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The Top 23 Java Bioinformatics Open Source Projects

Open source projects categorized as Java Bioinformatics
Categories > Data Processing > Bioinformatics
Adam ⭐ 966
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
dependent packages 17total releases 14most recent commit 3 months ago
Biojava ⭐ 564
📖🔬☕ BioJava is an open-source project dedicated to providing a Java library for processing biological data.
dependent packages 16total releases 56most recent commit 3 months ago
Cdk ⭐ 453
The Chemistry Development Kit
dependent packages 69total releases 17most recent commit 3 months ago
Jvarkit ⭐ 440
Java utilities for Bioinformatics
most recent commit 5 months ago
Intermine ⭐ 228
A powerful open source data warehouse system
dependent packages 2total releases 8most recent commit 2 years ago
P2rank ⭐ 193
P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.
most recent commit 3 months ago
Astral ⭐ 193
Accurate Species TRee ALgorithm
most recent commit 10 months ago
Artemis ⭐ 191
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
most recent commit a year ago
Pegasus ⭐ 168
Pegasus Workflow Management System - Automate, recover, and debug scientific computations.
dependent packages 2total releases 7most recent commit 3 months agopypi pegasus-wms.api} Downloads
Rnartist ⭐ 144
With RNArtist, you construct a collection of RNA structures that can be gathered into RNA families, projects,...
total releases 12most recent commit 5 months ago
Dnanalyzer ⭐ 122
Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools
most recent commit 5 months ago
Globalbioticinteractions ⭐ 114
Global Biotic Interactions provides access to existing species interaction datasets
most recent commit 3 months ago
Dockstore ⭐ 113
Our VM/Docker sharing infrastructure and management component
most recent commit 3 months ago
Bio4j ⭐ 112
Bio4j abstract model and general entry point to the project
most recent commit 7 years ago
Biojava Tutorial ⭐ 111
📖📚An introductory tutorial for BioJava
most recent commit 3 months ago
Molgenis ⭐ 106
MOLGENIS - for scientific data: management, exploration, integration and analysis.
dependent packages 39total releases 98most recent commit 4 months ago
Bioscala ⭐ 106
Bioinformatics for the Scala programming language
most recent commit 3 months ago
Genomicsdb ⭐ 88
High performance data storage for importing, querying and transforming variants.
dependent packages 2total releases 35most recent commit 3 months ago
Minced ⭐ 80
Mining CRISPRs in Environmental Datasets
most recent commit a year ago
Owltools ⭐ 76
OWLTools
most recent commit 3 years ago
Hadoop Bam ⭐ 66
Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework
dependent packages 33total releases 17most recent commit 5 years ago
Sirius ⭐ 66
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)
most recent commit 5 months ago
Caleydo ⭐ 57
Caleydo - Visualization for Molecular Biology
most recent commit 7 years ago
The 10 Most Depended On Java Bioinformatics Open Source Projects
Cdk ⭐ 453
The Chemistry Development Kit
dependent packages 69total releases 17latest release August 21, 2023most recent commit 3 months ago
Molgenis ⭐ 106
MOLGENIS - for scientific data: management, exploration, integration and analysis.
dependent packages 39total releases 98latest release August 03, 2020most recent commit 4 months ago
Bridgedb ⭐ 26
The BridgeDb Library source code
dependent packages 25total releases 38latest release November 21, 2023most recent commit 4 months ago
Bacting ⭐ 11
Bacting := acting as the Bioclipse TNG
dependent packages 14total releases 47latest release November 05, 2023most recent commit 3 months ago
Liblevenshtein Java ⭐ 40
Various utilities regarding Levenshtein transducers. (Java)
dependent packages 10total releases 4latest release May 29, 2016most recent commit 6 years ago
Jannovar ⭐ 51
Annotation of VCF variants with functional impact and from databases (executable+library)
dependent packages 5total releases 27latest release September 13, 2022most recent commit 3 months ago
Biodata ⭐ 27
Java library that models biological entities and their equivalents in different file formats typically used in bioinformatics
dependent packages 5total releases 79latest release November 20, 2023most recent commit 3 months ago
The 10 Latest Releases In Java Bioinformatics Open Source Projects
Bridgedb ⭐ 26
The BridgeDb Library source code
dependent packages 25total releases 38latest release November 21, 2023most recent commit 4 months ago
Biodata ⭐ 27
Java library that models biological entities and their equivalents in different file formats typically used in bioinformatics
dependent packages 5total releases 79latest release November 20, 2023most recent commit 3 months ago
Bacting ⭐ 11
Bacting := acting as the Bioclipse TNG
dependent packages 14total releases 47latest release November 05, 2023most recent commit 3 months ago
Genomicsdb ⭐ 88
High performance data storage for importing, querying and transforming variants.
dependent packages 2total releases 35latest release October 12, 2023most recent commit 3 months ago
Cdk ⭐ 453
The Chemistry Development Kit
dependent packages 69total releases 17latest release August 21, 2023most recent commit 3 months ago
Pegasus ⭐ 168
Pegasus Workflow Management System - Automate, recover, and debug scientific computations.
dependent packages 2total releases 7latest release October 28, 2022most recent commit 3 months agopypi pegasus-wms.api} Downloads
Cytomine Java Client ⭐ 13
Cytomine Java client
total releases 19latest release September 15, 2022most recent commit 9 months ago
Jannovar ⭐ 51
Annotation of VCF variants with functional impact and from databases (executable+library)
dependent packages 5total releases 27latest release September 13, 2022most recent commit 3 months ago
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