diff --git a/profile/README.md b/profile/README.md index cbd7bcb..6336e45 100644 --- a/profile/README.md +++ b/profile/README.md @@ -1,11 +1,14 @@ -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.