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    22 repositories

    • BCalm_experiments

      Public
      Repository containing the scripts for the experiments described in the BCalm manuscript.
      R
      •0•0•0•0•Updated Jan 17, 2025Jan 17, 2025

    • kircherlab.github.io

      Public
      Kircher Lab website
      HTML
      •0•1•0•0•Updated Jan 17, 2025Jan 17, 2025

    • MPRAsnakeflow

      Public
      With this snakemake pipeline you can process your MPRA sequencing data (assignment and count). It is the standard MPRA pipeline of the IGVF consortium and a further development of MPRAflow.
      Python
      •
      MIT License
      •5•4•7•2•Updated Jan 16, 2025Jan 16, 2025

    • cfDNA_GCcorrection

      Public
      Python
      •
      Other
      •1•4•1•0•Updated Jan 8, 2025Jan 8, 2025

    • BCalm

      Public
      HTML
      •
      MIT License
      •0•0•0•0•Updated Dec 19, 2024Dec 19, 2024

    • CADD-SV

      Public
      CADD-SV – a framework to score the effect of structural variants
      svvariant-annotationsvariant-effect-prediction
      Python
      •
      MIT License
      •3•14•3•0•Updated Dec 11, 2024Dec 11, 2024

    • CADD-scripts

      Public
      CADD scripts release for offline scoring. For more information about CADD, please visit our website
      Python
      •
      Other
      •33•75•9•3•Updated Dec 2, 2024Dec 2, 2024

    • cfDNA-UniFlow

      Public template
      Workflow for preprocessing cfDNA samples.
      Jupyter Notebook
      •
      MIT License
      •0•4•2•0•Updated Nov 11, 2024Nov 11, 2024

    • CADD-browserTracks

      Public
      UCSC genome browser tracks for CADD
      HTML
      •
      Other
      •0•1•0•0•Updated Nov 6, 2024Nov 6, 2024

    • IGVF_MPRA_seqspec_generator

      Public
      This little helper usues jinja2 and igvf_utils to generate seqspec files for mpra count and association data.
      Python
      •1•0•0•0•Updated Oct 30, 2024Oct 30, 2024

    • MPRAsnakeflow_tutorial

      Public
      Jupyter Notebook
      •0•0•1•0•Updated Sep 30, 2024Sep 30, 2024

    • MPRA_SaturationMutagenesis

      Public
      R Shiny website of the Saturation Mutagenesis manuscript
      R
      •
      GNU General Public License v3.0
      •2•3•2•1•Updated Aug 6, 2024Aug 6, 2024

    • HowToTrainDNN

      Public
      Tutorial for IGVF-MPRA-Workshop-2024, Lübeck, Germany
      MIT License
      •0•0•0•0•Updated Feb 20, 2024Feb 20, 2024

    • MPRAOligoDesign

      Public
      Basic scripts for creating an oligo design file
      Python
      •
      MIT License
      •0•0•6•2•Updated Feb 14, 2024Feb 14, 2024

    • snakemake_wrappers

      Public
      snakemake wrappers to share with others and to us ethem in multiple projects
      Python
      •
      MIT License
      •1•0•2•2•Updated Jul 7, 2023Jul 7, 2023

    • cfDNA

      Public
      cfDNA analysis workflow
      Python
      •
      MIT License
      •6•20•3•1•Updated Jun 15, 2023Jun 15, 2023

    • negative_training_sampler

      Public
      Python
      •
      MIT License
      •1•0•1•1•Updated Nov 15, 2022Nov 15, 2022

    • cookiecutter-snakemake-workflow

      Public
      A cookiecutter template for Snakemake workflows
      Python
      •
      MIT License
      •37•0•0•0•Updated Oct 17, 2022Oct 17, 2022

    • ReMM

      Public
      ReMM score snakemake workflow
      Python
      •
      MIT License
      •1•0•2•0•Updated Jul 19, 2022Jul 19, 2022

    • TF_enrichment_workflow

      Public
      Workflow to calculate enrichment of transcriptionfactors in open chromatin regions
      Python
      •0•0•0•0•Updated Feb 2, 2022Feb 2, 2022

    • cookiecutter-snakemake-wrappers

      Public
      Cookiecutter template for snakemake wrappers.
      Python
      •
      MIT License
      •1•0•0•0•Updated Feb 12, 2021Feb 12, 2021

    • hemoMIPs

      Public
      Automated analysis and result reporting for targeted sequencing data
      Python
      •
      MIT License
      •3•7•1•0•Updated Jun 18, 2020Jun 18, 2020