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    23 repositories

    • mrcepid-makebgen

      Public
      RAP platform turns a bcf into a bgen
      Python
      •
      MIT License
      •0•0•1•1•Updated Oct 22, 2024Oct 22, 2024

    • mrcepid-filterbcf

      Public
      Filter VCF/BCF according to MRCEpid parameters
      Python
      •
      MIT License
      •0•0•1•1•Updated Oct 18, 2024Oct 18, 2024

    • mrcepid-collapsevariants

      Public
      Python
      •
      MIT License
      •1•0•1•0•Updated Oct 18, 2024Oct 18, 2024

    • mrcepid-bcfsplitter

      Public
      Python
      •
      MIT License
      •0•0•1•0•Updated Aug 2, 2024Aug 2, 2024

    • mrcepid-runassociationtesting

      Public
      Interface for Association Tests on the UKB Research Access Platform
      Python
      •
      MIT License
      •2•7•1•0•Updated Jun 10, 2024Jun 10, 2024

    • general_utilities

      Public
      General Utilities for the RAP
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 10, 2024Jun 10, 2024

    • burden

      Public
      Burden module for mrcepid-runassociationtesting
      Python
      •
      MIT License
      •0•1•0•0•Updated May 22, 2024May 22, 2024

    • dockerimages

      Public
      Docker images to provide resourses to RAP applets
      Dockerfile
      •
      MIT License
      •1•1•0•0•Updated May 20, 2024May 20, 2024

    • phewas

      Public
      PheWAS module for mrcepid-runassociationtesting
      Python
      •
      MIT License
      •0•0•0•0•Updated May 16, 2024May 16, 2024

    • mrcepid-testing

      Public
      Testing utilities for the MRCEpid UKB RAP Pipeline
      Python
      •
      MIT License
      •0•0•0•0•Updated May 10, 2024May 10, 2024

    • extract

      Public
      Extract module for mrcepid-runassociationtesting
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 26, 2024Apr 26, 2024

    • QC_workflow_WGS

      Public
      Quality control of UKBB Whole Genome Sequencing
      Python
      •0•0•0•0•Updated Apr 10, 2024Apr 10, 2024

    • QC_workflow

      Public
      Example command lines for QC and burden testing
      HTML
      •0•1•0•0•Updated Nov 20, 2023Nov 20, 2023

    • mrcepid-test_loader

      Public archive
      A small applet for module import testing
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 18, 2023Aug 18, 2023

    • hg.r.utils

      Public
      R utilities for analysing associationtesting results
      R
      •0•0•0•0•Updated Aug 17, 2023Aug 17, 2023

    • mrcepid-buildgrms

      Public
      Do genotype QC and build GRMs
      Python
      •
      MIT License
      •0•1•0•0•Updated Apr 5, 2023Apr 5, 2023

    • mrcepid-lolliplotmaker

      Public
      R
      •0•0•0•0•Updated Mar 21, 2023Mar 21, 2023

    • .github

      Public
      1•0•0•0•Updated Aug 16, 2022Aug 16, 2022

    • mrcepid-annotatecadd

      Public archive
      Annotate VCFs with CADD
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 20, 2022Jun 20, 2022

    • mrcepid-extractvariants

      Public archive
      Extract individual level data from the RAP
      Python
      •0•0•0•0•Updated Mar 18, 2022Mar 18, 2022

    • mrcepid-mergecollapsevariants

      Public archive
      Merge variants from mrcepid-collapsevariants
      Python
      •0•0•0•0•Updated Feb 14, 2022Feb 14, 2022

    • mrcepid-collecthsmetrics

      Public
      Count mean coverage in cram files
      Python
      •1•0•0•0•Updated Jan 25, 2022Jan 25, 2022

    • mrcepid_raptutorial

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jan 25, 2022Jan 25, 2022