Search Results for "tutorials"
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Showing 14 open source projects for "tutorials"
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AlphaGenome
Programmatic access to the AlphaGenome model
The AlphaGenome API provides access to AlphaGenome, Google DeepMind’s unifying model for deciphering the regulatory code within DNA sequences. This repository contains client-side code, examples, and documentation to help you use the AlphaGenome API. AlphaGenome offers multimodal predictions, encompassing diverse functional outputs such as gene expression, splicing patterns, chromatin features, and contact maps. The model analyzes DNA sequences of up to 1 million base pairs in length and can... -
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OpenClinic GA
Open Source Integrated Hospital Information Management System
OpenClinic GA is an open source integrated hospital information management system covering management of administrative, financial, clinical, lab, x-ray, pharmacy, meals distribution and other data. Extensive statistical and reporting capabilities. OpenClinic GA and OpenClinic GMAO are owned by Frank Verbeke, MD, PhD at Post-Factum BV (https://www.post-factum.be) -
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The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments for bacterial and archaeal 16S rRNA sequences, fungal LSU and fungal ITS sequences, with confidence estimates for each assignment. More information and tutorials on how to install, use and retrain RDP Clasifier can be found on at https://github.com/rdpstaff/classifier and John Quensen's blog (https://john-quensen.com/). Citation: 1. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007 Aug;73(16):5261-7. 2. ...
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genppi
GENPPI: standalone software for creating protein interaction networks
...For instance, one can set parameters regarding the genus, metagenome, or pangenome. In addition to the parameterization of GENPPI, it is also the user's choice what set of genomes he is going to study. Please, to obtain the software and tutorials access: https://genppi.facom.ufu.br -
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MAGeCK
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. For instructions and documentations, please refer to the wiki page. MAGeCK is developed by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute/Harvard School of Public Health, and is maintained by Wei Li lab at Children's National Medical Center. We thank the support... -
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Cell Paint
cellPAINT allows users to create living illustrations of biology.
...There are currently several prototypes available: --cellPAINT_coronavirus includes a newly-redesigned user interface, and molecular building blocks for coronavirus, blood plasma, and a simple human cell --cellPAINT_exo includes hand-painted sprites created by Julia Jimenez during an internship, and also allows input of custom sprites through Mesoscope --cellPAINT_VR is a 3D virtual reality version of cellPAINT, with molecular building blocks for a red blood cell cytoskeleton --cellPAINT_2D is the initial alpha release of cellPAINT, with building blocks for HIV, blood plasma, and a human T-cell. For more information and tutorials, see our website at https://ccsb.scripps.edu/cellpaint Please submit any bug or feature requests to our ticket page. -
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NBT is an open source Matlab toolbox for the computation and integration of neurophysiological biomarkers. NBT allows for easy implementation of new biomarkers, and incorporates an online wiki with extensive help and tutorials.
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Pipeline Builder for NGS tools
Scripting tool for automatize and managing complex NGS analysis
...It allows for data independent reproducible analysis creating protected environment which separates data from results through variable exportation. It comes as a command-line tool with a wizard menus and step-by-step tutorials. Pipeline Builder is written in Perl and it is crossplatform. -
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TeachingDemos
Bioinformatics related demos and tutorials using the R programming lan
Bioinformatics related demos and tutorials using the R programming language for large biological data. Licence: Creative Commons Attribution-NonCommercial 4.0 International License -
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Protospacer
Rapid gRNA design and validation for CRISPR
...From here, users are able to evaluate potential off targeting, to export results in FASTA format or tabulated (e.g. for Microsoft Excel), and to connect to the Integrative Genomics Viewer (IGVref) and view target-sites in the context of genomic annotations, amino acid translations, and HT-Seq data (for off-target validation). We provide online video tutorials and a toy database from our main website. -
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The Blue Obelisk is a group of scientists driven by a belief in Open Source, Open Standards and Open Data, expressed in code, data, algorithms, specifications, tutorials, demonstrations, articles and anything that helps get the message across.
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Java API for implementing any kind of Genetic Algorithm and Genetic Programming applications quickly and easily. Contains a wide range of ready-to-use GA and GP algorithms and operators to be plugged-in or extended. Includes Tutorials and Examples.
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An open source, free DIY biotech/biohacking bootstrapping kit. Genetic engineering/therapy, BioBricks, synthetic biology - schematics, tutorials, etc.
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Microarray Explorer (MAExplorer) is a Java microarray data-mining bioinformatics program. It includes data management, graphics, statistics, clustering, reports, gene data-filtering, user written MAEPlugins, documentation, tutorials, demo data.
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