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    • BQSR-nf

      Public
      Nextflow script for base quality score recalibration of bam files using GATK
      Nextflow
      1020Updated Jan 27, 2026Jan 27, 2026
    • abra-nf

      Public
      Nextflow pipeline for ABRA (Assembly Based ReAligner)
      Nextflow
      3430Updated Jan 8, 2026Jan 8, 2026
    • Transcript-level RNA-seq analysis
      HTML
      2010Updated Jan 8, 2026Jan 8, 2026
    • Fusion-genes discovery from RNAseq data using STAR-Fusion
      Nextflow
      1010Updated Jan 8, 2026Jan 8, 2026
    • methylkey

      Public
      R
      3200Updated Jan 8, 2026Jan 8, 2026
    • Pipeline to run software quanTIseq in parallel to quantify immune cell content from RNA-seq data
      Shell
      1000Updated Jan 8, 2026Jan 8, 2026
    • RNAseq-nf

      Public
      RNAseq analysis pipeline
      HTML
      102740Updated Jan 7, 2026Jan 7, 2026
    • pavoa-nf

      Public
      Pipeline for variant detection. Preprocessing Alignment, Variant calling, Optimization, Annotation
      Nextflow
      0200Updated Jan 6, 2026Jan 6, 2026
    • Material for medical genomics course
      Jupyter Notebook
      6810Updated Nov 28, 2025Nov 28, 2025
    • IARC-nf

      Public
      List of IARC bioinformatics pipelines and resources
      105600Updated Nov 24, 2025Nov 24, 2025
    • mutect-nf

      Public
      Mutect pipeline with Nextflow
      Nextflow
      7900Updated Sep 22, 2025Sep 22, 2025
    • Repository with scripts from the lungNENomics manuscript
      HTML
      1000Updated Sep 10, 2025Sep 10, 2025
    • MESOMICS

      Public
      HTML
      0000Updated Aug 29, 2025Aug 29, 2025
    • Scripts used in panNEN organoids manuscript
      HTML
      0200Updated Aug 1, 2025Aug 1, 2025
    • Nextflow pipeline to perform RNA splicing analyses with SUPPA2
      Nextflow
      0000Updated Apr 10, 2025Apr 10, 2025
    • Annotate VCF files with Annovar
      R
      2100Updated Apr 1, 2025Apr 1, 2025
    • MS_SVA

      Public
      Repository with code used to produce the figures from Morrison et al. doi.org/10.1101/2023.11.23.23298821
      HTML
      0000Updated Mar 3, 2025Mar 3, 2025
    • Data and scripts associated with MESOMICS paper and data note
      R
      2410Updated Feb 24, 2025Feb 24, 2025
    • Nextflow pipeline to run somatic alteration calling from single-cell data using SComatic
      Nextflow
      2340Updated Feb 17, 2025Feb 17, 2025
    • Python scripts for MESOMICS2 single-cell analyses
      Jupyter Notebook
      0000Updated Jan 10, 2025Jan 10, 2025
    • R
      0000Updated Dec 12, 2024Dec 12, 2024
    • Jupyter Notebook
      0000Updated Dec 7, 2024Dec 7, 2024
    • Jupyter Notebook
      0000Updated Dec 6, 2024Dec 6, 2024
    • Nextflow pipeline for peaks calling with MACS
      Nextflow
      0000Updated Oct 7, 2024Oct 7, 2024
    • Whole Exome/Whole Genome Sequencing alignment pipeline
      Nextflow
      142960Updated Sep 18, 2024Sep 18, 2024
    • A nextflow pipeline to call somatic gene fusions
      Nextflow
      1101Updated Jul 12, 2024Jul 12, 2024
    • 0000Updated Jul 10, 2024Jul 10, 2024
    • numbat-nf

      Public
      Nextflow pipeline to run the numbat somatic copy number variant detection method on single-cell or spatial transcriptomics data
      HTML
      0000Updated Jun 24, 2024Jun 24, 2024
    • Nextflow pipeline to perform metagenomic analyses from next-generation sequencing data
      Nextflow
      0000Updated May 7, 2024May 7, 2024
    • A repository to convert BAM->CRAM files
      Nextflow
      1001Updated May 1, 2024May 1, 2024