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NathanielLee-Blues/README.md

Hi, I'm Nathaniel

MSc Genomics
Interested in Bioinformatics & Variant Analysis
Currently working on pathogenicity prediction

Projects

I am building a public bioinformatics portfolio focused on genomics, transcriptomics, variant analysis, workflow automation, and reproducible research.

Project Focus Skills demonstrated
alpharing-sarscov2-validation SARS-CoV-2 spike missense variant effect prediction R, Python, ROC/AUC, SHAP interpretation, structural bioinformatics
rnaseq-deseq2-workflow RNA-seq differential expression analysis DESeq2, R, PCA, volcano plots, heatmaps, transcriptomics
tcga-cancer-expression-analysis TCGA breast cancer expression and immune signature analysis Large-scale expression data, PCA, immune scoring, tumour transcriptomics
variant-calling-workflow Real-data bacterial variant calling FASTQ, FASTA, BAM, VCF, FastQC, BWA, SAMtools, BCFtools
nextflow-variant-calling-pipeline Workflow-managed variant-calling pipeline Nextflow, samplesheets, reproducible pipelines, workflow automation
bioinformatics-utilities Python utilities for FASTA, FASTQ and VCF parsing Python, CLI tools, file parsing, QC summaries, testing

Contact

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  1. alpharing-sarscov2-validation alpharing-sarscov2-validation Public

    Reproducible MSc Genomics project evaluating AlphaRING v2 for SARS-CoV-2 spike missense variant classification using ROC/AUC analysis and SHAP interpretation.

    R

  2. rnaseq-deseq2-workflow rnaseq-deseq2-workflow Public

    RNA-seq differential expression workflow using DESeq2 and the Bioconductor airway dataset in R.

    R

  3. bioinformatics-utilities bioinformatics-utilities Public

    Python command-line utilities for FASTA, FASTQ, and VCF parsing using real bioinformatics input data.

    Python

  4. tcga-cancer-expression-analysis tcga-cancer-expression-analysis Public

    Large-scale TCGA breast cancer gene expression analysis with PCA, immune signature scoring, and tumour expression interpretation.

    R