Repositories list

• GO-Compass

  Public
  Visual Navigation of Multiple Lists of GO terms

  JavaScript

  •0•4•6•7•Updated Mar 30, 2026Mar 30, 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•0•0•0•Updated Mar 27, 2026Mar 27, 2026

• phage_host_dual_transcriptomics

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Mar 27, 2026Mar 27, 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 Mar 26, 2026Mar 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

  •169•0•0•0•Updated Mar 26, 2026Mar 26, 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 Mar 18, 2026Mar 18, 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•0•Updated Mar 3, 2026Mar 3, 2026

• TrepoGen-auspice-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+ 1

  web-applicationproteomicsvisual-analyticspost-translational-modification

  HTML

  •

  GNU General Public License v3.0

  •1•6•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+ 2

  genomicssequence-alignmentvariant-annotationvariant-analysissequence-generation

  Java

  •

  GNU General Public License v3.0

  •1•5•0•0•Updated Dec 4, 2025Dec 4, 2025

• trustpca

  Public
  Python

  •

  GNU General Public License v3.0

  •0•2•0•0•Updated Nov 25, 2025Nov 25, 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

• 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 Sep 23, 2024Sep 23, 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

• rnaSeq-pipeline-rework

  Public
  Python

  •

  MIT License

  •1•1•0•0•Updated Apr 1, 2024Apr 1, 2024

• ClInt

  Public
  Nextflow

  •0•0•0•0•Updated Feb 16, 2024Feb 16, 2024

• FUNAGE-Pro-processing

  Public
  Python

  •0•0•0•0•Updated Jan 24, 2024Jan 24, 2024

• OmicsTIDE2.0

  Public
  Tool for the analysis of trends in multi-omics data

  JavaScript

  •1•3•2•0•Updated Jan 16, 2024Jan 16, 2024

• DamageProfiler

  Public
  A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage

  ngsdamageadna

  ngsdamageadna

  Java

  •

  GNU General Public License v3.0

  •3•18•11•0•Updated Nov 18, 2023Nov 18, 2023