Skip to content

@clinical-genomics-uppsala Clinical Genomics Uppsala

Change the repository type filter

All

    Repositories list

    55 repositories

    • GMS560_config

      Public
      A repository for storing Uppsala specific configurations of the pipeline in production
      0•0•0•3•Updated Nov 19, 2024Nov 19, 2024

    • fluffy_hematology_wgs

      Public
      Snakemake workflow to analyse hematological malignancies in whole genome data
      Python
      •
      GNU General Public License v3.0
      •1•0•1•3•Updated Nov 19, 2024Nov 19, 2024

    • validation_workflow

      Public
      workflow written in nextflow that will validate a list of files generated by hydra-genetics pipelines
      Nextflow
      •0•1•0•0•Updated Nov 15, 2024Nov 15, 2024

    • ductus-packs

      Public
      Python
      •1•0•6•1•Updated Nov 4, 2024Nov 4, 2024

    • poirot_config

      Public
      A repository for storing Uppsala specific configurations of the Poirot pipeline in production
      0•0•0•0•Updated Oct 24, 2024Oct 24, 2024

    • hastings_rd_wes

      Public
      Whole exome sequencing pipeline for inherited diseases
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 14, 2024Oct 14, 2024

    • poirot_rd_wgs

      Public
      Clinical Genomics Uppsala inheritance disease pipeline for WGS
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 14, 2024Oct 14, 2024

    • Geneious_metabarcoding

      Public
      Geneious workflow with Emu plugin to classify 16S amplicons
      HTML
      •0•0•0•0•Updated Sep 17, 2024Sep 17, 2024

    • pomfrey

      Public
      Python
      •
      GNU General Public License v3.0
      •2•0•4•0•Updated Sep 17, 2024Sep 17, 2024

    • poppy_uppsala

      Public
      Add-on and config for Poppy running Twist Myeloid panel
      GNU General Public License v3.0
      •0•0•0•1•Updated Sep 16, 2024Sep 16, 2024

    • SERA

      Public
      Perl
      •3•0•1•1•Updated Sep 2, 2024Sep 2, 2024

    • NIPTviewer

      Public
      Python
      •
      MIT License
      •0•0•4•1•Updated Aug 28, 2024Aug 28, 2024

    • pickett_bcr_abl_pipeline

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 23, 2024Aug 23, 2024

    • ductus_frontend_app

      Public
      Vue
      •0•0•0•0•Updated Jul 14, 2024Jul 14, 2024

    • ductus-core

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•5•0•Updated Jul 2, 2024Jul 2, 2024

    • marple_rd_tc

      Public
      Twist Cancer hydragenetics pipeline for HG38
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 4, 2024Jun 4, 2024

    • PrecMed1

      Public
      Precision Medicine course 1
      Python
      •0•0•1•0•Updated Mar 6, 2024Mar 6, 2024

    • ductus-analysis-upload-service

      Public
      simple service used to monitor a folder for new files and upload them using a rest api
      0•0•0•0•Updated Dec 14, 2023Dec 14, 2023

    • Geneious_SARS-CoV-2

      Public
      Geneious workflow for SARS-CoV-2 genome assembly
      0•1•0•0•Updated Dec 7, 2023Dec 7, 2023

    • Geneious_Nextclade_wrapper

      Public
      Geneious wrapper plugin with Nextclade for clade assignment, mutations calling and quality checks of SARS-CoV-2 genomes
      Python
      •0•0•0•0•Updated Dec 5, 2023Dec 5, 2023

    • Geneious_pangolin_wrapper

      Public
      Geneious wrapper plugin for Pangolin to assign pango lineages to SARS-CoV-2 genomes
      Python
      •0•1•0•0•Updated Dec 5, 2023Dec 5, 2023

    • ductus-clean-packs

      Public
      Stackstorm package used to remove folders after analysis and delivery has been performed
      0•0•0•0•Updated Sep 4, 2023Sep 4, 2023

    • arteria-bclconvert

      Public
      Python
      •
      MIT License
      •0•0•1•0•Updated Jun 19, 2023Jun 19, 2023

    • wgs_leukemia_tumor_only_konigskobra

      Public archive
      Snakemake workflow to analyse hematological malignancies in whole genome data
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jan 31, 2023Jan 31, 2023

    • TSO500_Marvin

      Public
      Python
      •0•0•0•0•Updated Dec 12, 2022Dec 12, 2022

    • arteria-packs

      Public
      StackStorm packs to automate sequencing center operations
      Python
      •
      MIT License
      •19•0•0•0•Updated Oct 5, 2022Oct 5, 2022

    • twist_exome_38

      Public
      Python
      •
      GNU General Public License v3.0
      •3•0•0•0•Updated Sep 23, 2022Sep 23, 2022

    • wts_leukemia_konigskobra

      Public archive
      Snakemake/Hydra workflow to analyse RNASeq data
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 20, 2022Sep 20, 2022

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •3.3k•0•0•0•Updated Aug 22, 2022Aug 22, 2022

    • Twist_RNA

      Public
      Python
      •3•0•0•0•Updated May 9, 2022May 9, 2022