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    31 repositories

    • 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 fur…
      Python
      •
      MIT License
      •9•15•13•3•Updated Apr 17, 2026Apr 17, 2026

    • Model-MPRA-Benchmark-Project

      Public
      Benchmarking DNA sequence models against multiple MPRA datasets with standardized pipelines
      Jupyter Notebook
      •0•0•0•0•Updated Apr 16, 2026Apr 16, 2026

    • MPRA_SaturationMutagenesis

      Public
      R Shiny website of the Saturation Mutagenesis manuscript
      R
      •
      GNU General Public License v3.0
      •2•4•1•1•Updated Apr 14, 2026Apr 14, 2026

    • CADD_threshold_app

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 14, 2026Apr 14, 2026

    • kircherlab.github.io

      Public
      Kircher Lab website
      HTML
      •0•1•0•0•Updated Apr 10, 2026Apr 10, 2026

    • MPRAlib

      Public
      Library to analyse, filter and plot MPRA count data.
      mpra
      mpra
      Python
      •
      MIT License
      •1•2•2•0•Updated Apr 7, 2026Apr 7, 2026

    • IGVF_MPRA_quantification

      Public
      With this workflow you can use the output of MPRAsnakeflow (reporter experiment barcode file) together with the MPRA library sequence design file to quantify t…
      R
      •
      MIT License
      •0•0•1•1•Updated Mar 5, 2026Mar 5, 2026

    • combined-kernel-gkmsvm

      Public
      C
      •0•0•0•0•Updated Mar 2, 2026Mar 2, 2026

    • BCalm

      Public
      HTML
      •
      MIT License
      •4•1•3•0•Updated Mar 2, 2026Mar 2, 2026

    • CADD_threshold_analysis

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 18, 2026Feb 18, 2026

    • CADD-SV

      Public
      CADD-SV – a framework to score the effect of structural variants
      svvariant-annotationsvariant-effect-prediction
      svvariant-annotationsvariant-effect-prediction
      Python
      •
      MIT License
      •6•18•7•0•Updated Feb 11, 2026Feb 11, 2026

    • CMPRA_figures

      Public
      Notebooks containing figures for the CMPRA project
      Jupyter Notebook
      •0•0•0•0•Updated Jan 14, 2026Jan 14, 2026

    • MPRAOligoDesign

      Public
      Basic scripts for creating an oligo design file
      Python
      •
      MIT License
      •1•0•6•0•Updated Jan 9, 2026Jan 9, 2026

    • CADD-scripts

      Public
      CADD scripts release for offline scoring. For more information about CADD, please visit our website
      Python
      •
      Other
      •42•92•3•4•Updated Oct 30, 2025Oct 30, 2025

    • mpra_capture_flow

      Public
      Python
      •
      MIT License
      •0•0•0•1•Updated Sep 29, 2025Sep 29, 2025

    • ISMB-2025_IGVF-MPRA-Tutorial

      Public
      Main resource repository for the ISMB 2025 Tutorial IP2: Massively parallel reporter assays in functional regulatory genomics and as part of the IGVF data resou…
      HTML
      •3•2•0•0•Updated Jul 20, 2025Jul 20, 2025

    • MPRAsnakeflow_tutorial

      Public
      Jupyter Notebook
      •2•1•1•0•Updated May 26, 2025May 26, 2025

    • cfDNA_GCcorrection

      Public
      Python
      •
      Other
      •1•6•1•0•Updated Jan 23, 2025Jan 23, 2025

    • snakemake_wrappers

      Public
      snakemake wrappers to share with others and to us ethem in multiple projects
      Python
      •
      MIT License
      •2•0•2•2•Updated Jan 21, 2025Jan 21, 2025

    • 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

    • cfDNA-UniFlow

      Public template
      Workflow for preprocessing cfDNA samples.
      Jupyter Notebook
      •
      MIT License
      •1•12•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•1•0•0•Updated Oct 30, 2024Oct 30, 2024

    • HowToTrainDNN

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

    • cfDNA

      Public
      cfDNA analysis workflow
      Python
      •
      MIT License
      •6•23•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
      •36•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
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