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    61 repositories

    • GO-Compass

      Public
      Visual analytics web tool for comparing multiple Gene Ontology (GO) term lists and reducing redundancy via semantic similarity clustering.
      JavaScript
      •1•4•3•2•Updated Oct 26, 2026Oct 26, 2026

    • TrepoGen-auspice

      Public
      Custom Auspice fork for visualizing global Treponema pallidum data with a focus on outer membrane proteins.
      JavaScript
      •
      GNU Affero General Public License v3.0
      •172•0•0•0•Updated Oct 23, 2026Oct 23, 2026

    • TrepoGen-nextstrain

      Public
      Nextstrain TrepoGen is a reproducible Nextstrain workflow for tracking bacterial diversity at both genome- and gene-level.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 22, 2026Oct 22, 2026

    • GO-Compass-Trrack

      Public
      Visual navigation of multiple lists of GO terms with Trrack.js for provenance tracking.
      JavaScript
      •1•1•0•0•Updated Oct 19, 2026Oct 19, 2026

    • deconv-bench-v2

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 13, 2026Oct 13, 2026

    • PhageGAP

      Public
      Interactive web application for functional annotation of bacteriophage proteins.
      web-serverprotein-function-predictionbiological-data-visualization
      web-serverprotein-function-predictionbiological-data-visualizationbacteriophagesprotein-language-model
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 29, 2026Sep 29, 2026

    • PhageGAP-model

      Public
      Training, testing and application of the ML model used for PhageGAP.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 29, 2026Sep 29, 2026

    • PhageExpressionAtlas

      Public
      PhageExpressionAtlas is a web application for interactive exploration of phage infections on the transcriptional level based on dual RNA-seq data.
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•Updated Aug 20, 2026Aug 20, 2026

    • Shiny_DESeq2

      Public
      R
      •0•1•6•0•Updated Aug 5, 2026Aug 5, 2026

    • trustpca

      Public
      Python
      •
      GNU General Public License v3.0
      •2•4•1•0•Updated Aug 5, 2026Aug 5, 2026

    • TSSpredator-Web

      Public
      TSSpredator-Web allows a web-based TSS predicition for prokaryotic data.
      JavaScript
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jul 16, 2026Jul 16, 2026

    • tss-captur-dsl2

      Public
      TSS-characterization pipeline for transcribed but unclassified RNA-transcripts
      HTML
      •
      GNU General Public License v3.0
      •2•2•0•0•Updated Jun 22, 2026Jun 22, 2026

    • PTMVision-Student

      Public
      Web application for the interactive visualization and exploration of post-translational modifications of proteins from open and closed search software.
      HTML
      •
      GNU General Public License v3.0
      •1•1•22•1•Updated May 5, 2026May 5, 2026

    • phage_host_dual_transcriptomics

      Public
      Jupyter Notebook
      •2•1•0•0•Updated Apr 29, 2026Apr 29, 2026

    • TrepoGen-docker

      Public
      Maintains the Dockerfile to run the custom TrepoGen auspice instance with the latest dataset.
      Dockerfile
      •0•0•0•0•Updated Feb 24, 2026Feb 24, 2026

    • PTMVision

      Public
      Web application for the interactive visualization and exploration of post-translational modifications of proteins from open and closed search software.
      web-applicationproteomicsvisual-analytics
      web-applicationproteomicsvisual-analyticspost-translational-modification
      HTML
      •
      GNU General Public License v3.0
      •1•7•0•0•Updated Feb 23, 2026Feb 23, 2026

    • Evidente2.0

      Public
      Go
      •1•1•27•1•Updated Feb 10, 2026Feb 10, 2026

    • MUSIAL

      Public
      Generate comprehensive statistics and alignments, and assess variability at the genome, gene and protein levels, based on VCF files produced from prokaryotic so…
      genomicssequence-alignmentvariant-annotation
      genomicssequence-alignmentvariant-annotationvariant-analysissequence-generation
      Java
      •
      GNU General Public License v3.0
      •1•5•0•0•Updated Dec 4, 2025Dec 4, 2025

    • tsne

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 13, 2025Nov 13, 2025

    • SID-Chart

      Public
      An automatic pipeline for the BGC characterization of genomes. Moreover, it should integrate further data layers, such as a phylogenetic tree and the similarity…
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 8, 2025Oct 8, 2025

    • StaphyDiversity

      Public
      Collection of script and data for the manuscript "A landscape of metallophore synthesis and uptake potential of the genus Staphylococcus"
      R
      •0•0•0•0•Updated Oct 1, 2025Oct 1, 2025

    • tuekitzmed-module

      Public
      JavaScript
      •0•0•0•0•Updated Aug 28, 2025Aug 28, 2025

    • VIPurPCA

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•1•0•Updated Jul 4, 2025Jul 4, 2025

    • MUSIAL-WEB

      Public archive
      ⚠️ This repository is deprecated and was archived, please see: https://github.com/Integrative-Transcriptomics/MUSIAL
      JavaScript
      •0•0•0•0•Updated Jun 17, 2025Jun 17, 2025

    • phagomics

      Public
      Nextflow
      •0•0•0•0•Updated May 21, 2025May 21, 2025

    • preserve-nextflow

      Public
      A repository for the Nextflow Pipeline that optimally predicts the structure of proteins and searches for structural homologs either within a set of references …
      Nextflow
      •1•1•0•0•Updated May 16, 2025May 16, 2025

    • lipo-search

      Public
      A repository for the Nextflow Pipeline that optimally predicts the structure of Lipoproteins and searches for structural homologs within a set of lipoprotein re…
      MIT License
      •1•0•0•0•Updated Nov 19, 2024Nov 19, 2024

    • tss-captur-dsl2-with-RNAseq

      Public
      TSS-characterization pipeline for transcribed but unclassified RNA-transcripts
      HTML
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Sep 24, 2024Sep 24, 2024

    • manual

      Public
      HTML
      •0•0•0•0•Updated Sep 10, 2024Sep 10, 2024

    • tss-prediction-comparison

      Public
      This repository includes the tool for the prediction, comparison and visualization of TSS predicted using RNAseq. The results are then compared to provide an ov…
      Jupyter Notebook
      •0•3•14•0•Updated Aug 31, 2024Aug 31, 2024
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