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@lumc-pgx

Leiden University Medical Center: Pharmacogenomics tools and methods

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  1. gene-viz gene-viz Public

    Interactive visualization of gene structure

    Python 1

  2. pgx-pipe pgx-pipe Public

    Pharmacogenomics pipeline of long amplicon sequences

    Python 1

  3. variant-tools variant-tools Public

    Tools for working with variants. Includes simple variant calling and comparison.

    Python

  4. locus-processing locus-processing Public

    Methods and tools for processing locus definition files used by the PGx pipeline.

    Python

  5. CCS-Amplicon CCS-Amplicon Public

    Create polished, phased allele sequences from PacBio amplicon data.

    Python

  6. pipe-helper pipe-helper Public

    Utility module to provide consistent handling of barcodes and loci by the PGx pipeline stages.

    Python

Repositories

Showing 10 of 14 repositories
  • pharmvar-tools Public
    lumc-pgx/pharmvar-tools’s past year of commit activity
    Python 0 MIT 1 1 0 Updated Jan 10, 2024
  • variant-tools Public

    Tools for working with variants. Includes simple variant calling and comparison.

    lumc-pgx/variant-tools’s past year of commit activity
    Python 0 MIT 0 0 1 Updated Jun 21, 2022
  • pgx-pipe Public

    Pharmacogenomics pipeline of long amplicon sequences

    lumc-pgx/pgx-pipe’s past year of commit activity
    Python 1 MIT 0 0 0 Updated May 25, 2021
  • variant_effects Public

    Pipeline module for predicting the effect of variants using ensembl VEP

    lumc-pgx/variant_effects’s past year of commit activity
    Python 0 1 0 0 Updated Feb 23, 2020
  • structural_variation Public

    Pipeline module for the identification of structural variants

    lumc-pgx/structural_variation’s past year of commit activity
    Python 0 0 0 0 Updated Feb 23, 2020
  • haplotyping Public

    Pipeline module for haplotype/diplotype determination

    lumc-pgx/haplotyping’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Feb 23, 2020
  • locus-processing Public

    Methods and tools for processing locus definition files used by the PGx pipeline.

    lumc-pgx/locus-processing’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Aug 22, 2019
  • variant-calling Public

    Normalized variant calling module for the PGx pipeline

    lumc-pgx/variant-calling’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Aug 22, 2019
  • phasing Public

    Pipeline stage for creating phased allele sequences from demultiplexed PacBio amplicon data

    lumc-pgx/phasing’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Aug 22, 2019
  • preprocessor Public

    Barcoding, demultiplexing and CCS generation from raw PacBio sequencing data.

    lumc-pgx/preprocessor’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Aug 21, 2019
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