Official code repository for GATK versions 4 and up
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Mar 31, 2025 - Java
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Bioinformatics
Bioinformatics is an interdisciplinary field that intersects with biology, computer science, mathematics and statistics. It concerns itself with the development and use of methods and software tools for collecting and analyzing biological data.
Here are 272 public repositories matching this topic...
📖🔬☕ BioJava is an open-source project dedicated to providing a Java library for processing biological data.
java bioinformatics genomics pdb parser-library protein-data-bank protein-structure protein-sequences sequence-alignment protein-modification structure-alignment structural-bioinformatics
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Mar 20, 2025 - Java
The Chemistry Development Kit
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Mar 31, 2025 - Java
Java utilities for Bioinformatics
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Mar 31, 2025 - Java
A powerful open source data warehouse system
python java api open-source clojure opensource bioinformatics genomics genetics clojurescript biology perl postgresql lgplv3 tomcat data-visualization data-warehouse data-visualisation webservices tomcat8
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Dec 3, 2023 - Java
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases
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Jun 15, 2024 - Java
Pegasus Workflow Management System - Automate, recover, and debug scientific computations.
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Mar 31, 2025 - Java
Democratizing on-device AI-powered DNA analysis for everyone, everywhere
machine-learning bioinformatics genomics computational-biology artificial-intelligence dna transcriptomics dna-sequencing regulatory-elements
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Mar 24, 2025 - Java
Global Biotic Interactions provides access to existing species interaction datasets
bioinformatics parasites biology diet ecology biodiversity diseases eol etl-framework food-webs ecoinformatics globi species-interactions pollinators
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Mar 27, 2025 - Java
The Pharmacogenomic Clinical Annotation Tool
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Mar 30, 2025 - Java
An app store for scientific workflows, tools, notebooks, and services
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Mar 31, 2025 - Java
Bio4j abstract model and general entry point to the project
java bioinformatics database graph proteins protein gene-ontology java-8 graph-database ncbi-taxonomy graph-databases property-graph graph-data uniprot bio4j graph-queries graph-schema titan bio4j-titan uniref
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Dec 16, 2016 - Java
MOLGENIS - for scientific data: management, exploration, integration and analysis.
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Dec 22, 2023 - Java
OWLTools
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Sep 9, 2024 - Java
SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)
java science bioinformatics cheminformatics molecular-structures sirius metabolomics mass-spectrometry ms-data denovo molecular-formulas ms-spectra structure-elucidation fragmentation-trees csi-fingerid fingerid isotope-pattern mass-spectra
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Jan 22, 2025 - Java
Apache cTAKES is a Natural Language Processing (NLP) platform for clinical text.
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Mar 18, 2025 - Java
Annotation of VCF variants with functional impact and from databases (executable+library)
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Mar 31, 2025 - Java
Version 4 of the EMBL-EBI Ontology Lookup Service (OLS)
bioinformatics linked-data rdf semantic-web owl knowledge-graph ontologies knowledge-management knowledge-representation fair-data
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Mar 28, 2025 - Java
Various utilities regarding Levenshtein transducers. (Java)
computer-science search-engine data-science machine-learning natural-language-processing information-retrieval bioinformatics genomics dictionary fuzzy-search computational-biology edit-distance levenshtein-distance approximate-string-matching distance-metric finite-state-automata finite-state-transducer levenshtein-automata spelling-correction universal-automata
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Dec 20, 2021 - Java