bean, a scope, a factory and a reference in object-oriented way. Pop treats a bean as the model of a web page (JSP or servlet), the webpage itself is a view of the bean. The model provides the data for the view, the view is responsible for rendering the data. The Pop itself acts as the general-purposed controller for all views and models. ... -
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RefVal
Program for statistical treatment of medical reference values
Computer implementation (for Windows) of the International Federation of Clinical Chemistry (IFCC) recommendation of the statistical treatment of reference values in laboratory medicine. Both source code and compiled program available for free download in the public domain. More details here: https://tinyurl.com/zhlaq5a -
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VoltMR
Pure java NGS mapping soft run on Hadoop 2.0
ＶｏｌｔＭＲ is pure java NGS (DNA/RNA) mapping and realignment soft that run on Hadoop 2.0 The accuracy is comparable to BWA-MEM and novoalgin with speed faster than those aligner. Using 100 core, VoltMR finish typical exome sample (10GB),mapping, sort, mark duplicate, local realignment in 30 minitue. It use about 10GB to 15GB RAM for each hadoop mapper and reducer. Currently, VoltMR take fastq as a input and output bam/ADAM format. For DNA mapping, GATK compatible realignment/recalbration... -
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Taurus
A python based User Interface library.
The Taurus Project has *moved* to: https://github.com/taurus-org/taurus This SourceForge page is *outdated* and kept for historical reference only. Taurus is a python framework for control and data acquisition CLIs and GUIs in scientific/industrial environments. It supports multiple control systems or data sources: Tango, EPICS, ... New control system libraries and data sources can be integrated through plugins. -
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mirPRo
Tool for miRNA-seq analysis in C++
...It can quantify known and novel miRNAs in single-end RNA-seq data and provide useful functions such as IsomiR detection and "arm switching" identification, miRNA family quantification, and read cataloging in terms of genome annotation. mirPRo only works for species that has reference genome. [1] Who are we? Please visit our website http://bioinfolab.miamioh.edu [2] How to cite mirPRo? Shi J, Dong M, Li L, Liu L, Luz-Madrigal A, Tsonis PA, Rio-Tsonis KD and Liang C (2015) mirPRo - a novel standalone program for differential expression and variation analysis of miRNAs. Sci Rep, 5:14617. http://www.nature.com/articles/srep14617 [3] mirPRo user manual For user manual, please visit the Wiki page of this website... -
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Volterra2.0
Volterra series Identification Tool
...Possibility to identify each Volterra kernel with an input with different variance. This feature reduces the identification noise on lower order kernels and improve the "resolution" on higher order kernels. For reference see: Simone Orcioni. Improving the approximation ability of Volterra series identified with a cross-correlation method. DOI:10.1007/s11071-014-1631-7. pp.2861-2869. In NONLINEAR DYNAMICS - ISSN:0924-090X vol. 78 (4) 2014. -
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Reference implementation for the proposed SII 5194 (Bidirectional Text Editing) Israeli standard (hopefully, a Unicode standard in the future). This is a fully functional text editor with complete BiDi support.
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Atera all-in-one platform IT management software with AI agentsAtera’s AI agents don’t just assist, they act. From detection to resolution, they handle incidents and requests instantly, taking your IT management from automated to autonomous.
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HD Eccentricity Correction
Eccentricity correction for the hole drilling strain gauge method
...The present functiones correct the measured strains in eccentric holes in the case of non-uniform residual stresses. In order to use the method in a practical way, the depths where the strains are measured in the ASTM E837-13 are taken as reference and specific functions are proposed. -
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dbuic2vdvbc
DB-AGs OLT Barcode to VDV Data Structure Reference Implementation
dbuic2vdvbc (DB Uic to VDV BarCode) gets the VDV relevant information out of the UIC -barcode to produce output in a VDV-KA compliant way. dbuic2vdvbc is a reference implementation, providing an API which can either be integrated in existing and future applications, or can be used as a guideline how UIC- Barcode processing works. It is entirely written in C, can be used to build a shared or static lib, or for linking the objects directly to the application. -
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This program is no longer needed due to changes made in the game. I am leaving it up for now for code reference and archival purposes. I do not plan to update it due to most people feeling there is no need for a calculator in the new Omega system.
