New Tools

profile/README.md

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-Genome Function Initiative Oxford is a GitHub repository for all Welcome Discovery Award related projects.
-
-This is a joint collaboration between [Hughes](https://www.rdm.ox.ac.uk/about/our-divisions/nuffield-division-of-clinical-laboratory-sciences/nuffield-division-of-clinical-laboratory-sciences-research/hughes-group) and [Davies](https://www.imm.ox.ac.uk/research/research-groups/davies-group-genome-function-and-advanced-cellular-therapy-development) Groups at the MRC Weatherall Institute of Molecular Medicine ([MRC WIMM](https://www.imm.ox.ac.uk/)), University of Oxford.
+# Genome Function Initiative Oxford
+## About
+Genome Function Initiative Oxford is a GitHub repository for all Welcome Discovery Award related projects. This is a joint collaboration between [Hughes](https://www.rdm.ox.ac.uk/about/our-divisions/nuffield-division-of-clinical-laboratory-sciences/nuffield-division-of-clinical-laboratory-sciences-research/hughes-group) and [Davies](https://www.imm.ox.ac.uk/research/research-groups/davies-group-genome-function-and-advanced-cellular-therapy-development) Groups at the MRC Weatherall Institute of Molecular Medicine ([MRC WIMM](https://www.imm.ox.ac.uk/)), University of Oxford.
 
+## Tools
 Here are some tools that we made publicly available:
-+ [UpStreamPipeline](https://github.com/Genome-Function-Initiative-Oxford/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](https://dx.doi.org/10.3791/65633): A High-Throughput Upstream-Pipeline for Bulk ATAC-Seq and ChIP-Seq Data, Published on 22/09/2023.
-+ [REgulamentary](https://github.com/Genome-Function-Initiative-Oxford/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.
++ [UpStreamPipeline](https://github.com/Genome-Function-Initiative-Oxford/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. They are built using the Snakemake framework, are designed to be user-friendly and to combat the issue of reproducibility in genomic data analysis. Among these pipelines includes:
+  + [CATCH-UP]([https://dx.doi.org/10.3791/65633](https://github.com/Genome-Function-Initiative-Oxford/UpStreamPipeline/tree/main/genetics/CATCH-UP)): A High-Throughput Upstream-Pipeline for Bulk ATAC-Seq and ChIP-Seq Data. Published to [JoVE](http://doi.org/10.3791/65633) 22/09/2023.
++ [REgulamentary](https://github.com/Genome-Function-Initiative-Oxford/REgulamentary): a Python-based Snakemake pipeline built to genome-wide annotate cis-regulatory elements, from sequenced data, in a cell-type specific manner. Published to [Bioinformatics Advances](https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbag079/8532518) 20/03/2026.
++ [Zone-Equalisation-Normalisation](https://github.com/Genome-Function-Initiative-Oxford/Zone-Equalisation-Normalisation): ZEN-norm is a Python package for normalising bigWigs of genomic signal, reversing prior normalisation and benchmarking normalisation method performance. Published to [bioRvix](https://www.biorxiv.org/content/10.64898/2025.12.10.693203v1) 12/12/2025.
++ [scATAC-Pseudobulk-Pipeline](https://github.com/Genome-Function-Initiative-Oxford/scATAC_Pseudobulk_Pipeline): A Snakemake pipeline for creating scATAC-seq pseudobulk replicates of equal cell number.
 
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