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chumawinnie/README.md

Hey There! 👋 I'm Chukwuma Winner Obiora

Role Profile Views

Clinical Genomics & Cancer Bioinformatics🎗️| Molecular Tumor Board Support | ML Scientist
Basel 🇨🇭, Bayern 🇩🇪

🧬 About Me

  • 🔬 Bioinformatics Researcher specializing in clinical genomics and cancer bioinformatics
  • 🏥 Developing automated pipelines for molecular tumor board presentations
  • 📊 Working with WES, WGS, Panel Sequencing, and RNA-seq (bulk & single-cell)
  • 📝 Published in the European Journal of Cancer
  • 🌱 Currently exploring opportunities in Switzerland's biotech sector

🔬 Clinical Genomics Pipeline Architecture

# WES Pipeline Flowchart

🛠️ Tech Stack

Python R Nextflow Bash

Docker Singularity Conda Git

Linux AWS Slurm VSCode

🧪 Bioinformatics Tools

nf-core Sarek GATK BWA Mutect2 Strelka2 VEP ANNOVAR Sequenza CNVkit SigProfiler MSIsensor OptiType HLA-HD pVACtools NetMHCpan STAR HISAT2 Salmon kallisto featureCounts StringTie DESeq2 edgeR Ballgown clusterProfiler Seurat Scanpy CellRanger Monocle

Featured Projects

HLA Neoantigen Pipeline WES Pipeline

TNBC RNA-Seq Bioinformatic WES

📊 GitHub Stats

GitHub Stats Top Languages

GitHub Streak

📫 Connect With Me

Email LinkedIn ORCID

"Translating genomic data into clinical insights" 🧬

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  1. TNBC-RNASeq-Analysis TNBC-RNASeq-Analysis Public

    Molecular subtyping of Triple Negative Breast Cancer (TNBC) using RNA-Seq analysis and immune deconvolution to identify novel biomarkers for early diagnosis and effective prognosis.

    R

  2. ballgown-rnaseq-analysis ballgown-rnaseq-analysis Public

    Complete RNA-seq analysis pipeline: Ballgown DE, biomaRt annotation, GO/KEGG enrichment, and immune deconvolution

    R

  3. scRNA-melanoma-TME scRNA-melanoma-TME Public

    Single-cell RNA-seq analysis of acral vs cutaneous melanoma tumor microenvironment. Reproduction of Zhang et al. (2022) Nature Communications.

    R

  4. Basel_ovarian_cancer_project Basel_ovarian_cancer_project Public

    inferCNV analysis of scRNA-seq data comparing CNV profiles between solid tumor and ascites in HGSOC (Vasquez-Garcia et al., 2022, SPECTRUM cohort, 25 patients, 70K cells)

    R