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UPascal
My common Pascal units for Lazarus/FreePascal
...Its going to take some time, since I've built up a lot of code over the years. But, give it a few months, and everything should be here. The idea is to have a common code base for all my goodies, and a reference point for any "how do I" questions. cheers Derek -
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Density-ratio based clustering
Discovering clusters with varying densities
...An existing density-based clustering algorithm, which is applied to the rescaled dataset, can find all clusters with varying densities that would otherwise impossible had the same algorithm been applied to the unscaled dataset. Reference: Zhu, Y., Ting, K. M., & Carman, M. J. (2016). Density-ratio based clustering for discovering clusters with varying densities. Pattern Recognition. http://www.sciencedirect.com/science/article/pii/S0031320316301571 -
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Kavvvka
Automated tabletennis competition form for match in KAVVV Leage (BE)
Linux Desktop program to calculate results of competition home-match, based on layout of original paper form. Form default is the "old" 21 points / set, 2 winning sets. Teams are 3 players, and they play 9 games + one double game. Calculation of the individual winning sets (and lost), and winning matches (and lost) is done, like needed to fill the official form. Print function for empty or filled form and official form to send in. If you want to try the program, just download the... -
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ENGH Dictionary
English-Hindi Dictionary
English-Hindi Dictionary. A compact reference for general readers. Over Thousand of word and phrases! -
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LibNucNucGam
Nuclear collision secondary particle production cross sections.
This Python library contains the parametrization of the Nucleus-Nucleus pi-meson (including subthreshold pions) and the direct hard photon gamma-ray production cross sections channels for calculating the secondary gamma-ray and electron/positron spectra based on arXiv:1608.03348. Please, if you use this library DO NOT reference to this webpage, instead reference to arXiv:1608.03348, "Parametrization of the nucleus-nucleus gamma-ray production cross sections below 100 GeV/nucleon: Subthreshold pions and Hard photons" by Ervin Kafexhiu COMING SOON... -
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6. DHOEM (Windows)
R function which incorporates simulated markers to a real data set
...The function allows the user to specify a desired level of marker density, with a minor allele frequency (MAF) limit, which is produced in a reasonable computation time. Reference: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0830-7 -
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5.Kernelized qtl-haplotype mapping (HPC)
Fortran/R program for kernelized qtl-haplotype mapping by mixed model
...The haplotypes are defined by a sliding window of L SNP markers (L is an integer greater or equal to 1). Hence, 2^L haplotypes can be (not necessarily) observed for a sliding window (e.g. 2^6=64 for L=6). Reference: http://gsejournal.biomedcentral.com/articles/10.1186/1297-9686-46-45 -
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REDD Abacus SP
a land use planning tool for climate change research
**REDD Abacus SP** is a public domain software developed by the [World Agroforestry Centre (ICRAF)](http://www.worldagroforestry.org/sea) to: * Estimate emission from land use and land cover changes allowing for dynamic heterogeneity of soil types, elevations, climate and other biophysical characteristics in the landscapes * Analyze trade-offs between emissions and financial gain (opportunity cost analysis) and produce abatement cost curves Project ex-ante emissions and financial gain of business-as-usual scenarios for setting Reference Emission Level (REL) * Simulate zone-specific policies and other emission reduction scenarios within the landscapes, and estimate the potential emission reductions and opportunity costs of them **REDD Abacus SP** can serve as a main tool in: * Developing land use plan for low emission development strategies at the province or district level * Assessing carbon efficiency of a large scale land-based enterprise * Estimating abatement cost o -
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An Excel that creates a powerpoint presentation of nicely formatted slides from the rows in a spreadsheet. Create your own ttemplates to include any fields from the spreadsheet customize your layout. More info on Tiran: http://tirandagan.com
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SVN Externals Updater
Tool for SVN externals update of multiple repositories
A tool that allows management of SVN externals of multiple SVN repositories. If you have many SVN repositories that reference each other using SVN externals it is not simple to keep these externals updated. This tool allows you to manage the repositories using a graphical user interface that is simple to use. I created this tool for help in my own official work as I manage SVN repositories of the software developed by my company. There are quite a few repositories for the applications and components used in the software and these link to each other via SVN externals. ... -
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BRACIL-IA
Inference of Genome Accessibility in Bacteria from ChIP-seq data.
...This is performed by a linear mixed effect model that considers two parameters: DNA affinity and DNA accessibility. The fundaments for this code and its biological relevance is described in the following reference: Gomes ALC, Wang HH (2016) The Role of Genome Accessibility in Transcription Factor Binding in Bacteria. PLoS Comput Biol 12(4): e1004891. doi:10.1371/journal.pcbi.1004891 -
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CT collimation measurements using CR plates. Please reference Bjarnason TA, Yang CY. CT radiation profile width measurement using CR raw data. Journal of Applied Clinical Medical Physics. 2015;16:501-507. Available from: http://www.jacmp.org/index.php/jacmp/article/view/5512
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OpenVPN for Docker
OpenVPN server in a Docker container complete with an EasyRSA PKI CA
...Extensively tested on Digital Ocean $5/mo node and has a corresponding Digital Ocean Community Tutorial. Pick a name for the $OVPN_DATA data volume container. It's recommended to use the ovpn-data- prefix to operate seamlessly with the reference systemd service. Users are encourage to replace example with a descriptive name of their choosing. Initialize the $OVPN_DATA container that will hold the configuration files and certificates. The container will prompt for a passphrase to protect the private key used by the newly generated certificate authority. Miscellaneous write-ups for advanced configurations are available in the docs folder. ...
