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86 search results found

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

Biojava ⭐ 564

📖🔬☕ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

The Chemistry Development Kit

Jvarkit ⭐ 440

Java utilities for Bioinformatics

Intermine ⭐ 228

A powerful open source data warehouse system

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.

Accurate Species TRee ALgorithm

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

Pegasus ⭐ 168

Pegasus Workflow Management System - Automate, recover, and debug scientific computations.

Rnartist ⭐ 144

With RNArtist, you construct a collection of RNA structures that can be gathered into RNA families, projects,...

Dnanalyzer ⭐ 122

Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools

Globalbioticinteractions ⭐ 114

Global Biotic Interactions provides access to existing species interaction datasets

Dockstore ⭐ 113

Our VM/Docker sharing infrastructure and management component

Bio4j abstract model and general entry point to the project

Biojava Tutorial ⭐ 111

📖📚An introductory tutorial for BioJava

Molgenis ⭐ 106

MOLGENIS - for scientific data: management, exploration, integration and analysis.

Bioscala ⭐ 106

Bioinformatics for the Scala programming language

Genomicsdb ⭐ 88

High performance data storage for importing, querying and transforming variants.

Mining CRISPRs in Environmental Datasets

Owltools ⭐ 76

Hadoop Bam ⭐ 66

Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework

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)

Caleydo - Visualization for Molecular Biology

Jannovar ⭐ 51

Annotation of VCF variants with functional impact and from databases (executable+library)

Sirius Libs ⭐ 45

sirius-libs - Metabolomics mass spectrometry framework for molecular formula identification of small molecules written in Java

Peptide Shaker ⭐ 41

Interpretation of proteomics identification results

Liblevenshtein Java ⭐ 40

Various utilities regarding Levenshtein transducers. (Java)

GORpipe is a tool based on a genomic ordered relational architecture and allows analysis of large sets of genomic and phenotypic tabular data using declarative query language, in a parallel execution engine.

Searchgui ⭐ 36

Highly adaptable common interface for proteomics search and de novo engines

PDV: an integrative proteomics data viewer

Metaomgraph ⭐ 30

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

Aracne Ap ⭐ 30

Network Reverse Engineering through AP inference of Mutual Information

CGView is a Java package for generating high-quality, zoomable maps of circular genomes.

Java library that models biological entities and their equivalents in different file formats typically used in bioinformatics

This is the SeqWare Project's main repo.

Causalpath ⭐ 27

A project for exploring differentially active signaling paths related to proteomics datasets

Bridgedb ⭐ 26

The BridgeDb Library source code

Version 4 of the EMBL-EBI Ontology Lookup Service (OLS)

Compomics Utilities ⭐ 26

Open source Java library for computational proteomics

Efficient and accurate pathogenicity prediction for coding and regulatory structural variants in long-read genome sequencing

Rnartistcore ⭐ 25

A Kotlin DSL to create and plot RNA 2D structures. The drawing engine behind RNArtist to be used from the command line.

ASAP : Automated Single-cell Analysis Pipeline

an implementation of NSGA-II in java

Aptasuite ⭐ 20

A full-featured bioinformatics software collection for the comprehensive analysis of aptamers in HT-SELEX experiments.

UFCG: Universal Fungal Core Genes

Repository of our application for human-augmented binning

MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers

Metacherchant ⭐ 19

Synteny Mapping and Analysis Program

Genomics data re-analysis

Nextprot Api ⭐ 16

neXtProt API - From SIB CALIPHO group; neXtProt project

Omicssuite.github.io ⭐ 15

OmicsSuite website for releasing new version.

Scriptmanager ⭐ 14

Wqfm 2020 ⭐ 13

wQFM implementation in Java

Cytomine Java Client ⭐ 13

Cytomine Java client

Chia Pet_tool_v3 ⭐ 13

ChIA-PET, HiChIP, PLAC-Seq data analysis, with linker detection, linker filter, or restriction process for HiChIP, mapping, call cluster and visulization

BACNET is a Java based platform to develop website for multi-omics analysis

Watchdog ⭐ 12

Workflow management system for the automated and distributed analysis of large-scale experimental data.

Bacting := acting as the Bioclipse TNG

BioDWH2 is an easy-to-use, automated, graph-based data warehouse and mapping tool for bioinformatics and medical informatics.

PRNGine - Pseudo Random Number Engines for Monte Carlo simulations

Linkedisa ⭐ 10

Package to convert ISA-TAB files into RDF data relying on different semantic frameworks (OWL ontologies).

Karkinos ⭐ 10

Tumor genotyper, that detects SNV, absolute CNV and Tumor contents

Python Library for data analysis based on GMQL

Improved Meta-aligner and Minimap2 On Spark. A distributed long read aligner.

Gene Ontology Semantic Similarity Tool

Gluetools ⭐ 9

An open, platform-independent software toolkit for storage and interpretation of sequence data, implemented in Java.

🍃 SiNGA (Simulation of Natural Systems using Graph Automata) is an open-source library containing tools especially for structural bioinformatics and systems biology.

Prion-Like Amino Acid Composition

Java based bioinformatics data analysis tool kits

A command line tool (in Kotlin/JVM) for intuitively visualizing BAM alignments.

Fonda is a framework which offers scalable and automatic analysis of multiple NGS sequencing data types

🔍 Fit3D - An application for template-based detection of small structural motifs in protein structures and macromolecular structure data.

Decision-driven action launching system

Ambit Mirror ⭐ 6

GitHub read-only mirror of AMBIT

Cluster up to millions of peptide sequences on shared sequence motifs.

Dishevelled Bio ⭐ 6

dishevelled.org bio

Spectrum_similarity ⭐ 5

Scoring functions to compare MS/MS spectra

Spollineages ⭐ 5

Rapid and precise prediction of Mycobacterium tuberculosis complex families

Treegraph2 ⭐ 5

A feature rich and easy to use phylogenetic tree editor

Platform for Distributed Proteomics Software

Evanalyzer ⭐ 5

EV analyzing plugin for Fiji

Recon2neo4j ⭐ 5

This framework is part of the DiseaseNetworks module, eTRIKS Lab. The Metabolic Framework uses the neo4j graph platform for the management of data on human metabolism (basis: Recon2).

SEquence DAtaset builder

A 03-713 Bioinformatics Practicum project. It focuses on virus transcriptome detection of a given diseased model (i.e. human cancer) using RNA-seq data, and in the future, some further analyses including SNP analysis etc.

Bioinformatics projects and code shared by Zhi John Lu

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