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    73 repositories

    • AILMENT_ML_GUT

      Public
      ML framework for metatranscriptomics and metagenomics for species and tumour traits
      Jupyter Notebook
      •0•0•0•0•Updated Jun 27, 2025Jun 27, 2025

    • src-component-pulsar

      Public
      SRC Pulsar Component
      HTML
      •
      GNU Lesser General Public License v2.1
      •1•1•0•1•Updated May 13, 2025May 13, 2025

    • nextNEOpi

      Public
      nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
      Nextflow
      •
      Other
      •25•0•0•0•Updated Apr 14, 2025Apr 14, 2025

    • molclass

      Public
      Moleculair classification tool, search for a variant and get results from many sources
      Python
      •1•1•0•0•Updated Apr 2, 2025Apr 2, 2025

    • geneyx.analysis.api

      Public
      Geneyx Analysis API
      Python
      •7•0•0•0•Updated Mar 26, 2025Mar 26, 2025

    • AMR-Pathfinder

      Public
      SCSS
      •
      Creative Commons Zero v1.0 Universal
      •1•0•0•0•Updated Feb 18, 2025Feb 18, 2025

    • EMC-MetaMicrobes

      Public
      Nextflow pipeline to detect and classify microbial reads in sequencing data from human samples.
      bioinformatics-pipelinemetatranscriptomicsnextflow-pipelinemicrobiome-analysis-pipelines
      Nextflow
      •
      MIT License
      •2•3•1•0•Updated Dec 12, 2024Dec 12, 2024

    • SuReCAN

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Dec 1, 2024Dec 1, 2024

    • infrastructure

      Public
      Jinja
      •1•0•1•0•Updated Oct 22, 2024Oct 22, 2024

    • musica

      Public
      MuSiCa - Mutational Signatures in Cancer
      R
      •
      MIT License
      •13•0•0•0•Updated Sep 26, 2024Sep 26, 2024

    • DL_LCNEC_pRBsubtyping_HE

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Sep 26, 2024Sep 26, 2024

    • two-step-TL

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Sep 16, 2024Sep 16, 2024

    • BenchAMRking-scripts

      Public
      Code for figures
      Python
      •0•1•0•0•Updated Sep 13, 2024Sep 13, 2024

    • benchAMRking

      Public
      SCSS
      •
      Creative Commons Zero v1.0 Universal
      •1•3•0•0•Updated Sep 5, 2024Sep 5, 2024

    • transferlearningproject

      Public
      Python
      •0•0•0•0•Updated Sep 3, 2024Sep 3, 2024

    • EMC-Neoantigen

      Public
      nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
      Nextflow
      •
      Other
      •25•0•0•0•Updated Sep 2, 2024Sep 2, 2024

    • TME_Analyzer

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 26, 2024Jul 26, 2024

    • EMC-MetaMicrobes_old

      Public
      Nextflow pipeline to detect and classify microbial reads in sequencing data from human samples.
      Nextflow
      •
      MIT License
      •2•0•0•0•Updated Jul 9, 2024Jul 9, 2024

    • reconCNV

      Public
      visualize CNV data from targeted capture based sequencing data
      Python
      •
      GNU General Public License v3.0
      •10•0•0•0•Updated Jun 14, 2024Jun 14, 2024

    • shm_csr

      Public
      Somatic hypermutation and class switch recombination pipeline
      R
      •
      MIT License
      •2•1•0•0•Updated Jan 10, 2024Jan 10, 2024

    • SigMA

      Public
      Mutational signature analysis for low statistics SNV data
      R
      •
      Other
      •21•0•0•0•Updated Nov 29, 2023Nov 29, 2023

    • HPV-EM

      Public
      HPV-EM is an HPV genotyping tool that utilizes an expectation maximization algorithm to identify the presence of HPV genotypes in a sample from RNA-seq data
      Python
      •5•0•0•0•Updated Sep 21, 2023Sep 21, 2023

    • OrganoTrack

      Public
      Image analysis pipeline of organoid images
      Python
      •0•0•0•0•Updated Aug 28, 2023Aug 28, 2023

    • MasterProjectAI_Daria-

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Jul 14, 2023Jul 14, 2023

    • TOSCA

      Public
      Snakemake workflow for somatic mutation detection without matched normal samples
      Python
      •
      MIT License
      •2•0•0•0•Updated Jun 15, 2023Jun 15, 2023

    • installed-tools

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated May 9, 2023May 9, 2023

    • tmz-analysis

      Public
      Bioinformatics analysis of the tmz paper
      R
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated May 5, 2023May 5, 2023

    • galaxy

      Public
      Data intensive science for everyone.
      Python
      •
      Other
      •1.1k•0•0•0•Updated Jan 31, 2023Jan 31, 2023

    • erasmusmc-bioinformatics.github.io

      Public
      ErasmusMC Bioinformatics Landing Page
      HTML
      •
      MIT License
      •1•0•4•9•Updated Jan 27, 2023Jan 27, 2023

    • iobio_containers

      Public
      Clin.iobio and gene.iobio dockerized.
      JavaScript
      •0•1•0•0•Updated Jan 26, 2023Jan 26, 2023