Search Results for "genomics"
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Showing 19 open source projects for "genomics"
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...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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Lirex
A Package for Identification of Long Inverted Repeats in Genomes
...Lirex, as a cross-platform tool to identify LIRs in a genome, may assist in designing following experiments to explore the function of LIRs. Our tool can identify more LIRs than other LIR searching tools. For more details, please refer to Genomics, Proteomics and Bioinformatics 2017, 15:141-146 by Y. Wang and J.M. Huang. -
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oasis-genomics
Oasis Genomics cancer omics integration portal
OASIS is an application that enables complex analytical queries across somatic mutations; copy number changes (CNV); and gene expression data. OASIS has been built on top of the BIoMart frameworks and has been extended to incorporate unique tools and visualizations to facilitate analysis of complex cancer "Omics" datasets. -
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GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded. This project has moved to GitHub: https://github.com/GenomeView/genomeview
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MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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locusvu
Tool for genomics;automates data retrieval from db;enables workflows
...Thus, LocusVu provides a basic framework that can be used by users and developers alike in simplifying existing workflows and creating newer ones to support data analysis in genomics. -
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TreeLiker
TreeLiker is a collection of fast algorithms for working with complex
...In experiments with real-life data, the algorithms were shown to be able to construct complete non-redundant sets of patterns for chemical datasets involving several thousands of molecules as well as for comparably large datasets from genomics or proteomics. The included relational learning algorithms are tailored towards so-called tree-like features for which some otherwise very hard sub-problems (NP-hard) become tractable. -
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locsmoc
piecewise polynomial curves for genomic signals
Locsmoc produces piecewise polynomial models for one-dimensional signals of the type encountered in genomics. The project wiki contains an overview of the tool and usage examples. -
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Intrepid Bioinformatic's Integrative Genomics Viewer (IGV) modifications for viewing NGS files on IGV with data located on remote servers, accessed by web services.
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The Celera Genome Browser, developed at Celera Genomics as part of Celera's sequencing and annotation of the human genome, and released as open source in 2006.
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SyMBA is a Data Archive and Integrator that is based on the Functional Genomics Object Model (http://fuge.sf.net) and which archives, stores, and retrieves raw high-throughput data. See http://symba.sf.net and http://www.cisban.ac.uk
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CloudBurst is a parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics.
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MOLGENIS can be used to generate databases for life science experiments (micrroarray, mass spectrometry, genomics) having a web user interface, csv exchange format, and programmatic interfaces (web services, rest, and r-project). See NatRevGen 8.
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Opensource software projects for genetics and genomics from Sage Bionetworks.
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DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV
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TRANSFOG DAS (Translational and Functional Onco-Genomics Distributed Annotation System) is an XML-based annotation system to allow the discovery and analysis of candidate genes potentially involved in cancer onset and progression.
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Io (ISREC ontologizer) is a program to classify high-throughput genomics data (e.g. microarray results) in the Gene Ontology. Io includes a statistical estimation of the significance of data in the GO nodes and reannotation files for Affymetrix chips.
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eQTLexplorer is a database application for the visualization and integrated mining of genetical genomics experiments.
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