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    117 repositories

    • MESOMICS_data

      Public
      Data and scripts associated with MESOMICS paper and data note
      R
      •
      GNU General Public License v3.0
      •2•3•1•0•Updated Jan 27, 2025Jan 27, 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

    • methylkey

      Public
      R
      •3•2•0•0•Updated Jan 10, 2025Jan 10, 2025

    • IARC-nf

      Public
      List of IARC bioinformatics nextflow pipelines
      bioinformaticspipelinenextflowcancerngs
      GNU General Public License v3.0
      •10•49•0•0•Updated Jan 9, 2025Jan 9, 2025

    • 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

    • medical_genomics_course

      Public
      Material for medical genomics course
      R
      •
      GNU General Public License v3.0
      •5•8•1•0•Updated Nov 27, 2024Nov 27, 2024

    • MS_panNEN_organoids

      Public
      Scripts used in panNEN organoids manuscript
      HTML
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Nov 6, 2024Nov 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
      ngsalignmentbwawhole-exome-sequencingwhole-genome-sequencingnextflowgatk
      Nextflow
      •
      GNU General Public License v3.0
      •14•28•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

    • 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 Jun 26, 2024Jun 26, 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

    • mutect-nf

      Public
      Mutect pipeline with Nextflow
      nextflowmutect
      Nextflow
      •
      GNU General Public License v3.0
      •7•9•0•0•Updated Apr 30, 2024Apr 30, 2024

    • purple-nf

      Public
      Nextflow pipeline for CNV calling with PURPLE
      Nextflow
      •
      MIT License
      •1•3•0•0•Updated Apr 29, 2024Apr 29, 2024

    • SComatic-nf

      Public
      Nextflow pipeline to run somatic alteration calling from single-cell data using SComatic
      Nextflow
      •
      GNU General Public License v3.0
      •1•1•4•0•Updated Apr 29, 2024Apr 29, 2024

    • gama_annot-nf

      Public
      Annotate VCF files with Annovar
      R
      •
      GNU General Public License v3.0
      •2•1•0•0•Updated Apr 25, 2024Apr 25, 2024

    • TCR-BCR-nf

      Public
      A nextflow pipeline to genotype Tcell and Bcell receptors from bulk or single-cell RNAseq data
      Nextflow
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 10, 2024Apr 10, 2024

    • hla-neo-nf

      Public
      Pipeline to make neonantigen prediction from WGS data
      Perl
      •1•1•0•0•Updated Apr 3, 2024Apr 3, 2024

    • DPclust-nf

      Public
      Nextflow workflow to run DPclust on a series of samples
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 10, 2024Mar 10, 2024

    • strelka2-nf

      Public
      Nextflow
      •
      GNU General Public License v3.0
      •4•4•1•0•Updated Feb 28, 2024Feb 28, 2024

    • SpatialPCAForWSIs

      Public
      R
      •0•1•0•0•Updated Feb 23, 2024Feb 23, 2024

    • DRMetrics

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Feb 19, 2024Feb 19, 2024

    • PathonetLNEN

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 12, 2024Jan 12, 2024

    • RNAseq-fusion-nf

      Public
      Fusion-genes discovery from RNAseq data using STAR-Fusion
      Nextflow
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jan 11, 2024Jan 11, 2024

    • TumorSegmentationCFlowAD

      Public
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•1•Updated Jan 4, 2024Jan 4, 2024

    • WSIPreprocessing

      Public
      The WSI pre-processing repository includes the patching process and the Vahadane colour normalisation method.
      Python
      •0•0•0•0•Updated Dec 16, 2023Dec 16, 2023