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@jhuapl-bio JHU Applied Physics Laboratory Biological Sciences

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    18 repositories

    • taxtriage

      Public
      TaxTriage is a Nextflow workflow designed to agnostically identify and give confidences of microbial organisms within short- or long-read metagenomic NGS data. …
      taxonomymetagenomicsclassification
      taxonomymetagenomicsclassificationmultiqctriage
      JavaScript
      •
      MIT License
      •10•80•10•1•Updated Aug 14, 2026Aug 14, 2026

    • mytax

      Public
      mytax is a tool for building custom taxonomies, useful for nucleotide sequence classification
      JavaScript
      •
      GNU Affero General Public License v3.0
      •2•14•1•1•Updated Aug 12, 2026Aug 12, 2026

    • datasets

      Public
      General repository for example datasets
      HTML
      •0•0•0•0•Updated Jul 31, 2026Jul 31, 2026

    • fungai

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated Mar 5, 2026Mar 5, 2026

    • What_You_Read_ExplainableAI

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Mar 2, 2026Mar 2, 2026

    • microbert

      Public
      Leveraging Language Models for Analysis of Metagenomic Sequencing Data
      Python
      •
      MIT License
      •0•3•0•0•Updated Sep 23, 2025Sep 23, 2025

    • Basestack

      Public archive
      Basestack is a platform for rapid and real time analysis of NGS data. It provides a executable application that connects standard bionformatics tools to a user …
      linuxdockermac
      linuxdockermacguiinterfacewindows-10suiteconsensus-generation
      JavaScript
      •
      GNU General Public License v3.0
      •1•27•3•1•Updated Jan 7, 2025Jan 7, 2025

    • DeepPaint

      Public
      A python package for exploration and classification of Cell Painting data.
      Jupyter Notebook
      •
      Apache License 2.0
      •1•6•0•0•Updated Sep 30, 2024Sep 30, 2024

    • TgIF

      Public
      Trans-gene Insertion Finder
      Shell
      •
      MIT License
      •0•1•0•0•Updated Sep 25, 2024Sep 25, 2024

    • ONT-DART

      Public
      Vue
      •
      Apache License 2.0
      •1•0•0•0•Updated Jun 14, 2024Jun 14, 2024

    • omics_workshop

      Public
      This is the central repository for data and example commands for bioinformatics workshop used for JHU-APL faculty and participant use
      HTML
      •0•1•0•0•Updated Apr 29, 2024Apr 29, 2024

    • AGAVE

      Public
      Automated Genomics Application for Variant Exploration (AGAVE)
      vuevariant-analysisvirology
      vuevariant-analysisvirology
      Vue
      •
      GNU General Public License v3.0
      •0•2•3•0•Updated Feb 14, 2024Feb 14, 2024

    • GE-Workshop-Sandbox

      Public
      Dockerfile
      •0•0•0•0•Updated Sep 18, 2023Sep 18, 2023

    • mytax_marine

      Public
      Shell
      •0•0•0•0•Updated May 12, 2023May 12, 2023

    • mytax_marine_old

      Public
      mytax with added information on marine organisms, including common names, pictures, and population distribution
      Vue
      •
      GNU Affero General Public License v3.0
      •2•0•0•0•Updated Sep 14, 2022Sep 14, 2022

    • pathogenesis-gene-ontology

      Public
      An ontology for the functional annotation of genes and gene products involved in pathogenesis
      bioinformaticsontology
      bioinformaticsontology
      C++
      •1•1•36•0•Updated Mar 8, 2022Mar 8, 2022

    • basestack_consensus

      Public
      This repository is a Dockerized pipeline for creating consensus viral genomes from Oxford Nanopore data. This pipeline leverages the ARTIC Network bioinformatic…
      Shell
      •
      GNU General Public License v3.0
      •2•3•16•1•Updated Sep 1, 2021Sep 1, 2021

    • nCovIllumina

      Public
      Python
      •2•0•1•0•Updated Feb 20, 2021Feb 20, 2021
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