Search Results for "linux command" - Page 27
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Showing 2463 open source projects for "linux command"
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Copy Number Analysis for Targeted Resequencing (CONTRA) is a tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data.
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mRIN
Assessing mRNA integrity directly from RNA-Seq data
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A broad collection of command-line-interface tools for performing machine learning operations. Each tool is a thin wrapper around functionality in a well-documented C++ class library. Waffles tools are designed to be simple, script-friendly, and to
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denovo_hit
Outputs potential denovo variants from VCF given pedigree information.
Program takes variants calls and determines if the call is novel for a child compared to parents. Program can handle both annotated and unannotated VCF files, however output file is not compatible with GATK's snpEff, so you should annotate prior to using denovo_hit. Usage: ./denovo_hit <VCF file> <PED file> Output: ./potential_denovo.txt To compile: g++ -std=c++11 denovo_hit.cpp -o denovo_hit Please see files for example VCF file, and pedigree file. Format VCF file (tab... -
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Theodore is a tool for semi-automated hybrid assembly of genomes, improving assembly quality by combining multiple information sources.
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Application to estimate haplotypes and other genetics data, based on maximum likehood approach. It can handle present-absent as well as multiallelic loci.
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WODA solver
A finite volume groundwater simulator
WODA (Well Outline and Design Aid) is a groundwater simulator developed at the Group for Numerical Analysis, Jaroslav Cerni Institute, Belgrade, Serbia. WODA does not have its own graphical user interface, but it can work with groundwater models constructed using the freely available Lizza interface, http://www.bioirc.ac.rs/index.php/groundwater-flow-software. -
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PLP
Powerfull pre-processor
Powerful Verilog Preprocessor. PLP stands for Perl Pre-processor. Perl is used as "control language" that is embedded in the Verilog code (or any other code) to generate code on the fly. It is used commonly as a Verilog pre-processor but can be used with any target/output language (C, C++, Java, VHDL, plain text etc) -
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CSV Transformer
transforms xml to csv
The CSV Transformer is a data processing tool which transforms .xml-Files to comma separated values. The CSV Transformer was created in a load and performance testing project, the use case was to be able to transform 2800 configuration files of a big banking application to a single .csv-File. With this single file it was possible to compare the whole configuration between two releases with the already available tool CSV Comparator. This enabled the team to verify if there were any... -
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EV3Utils
LEGO EV3 Utilities and Assembler
EV3Utils are Communication and Assembler utilities written in JAVA for working with the LEGO Mindstorms EV3 from Linux. A command line interface is provided which can be used to up- or download projects as well as assemble new bytecode files. Communication with the brick is currently limited to USB-only, but other transports should be easy to add. The assembler supports all of the functionality of the one provided by LEGO, but uses a slightly different syntax and supports far more error checking. ... -
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jAudio is a project implementing a number of common feature extraction algorithms for analyzing audio in java. Output is either in Weka's ARFF format or the ACE format. Can be used either as a GUI application, command-line application, or embedded. The primary repository is on github (dmcennis) which pushes to this projects github repository.
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Easy CNC
Modular CNC software for Arduino controller
The goal of the project is the realization of a modular firmware that allows to control a CNC machine with different utensils. For instance, a CNC with a drill, with few changes can become a plotter with a pen or cutting machine to cut cardboard or stickers. In order to do that, we want project a CNC router with a mechanism that allows a fast utensil change and a controlling firmware which can use different utensils changing some configuration parameters. -
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Yet Another Audio Feature Extractor is a toolbox for audio analysis. Easy to use and efficient at extracting a large number of audio features simultaneously. WAV and MP3 files supported, or embedding in C++, Python or Matlab applications.
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RTLSDR Scanner
A cross platform Python frequency scanning GUI for rtl-sdr
A cross platform Python frequency scanning GUI for USB TV dongles, using the OsmoSDR rtl-sdr library. In other words a cheap, simple Spectrum Analyser. More information can be found at: http://eartoearoak.com/software/rtlsdr-scanner An installer and standalone versions for Windows are located here: https://github.com/EarToEarOak/RTLSDR-Scanner/releases Sources are available on GitHub: https://github.com/EarToEarOak/RTLSDR-Scanner ** The up to date installer is no longer... -
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RandomLib
Random number library
RandomLib is a C++ interface to the Mersenne Twister random number generator MT19937 and to the SIMD-oriented Fast Mersenne Twister random number generator, SFMT19937. For documentation, visit http://randomlib.sf.net -
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CRISPR-Offinder
a CRISPR guide RNA design and off-target searching to
Summary: Design efficient and specific CRISPR small guide RNAs (sgRNAs) is one of the keys for a successful application of CRISPR technology. Importantly, more and more new RNA-guided endonucleases with different protospacer adjacent motif (PAM) have been discovered. Therefore, there is an urgent need to develop a versatile tool to design sgRNA to satisfy the requirement of different RNA-guided DNA endonucleases. To this end, a flexible sgRNA design program named “CRISPR-offinder” was... -
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Calculator
My Project is a calculator i created for a school project.
My project is a calculator i created for a school project. Enjoy! Download Calculator.cpp if you want to make your own calculator. Please Consider writing a ticket if you find a bug, or writing a review. If you download Calculator.cpp, you need to have an IDE that supports the language. Here are a few suggestions: Visual Studio: https://www.visualstudio.com/en-us/products/visual-studio-community-vs.aspx (Only on Windows) Netbeans: https://netbeans.org/index.html (on Microsoft... -
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olego
OLego – short or long RNA-seq read mapping to discover exon junction
OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a seeding and extension scheme, and does not rely on a separate external mapper. It achieves high sensitivity of junction detection by using very small seeds (12-14 nt), efficiently mapped using Burrows-Wheeler transform (BWT) and FM-index. This also makes it particularly sensitive for discovering small exons. It is implemented in C++ with full support of multiple threading, to allow fast... -
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Atlas is a suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in Whole Exome Capture Sequecing (WECS) data.
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GSA-SNP is a gene set analysis software that can process SNP data as well as gene and haplotype data.
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COFILOS
A Development Framework for Coldfire
Contains a framework for Coldfire MCUs like 52254. The framework supports a Command Line Interface (CLI) that may work from Serial port, USB or ENET. The framework uses Processor Expert and IDE requirement is MCU Eclipse 10.4 from Freescale. Includes the FunkOS Realtime Operating System by Funkenstein Software Consulting, available at http://funkos.sourceforge.net Mainly it is a support package for the development board Perseus, but I have ported also the RTOS to MCF52233DEMO... -
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Notice: RMG-Java is no longer in active development. Please find the latest version written in Python at http://reactionmechanismgenerator.github.io To see the website o the old Java version of RMG, visit http://rmg.sourceforge.net RMG (Java version) is an automatic chemical reaction mechanism generator that constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react (currently limited to C, H, O, and S atoms).
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O.N.O.S
Open Network Object System
...Internet of things made easy for everyone. Open source , simple to use , no need to know any programming language , you can add your programs easy , it runs bash command!every linux system will run it , portable . No installation required! just copy the folder where you want, connect your arduino to the usb and run the python program on the pc. -
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iMSAT represents a full update of the vcf2MSAT program. This command line python program allows for a user to use the polymorphism data generated using SAM- and BAM-tools and a .fasta alignment file to search for polymorphic microsatellite markers (MSATs or STRs). By identifying polymorphic makers, rather than simple repeat regions as previous programs have done, iMSAT greatly increases the speed at which polymorphic MSATs that can be identified -- saving researchers precious time and...
