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.