Graph theory (a.k.a. network) library for analysis and visualisation
Embeddable genomic visualization component based on the Integrative Genomics Viewer
RCSB 1D Feature Viewer
JavaScript/TypeScript molecular visualization library
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Nucleotide sequence manipulation and analysis library
This project is a Galaxy visualization package that integrates [Cytoscape](https://cytoscape.org/) into the Galaxy platform using the [Galaxy Charts](https://galaxyproject.github.io/galaxy-charts/) and [Cytoscape package](https://www.npmjs.com/package/@ga
Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.
RCSB 1D Saguaro Web App
AI-powered CLI for Seqera Platform - bioinformatics workflow management
RCSB Molstar/Saguaro Web App
A WebGL based 3D data visualization engine.
an open source bioinformatics package for retrieving, processing and analyzing the sequences and structures of biomolecules, such as proteins and nucleotides.
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A network visualisation that displays molecular interaction data, including detailed residue-level information such as binding sites. Used in EBI's Complex Portal and elsewhere.
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Generate interactive visualizations of statistical genetic data
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TypeScript MCP server for biocontext7 — bioinformatics tool discovery and documentation
CLI for Xiantao bioinformatics tools
A bunch of useful classes for bioinformatics
BioRuby Shell is a command line interface on BioRuby open source bioinformatics library. It provides easy-to-use analysis environment for bioinformatics.
A gem to automate using the Scribl bioinformatics graphics library with Rails 3 asset pipeline
This is an RDF.rb reader plugin for Variant Call Format (VCF) files, widely used in bioinformatics.
A Ruby Gem used for consolidating files containing lists with a unique identifier (such as genetic sequence) and their associated value, count, or sum (in asc or desc order) into a single file. We've used it for sequencing and genomic searches for assay development in molecular diagnostics to consolidate distributed processes and pipelines. Also helpful for bioinformatics and NLP applications to summarize occurences of frequency.
Biogem is a software generator for those bioinformaticans who want to start coding an application or a library for using/extending BioRuby core library and sharing it through rubygems.org . The basic idea is to simplify and promote a modular approach to bioinformatics software development
This library provides support for BGZF (Blocked GZip Format) in Ruby. BGZF, originally defined as part of the SAM/BAM specification, is used to compress record-oriented data in a way that facilitates random access, unlike plain gzip. BGZF is principally used for bioinformatics data but would be useful in other contexts as well.
Pipet is a package manager for bioinformatics databases that allows users to easily retrieve databases from their sources using the command line. Pipet also checks for database integrity via checksum
SolveBio is a platform for biomedical datasets. With SolveBio you can forget about parsing complex flat files and sifting through cryptic datasets. Just use the Ruby Client and API to explore massive datasets and automate just about any bioinformatics workflow. See https://www.solvebio.com/ for more information.
Macroape is an abbreviation for MAtrix CompaRisOn by Approximate P-value Estimation. It's a bioinformatic tool for evaluating similarity measure and best alignment between a pair of Position Weight Matrices(PWM), finding thresholds by P-values and vice versa and even searching a collection of motifs for the most similar ones. Used approach and application described in manual at https://docs.google.com/document/pub?id=1_jsxhMNzMzy4d2d_byAd3n6Szg5gEcqG_Sf7w9tEqWw
A Ruby Gem used for calculating a consensus (most frequent) DNA sequence from an array of ALIGNED sequences. Useful for bioinformatics pipelines to create a reference sequence when using another sequence aligning utility. Also, helpful in finding consensus regions for primer design or viral genotyping.
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