Search Results for "variation"
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Showing 40 open source projects for "variation"
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Soot
Soot - A Java optimization framework
...Baf: a streamlined representation of bytecode which is simple to manipulate. Jimple: a typed 3-address intermediate representation suitable for optimization. Shimple: an SSA variation of Jimple. Grimp: an aggregated version of Jimple suitable for decompilation and code inspection. -
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BRIG is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. Please cite the BRIG paper if BRIG is used to generate figures for publications: NF Alikhan, NK Petty, NL Ben Zakour, SA Beatson (2011) BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons, BMC Genomics, 12:402. PMID: 21824423
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NGSEP
NGSEP (Next Generation Sequencing Experience Platform)
...The current version provides functionalities for both de-novo and reference guided analysis of sequencing data, including genome assembly, read mapping, variants detection and genotyping and de-novo analysis of data generated from reduced representation protocols. NGSEP also provides modules for analysis of genomic variation databases (VCF files), including functional annotation, filtering, format conversion, comparison, clustering, imputation, introgression analysis and different kinds of statistics. Since version 4, we provide functionalities for management of genomes and transcriptomes, including genome alignment and annotation of transposable elements. ... -
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NGSpop
NGSpop: identifying & visualizing sequence variation in deepvariant
*NOTICE* The official software(NGSpop) will be updated soon, so please visit us in 2/29. Thank you. -
Train ML Models With SQL You Already KnowBuild and deploy ML models using familiar SQL. Automate data prep with built-in Gemini. Query 1 TB and store 10 GB free monthly.
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TVscript
Exploration of the removal of count variable transcripts.
> See TVscript wiki: https://sourceforge.net/p/tvscript/wiki/Home/ Related Software: 1. CStone: https://sourceforge.net/projects/cstone/ 2. CSReadGen: https://sourceforge.net/projects/csreadgen/ 3. CView: https://sourceforge.net/projects/cview/ 4. ChimSim: https://sourceforge.net/projects/chimsim/ 5. TVScript: (See wiki) 6. SeQuester: https://sourceforge.net/projects/sequester/ 7. TreeScope: https://sourceforge.net/projects/treescope/ -
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Optimized Storage for temporal Data
open Optimized Storage of time series data
...Base class for optimized storage of time series data. Uses any kind of relational database. Cross plateform with multiple languages (C++, C#, Java). Conditional storage based on value variation : DeltaValue and DeltaTime params. Get back data without losts. -
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NOTE: For latest version, please visit https://github.com/ispasic/FlexiTerm. FlexiTerm is an open-source software tool for automatic term recognition. FlexiTerm uses a range of methods to neutralise the main sources of term variation. FlexiTerm is robust enough for less formally structured texts, such as those found in patient blogs or medical notes.
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REHUNT
REHUNT (Restriction Enzymes HUNTing)
REHUNT (Restriction Enzymes HUNTing) is a free and open source package implemented in JAVA for providing many useful methods for biological sequence analysis (especially in SNP genotyping) around restriction enzymes. All academic researchers are encouraged to use REHUNT in their studies or to integrate it into their systems and applications. Non-academic users or commercial needs are also welcome to use it. For further information or additional applications, please contact the author... -
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Clustering Variation looks for a good subset of attributes in order to improve the classification accuracy of supervised learning techniques in classification problems with a huge number of attributes involved. It first creates a ranking of attributes based on the Variation value, then divide into two groups, last using Verification method to select the best group.
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GeneticThesaurus
Annotation of genetic variants in repetitive regions
GeneticThesaurus enables analysis of genetic variation in repetitive regions. See project wiki for details. -
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JLWR
Java Locally weighted regression (JLWR)
Locally weighted regression (LWR) is a variation of the standard linear regression technique in which training points close to the query point have more influence over the fitted regression surface. Given a set of training points, linear regression ts the linear model that minimizes squared prediction error over the whole training set. source on git :https://github.com/ahrnazemi/jlwr This implicitly assumes that we know the global form of the underlying function that generated the data. -
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cnvCapSeq
detecting & genotyping CNV in long-range targeted resequencing.
cvnCapSeq is a set of Java-based command-line tools for detecting and genotyping copy number variation (CNV) in targeted resequencing experiments of large contiguous genomic regions. -
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cnvOffSeq
detecting & genotyping intergenic CNVs using off-target exome data
cnvOffSeq is a set of Java-based command-line tools for detecting and genotyping intergenic copy number variation (CNV) using off-target data from whole-exome sequencing experiments. -
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VarImpact
Extracting effects of mutations on molecular properties from text.
Genetic variants alter cellular behavior in a variety of ways, changing biochemical properties of DNA, mRNA, and proteins. Many large-scale sequencing projects are under way to detect human variation in health and disease. Although broad disease associations can be discovered by GWAS studies, the low-level impact of mutations is hardly available in structured form. The results of thousands of small-scale experiments, on the other hand, are present in the literature and discuss observations made ranging from alteration of active sites to changes in drug response resulting. ... -
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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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Chmuk
GPS data visualisation and exploration
A really wonderful software to visualise and analyse GPS traces in many different ways (speed and elevation variation, etc.), with different background maps (hiking map, road map, orienteering map, aerial image, cycling map, etc.). It is possible to make KML exports. -
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FishingCNV
Copy number variation (CNV) detection in exome sequencing data
FishingCNV, a software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data. The inputs are standard coverage files produced by Genome Analysis ToolKit (GATK), and the output is a file containing putative CNVs. The program comes in 2 different releases * GUI version (FishingCNV_X.X.X.zip) * Command line version (FishingCNV_X.X_pipeline) Browse through our files to find the different releases. -
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A web database and bioinformatics analysis tool for gene families involved in antigenic variation and immune system evasion in pathogens.
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Seurat
A sequence analysis tool for normal/tumor DNA and RNA data.
THIS IS NO LONGER THE HOME FOR SEURAT. PLEASE GO TO https://sites.google.com/site/seuratsomatic/ --- Seurat is an sequence analysis program for somatic mutation and allelic imbalance discovery in paired tumor and normal genome and transcriptome data. -
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Mario Survival
A variation of the classic Mario game with a custom map editor.
This is a variation of the classic Mario game in which you, Mario, must survive against a never ending onslaught of enemy Mario's. The application includes an in-game map editor, so you can create your own custom maps to play on, as well. -
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A cross platform steganography software written completely in java, with a juicy AES support. The project is pretty extensible, so new smarter steganography algorithms's are fully implementable.
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super-lines is a variation of commonly known dos-game COLOR LINES. It is written in java, supports user authentication, game progress saving and online-mode when users score is sent to server and saved in database.
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Genevar (GENe Expression VARiation) is a platform of database and web services for the integrative analysis and visulization of SNP-gene assocaitaions in eQTL studies.
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No Latte is an interpreter for a variation of the Latte language (cf. http://www.latte.org/) for writing XHTML documents in a functional-programming style---LaTeX sensibilities with LISP semantics.
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Bistro is a new programming language that integrates the best features of Smalltalk and Java. Bistro is a variation of Smalltalk that runs on top of any Java virtual machine (VM) that conforms to Sun's Java specifications.
