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    146 repositories

    • Dx_resources

      Public
      Resources used in diagnostics pipelines
      Python
      •
      MIT License
      •0•3•15•3•Updated Mar 6, 2025Mar 6, 2025

    • Epi2Me_wf-human-variation

      Public
      Nextflow
      •
      Other
      •57•0•0•1•Updated Mar 5, 2025Mar 5, 2025

    • CustomModules

      Public
      R
      •
      MIT License
      •0•1•0•2•Updated Mar 4, 2025Mar 4, 2025

    • clarity_epp

      Public
      Clarity LIMS epp scripts
      Python
      •
      MIT License
      •0•1•0•0•Updated Mar 4, 2025Mar 4, 2025

    • Dx_tracks

      Public
      Verilog
      •
      Other
      •0•2•2•0•Updated Mar 3, 2025Mar 3, 2025

    • DxNextflowRNA

      Public
      R
      •0•0•0•4•Updated Mar 3, 2025Mar 3, 2025

    • GIABEval

      Public
      Genome-in-a-bottle evaluation tool to determine statistics
      Nextflow
      •
      MIT License
      •0•1•0•1•Updated Feb 28, 2025Feb 28, 2025

    • DIMS

      Public
      Direct Infusion Mass Spectrometry pipeline
      Nextflow
      •
      MIT License
      •2•2•11•1•Updated Feb 26, 2025Feb 26, 2025

    • DxNextflowWES

      Public
      Genome Diagnostics Nextflow WES workflow
      Nextflow
      •
      MIT License
      •1•6•6•0•Updated Feb 25, 2025Feb 25, 2025

    • USEQ_tools

      Public
      Utility scripts to work with Genologics Clarity LIMS
      Python
      •
      MIT License
      •0•2•0•2•Updated Feb 17, 2025Feb 17, 2025

    • AdvancedBioinformaticsCourse

      Public
      Creative Commons Zero v1.0 Universal
      •0•4•0•0•Updated Feb 16, 2025Feb 16, 2025

    • cuplr

      Public
      Predicting tumor type using WGS derived features
      R
      •
      GNU General Public License v3.0
      •2•5•1•0•Updated Feb 13, 2025Feb 13, 2025

    • mutSigExtractor

      Public
      An R package for extracting mutational signatures from vcf files
      R
      •
      GNU General Public License v3.0
      •6•10•4•0•Updated Feb 13, 2025Feb 13, 2025

    • CHORD

      Public
      An R package for predicting HR deficiency from mutation contexts
      R
      •
      GNU General Public License v3.0
      •7•28•3•0•Updated Feb 13, 2025Feb 13, 2025

    • hpcguix-web

      Public
      The code that drives https://hpc.guix.info/browse.
      JavaScript
      •
      GNU Affero General Public License v3.0
      •3•11•2•0•Updated Feb 10, 2025Feb 10, 2025

    • rsync_to_rdisc

      Public
      Daemon to rsync data from HPC to bgarray
      Python
      •
      MIT License
      •0•0•0•1•Updated Feb 7, 2025Feb 7, 2025

    • aptaflow_useq

      Public
      Modified apaflow pipeline for useq output and umcu hpc
      Nextflow
      •3•0•0•0•Updated Feb 4, 2025Feb 4, 2025

    • pypgx

      Public
      A Python package for pharmacogenomics (PGx) research
      Python
      •
      MIT License
      •16•0•0•0•Updated Feb 3, 2025Feb 3, 2025

    • ManuscriptSMNGeneConversion

      Public
      Scripts and files related to the SMN gene conversion manuscript
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 31, 2025Jan 31, 2025

    • HapSMA

      Public
      Nextflow Oxford Nanopore Technologies workflow for SMA dataprocessing
      Nextflow
      •
      MIT License
      •0•0•1•0•Updated Jan 31, 2025Jan 31, 2025

    • ExonCov

      Public
      ExonCov: Exon coverage statistics from BAM files
      Python
      •
      MIT License
      •3•4•4•4•Updated Jan 30, 2025Jan 30, 2025

    • DIMSdb

      Public
      database for Direct Infusion Mass Spectrometry pipeline
      MIT License
      •0•0•0•0•Updated Jan 24, 2025Jan 24, 2025

    • NextflowModules

      Public
      UMCU Genetics Nextflow modules
      Nextflow
      •
      MIT License
      •10•28•0•2•Updated Oct 25, 2024Oct 25, 2024

    • rnaseq-voila

      Public
      Jupyter Notebook / Voila App for analysis and filtering of RNA-Seq data for clinical genetics diagnostics
      Jupyter Notebook
      •
      MIT License
      •2•0•0•0•Updated Sep 4, 2024Sep 4, 2024

    • NanoRCS

      Public
      NanoRCS: Multimodal genome-wide cfDNA sequencing and analysis
      Python
      •
      GNU General Public License v3.0
      •3•0•0•0•Updated Aug 30, 2024Aug 30, 2024

    • alissa_interpret_client

      Public
      Alissa Interpret Public API Client
      Python
      •
      MIT License
      •0•0•0•1•Updated Jul 2, 2024Jul 2, 2024

    • clarity_portal

      Public
      Clarity LIMS portal app
      Python
      •
      MIT License
      •0•0•1•0•Updated Jul 2, 2024Jul 2, 2024

    • DIMSpect_GUI

      Public
      0•0•0•0•Updated Jul 1, 2024Jul 1, 2024

    • franklin_client

      Public
      Python package for Franklin API
      MIT License
      •0•0•0•0•Updated Jun 21, 2024Jun 21, 2024

    • DxNextflowWGS

      Public
      Genome Diagnostics Nextflow WGS workflow
      Nextflow
      •
      MIT License
      •0•0•2•0•Updated Jun 11, 2024Jun 11, 2024