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@lumc-pgx Leiden University Medical Center: Pharmacogenomics tools and methods

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    14 repositories

    • pharmvar-tools

      Public
      Python
      •
      MIT License
      •1•0•1•0•Updated Jan 10, 2024Jan 10, 2024

    • variant-tools

      Public
      Tools for working with variants. Includes simple variant calling and comparison.
      Python
      •
      MIT License
      •0•0•0•1•Updated Jun 21, 2022Jun 21, 2022

    • pgx-pipe

      Public
      Pharmacogenomics pipeline of long amplicon sequences
      Python
      •
      MIT License
      •0•1•0•0•Updated May 25, 2021May 25, 2021

    • variant_effects

      Public
      Pipeline module for predicting the effect of variants using ensembl VEP
      Python
      •1•0•0•0•Updated Feb 23, 2020Feb 23, 2020

    • structural_variation

      Public
      Pipeline module for the identification of structural variants
      Python
      •0•0•0•0•Updated Feb 23, 2020Feb 23, 2020

    • haplotyping

      Public
      Pipeline module for haplotype/diplotype determination
      Jupyter Notebook
      •0•0•0•0•Updated Feb 23, 2020Feb 23, 2020

    • locus-processing

      Public
      Methods and tools for processing locus definition files used by the PGx pipeline.
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 22, 2019Aug 22, 2019

    • variant-calling

      Public
      Normalized variant calling module for the PGx pipeline
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 22, 2019Aug 22, 2019

    • phasing

      Public
      Pipeline stage for creating phased allele sequences from demultiplexed PacBio amplicon data
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 22, 2019Aug 22, 2019

    • preprocessor

      Public
      Barcoding, demultiplexing and CCS generation from raw PacBio sequencing data.
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 21, 2019Aug 21, 2019

    • pipe-runner

      Public
      Very simple helper for invoking snakemake workflows with sensible parameters for use on the LUMC SGE Shark cluster
      Python
      •
      MIT License
      •1•0•0•0•Updated Aug 15, 2019Aug 15, 2019

    • pipe-helper

      Public
      Utility module to provide consistent handling of barcodes and loci by the PGx pipeline stages.
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 15, 2019Aug 15, 2019

    • CCS-Amplicon

      Public
      Create polished, phased allele sequences from PacBio amplicon data.
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 8, 2019Aug 8, 2019

    • gene-viz

      Public
      Interactive visualization of gene structure
      Python
      •
      MIT License
      •0•1•0•0•Updated Jul 23, 2019Jul 23, 2019