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    121 repositories

    • BQSR-nf

      Public
      Nextflow script for base quality score recalibration of bam files using GATK
      Nextflow
      •
      GNU General Public License v3.0
      •1•0•2•0•Updated Jan 27, 2026Jan 27, 2026

    • abra-nf

      Public
      Nextflow pipeline for ABRA (Assembly Based ReAligner)
      pipelinenextflowassemblyngsalignment
      Nextflow
      •
      GNU General Public License v3.0
      •3•4•3•0•Updated Jan 8, 2026Jan 8, 2026

    • RNAseq-transcript-nf

      Public
      Transcript-level RNA-seq analysis
      HTML
      •
      GNU General Public License v3.0
      •2•0•1•0•Updated Jan 8, 2026Jan 8, 2026

    • RNAseq-fusion-nf

      Public
      Fusion-genes discovery from RNAseq data using STAR-Fusion
      Nextflow
      •
      GNU General Public License v3.0
      •1•0•1•0•Updated Jan 8, 2026Jan 8, 2026

    • methylkey

      Public
      R
      •3•2•0•0•Updated Jan 8, 2026Jan 8, 2026

    • quantiseq-nf

      Public
      Pipeline to run software quanTIseq in parallel to quantify immune cell content from RNA-seq data
      Shell
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jan 8, 2026Jan 8, 2026

    • RNAseq-nf

      Public
      RNAseq analysis pipeline
      rna-seqpipelinenextflowngs
      HTML
      •
      GNU General Public License v3.0
      •10•27•4•0•Updated Jan 7, 2026Jan 7, 2026

    • pavoa-nf

      Public
      Pipeline for variant detection. Preprocessing Alignment, Variant calling, Optimization, Annotation
      Nextflow
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Jan 6, 2026Jan 6, 2026

    • medical_genomics_course

      Public
      Material for medical genomics course
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •6•8•1•0•Updated Nov 28, 2025Nov 28, 2025

    • IARC-nf

      Public
      List of IARC bioinformatics pipelines and resources
      bioinformaticspipelinenextflowcancerngs
      GNU General Public License v3.0
      •10•56•0•0•Updated Nov 24, 2025Nov 24, 2025

    • mutect-nf

      Public
      Mutect pipeline with Nextflow
      nextflowmutect
      Nextflow
      •
      GNU General Public License v3.0
      •7•9•0•0•Updated Sep 22, 2025Sep 22, 2025

    • MS_lungNENomics

      Public
      Repository with scripts from the lungNENomics manuscript
      HTML
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Sep 10, 2025Sep 10, 2025

    • MESOMICS

      Public
      HTML
      •0•0•0•0•Updated Aug 29, 2025Aug 29, 2025

    • MS_panNEN_organoids

      Public
      Scripts used in panNEN organoids manuscript
      HTML
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Aug 1, 2025Aug 1, 2025

    • RNAsplicing-nf

      Public
      Nextflow pipeline to perform RNA splicing analyses with SUPPA2
      Nextflow
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 10, 2025Apr 10, 2025

    • gama_annot-nf

      Public
      Annotate VCF files with Annovar
      R
      •
      GNU General Public License v3.0
      •2•1•0•0•Updated 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
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 3, 2025Mar 3, 2025

    • MESOMICS_data

      Public
      Data and scripts associated with MESOMICS paper and data note
      R
      •
      GNU General Public License v3.0
      •2•4•1•0•Updated Feb 24, 2025Feb 24, 2025

    • SComatic-nf

      Public
      Nextflow pipeline to run somatic alteration calling from single-cell data using SComatic
      Nextflow
      •
      GNU General Public License v3.0
      •2•3•4•0•Updated Feb 17, 2025Feb 17, 2025

    • singlecell_scripts

      Public
      Python scripts for MESOMICS2 single-cell analyses
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 10, 2025Jan 10, 2025

    • MS-EPIC-RareCancers

      Public
      R
      •0•0•0•0•Updated Dec 12, 2024Dec 12, 2024

    • LNENBarlowTwins

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Dec 7, 2024Dec 7, 2024

    • LeidenForTilesCommunity_accGPU

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Dec 6, 2024Dec 6, 2024

    • bam2peaks-nf

      Public
      Nextflow pipeline for peaks calling with MACS
      Nextflow
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 7, 2024Oct 7, 2024

    • alignment-nf

      Public
      Whole Exome/Whole Genome Sequencing alignment pipeline
      nextflowngsgatkalignmentbwawhole-exome-sequencingwhole-genome-sequencing
      Nextflow
      •
      GNU General Public License v3.0
      •14•29•6•0•Updated Sep 18, 2024Sep 18, 2024

    • gene-fusions-nf

      Public
      A nextflow pipeline to call somatic gene fusions
      Nextflow
      •
      MIT License
      •1•1•0•1•Updated Jul 12, 2024Jul 12, 2024

    • ESMOOpen_LungNENomicsCohort

      Public
      0•0•0•0•Updated 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
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 24, 2024Jun 24, 2024

    • metagenomics-nf

      Public
      Nextflow pipeline to perform metagenomic analyses from next-generation sequencing data
      Nextflow
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 7, 2024May 7, 2024

    • bam2cram-nf

      Public
      A repository to convert BAM->CRAM files
      Nextflow
      •
      MIT License
      •1•0•0•1•Updated May 1, 2024May 1, 2024