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@Genome-Function-Initiative-Oxford

Genome-Function-Initiative-Oxford

README.md

Genome Function Initiative Oxford is a GitHub repository for all Welcome Discovery Award related projects.

This is a joint collaboration between Hughes and Davies Groups at the MRC Weatherall Institute of Molecular Medicine (MRC WIMM), University of Oxford.

Here are some tools that we made publicly available:

  • UpStreamPipeline: "upstream" includes the necessary steps to go from raw data output (usually fastq files) to a format which is visually interpretable by a researcher (e.g., bigwigs). These upstream pipelines allow wet-lab scientists to reproducibly analyse their own data without needing any prior knowledge of bioinformatics. These pipelines are built using the snakemake framework and designed to be both user-friendly and to combat the issue of reproducibility in genomic data analysis. Among these pipelines:
    • CATCH-UP: A High-Throughput Upstream-Pipeline for Bulk ATAC-Seq and ChIP-Seq Data, Published on 22/09/2023.
  • REgulamentary: a Python-based Snakemake pipeline built to genome-wide annotate cis-regulatory elements, from sequenced data, in a cell-type specific manner. Currently under revision.

Popular repositories Loading

  1. UpStreamPipeline UpStreamPipeline Public

    HTML 2 1

  2. REgulamentary REgulamentary Public

    Jupyter Notebook 1

  3. scATAC_Pseudobulk_Pipeline scATAC_Pseudobulk_Pipeline Public

    Snakemake pipeline for scATAC-seq pseudobulk replicate creation

    Python 1

  4. Zone-Equalisation-Normalisation Zone-Equalisation-Normalisation Public

    ZEN-norm is a Python package for normalising bigWigs of genomic signal, reversing prior normalisation and benchmarking normalisation method performance.

    Jupyter Notebook 1

  5. .github .github Public

  6. EdsTools EdsTools Public

    BedTools style repository for passing VCF/BED files.

    Python

Repositories

Showing 10 of 10 repositories
  • Zone-Equalisation-Normalisation Public

    ZEN-norm is a Python package for normalising bigWigs of genomic signal, reversing prior normalisation and benchmarking normalisation method performance.

    Genome-Function-Initiative-Oxford/Zone-Equalisation-Normalisation’s past year of commit activity
    Jupyter Notebook 1 MIT 0 0 0 Updated Mar 18, 2026
  • scATAC_Pseudobulk_Pipeline Public

    Snakemake pipeline for scATAC-seq pseudobulk replicate creation

    Genome-Function-Initiative-Oxford/scATAC_Pseudobulk_Pipeline’s past year of commit activity
    Python 1 0 0 0 Updated Jan 22, 2026
  • MCCGeneSkew Public
    Genome-Function-Initiative-Oxford/MCCGeneSkew’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Dec 17, 2025
  • REnformer Public
    Genome-Function-Initiative-Oxford/REnformer’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Dec 17, 2025
  • CREST-GV Public
    Genome-Function-Initiative-Oxford/CREST-GV’s past year of commit activity
    Python 0 0 0 0 Updated Dec 17, 2025
  • REgulamentary Public
    Genome-Function-Initiative-Oxford/REgulamentary’s past year of commit activity
    Jupyter Notebook 1 GPL-3.0 0 0 3 Updated Jun 19, 2025
  • UpStreamPipeline Public
    Genome-Function-Initiative-Oxford/UpStreamPipeline’s past year of commit activity
    HTML 2 MIT 1 1 0 Updated Apr 16, 2024
  • .github Public
    Genome-Function-Initiative-Oxford/.github’s past year of commit activity
    0 0 0 0 Updated Apr 5, 2024
  • ALTSPLICE Public

    Neural network models for the prediction of Alternative Splicing

    Genome-Function-Initiative-Oxford/ALTSPLICE’s past year of commit activity
    0 0 0 0 Updated Oct 16, 2023
  • EdsTools Public

    BedTools style repository for passing VCF/BED files.

    Genome-Function-Initiative-Oxford/EdsTools’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Sep 1, 2023

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