I'm a postdoctoral research scientist, working in the Koo lab at Cold Spring Harbor Laboratory. My work focuses on deep learning for genomics.See mypersonal website to learn more about my work and experience.

Software:

• MungeSumstats -Maintainer & Creator - Bioconductor R package for the standardisation and quality control of GWAS summary statistics to address the lack of standardisation in the field. MungeSumstats can handle the most common summary statistic formats, including variant call format (VCF) producing a reformatted, standardised, tabular summary statistic file, VCF or R native data object.
• Enformer Celltyping -Maintainer & Creator - a deep learning model which incorporates distal effects of DNA interactions, up to 100,000 base-pairs away, to predict epigenetic signals in previously unseen cell types using DNA and chromatin accessibility data.
• ChromExpress -Maintainer & Creator - Deep learning models for the predictions of gene expression from histone mark signals

Helpful documentation:

• Complete Documentation for Creating and Maintaining a Bioconductor package
• Intro to ML for geonomics
• Job scripts for a PBS high performance compute cluster (HPC)

Popular repositoriesLoading

1. MungeSumstatsMungeSumstatsPublic

   Rapid standardisation and quality control of GWAS or QTL summary statistics

   R 78 16

2. SumstatFormatsSumstatFormatsPublic

   Meta-analysis of the most common GWAS Summary Statistic file formats

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3. reanalysis_scRNA_seq_benchmarkreanalysis_scRNA_seq_benchmarkPublic

   A reanalysis the results of the paper: A practical solution to pseudoreplication bias in single-cell studies (https://www.nature.com/articles/s41467-021-21038-1)

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4. Al-MurphyAl-MurphyPublic

5. ega-download-clientega-download-clientPublic

   Forked fromEGA-archive/ega-download-client

   A basic Python-based EGA download client

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6. echocondaechocondaPublic

   Forked fromRajLabMSSM/echoconda

   echoverse module: conda environment handling

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