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Femrebora/README.md

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🧬 About Me

  • πŸŽ“ M.Sc. Biotechnology student @ Bezmialem VakΔ±f University
  • πŸ”¬ Currently working on CRISPR-based functional screening
  • πŸ€– Learning ML for genomics
  • πŸ›  Building reproducible pipelines with Nextflow & Snakemake
  • πŸ’‘ Passionate about turning raw biological data into actionable insights
  • 🎯 Goal: publish an open-source bioinformatics tools
  • 🌍 Based in Istanbul, Turkey


πŸ§ͺ Bioinformatics Expertise

Genomics & NGS        β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆ  Variant calling, alignment, QC
RNA-seq & scRNA-seq   β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–‘β–‘β–‘β–‘  DESeq2, Seurat, Scanpy, STAR
CRISPR Screening      β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–‘β–‘β–‘β–‘β–‘β–‘β–‘β–‘  MAGeCK, functional screens
ML in Genomics        β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–‘β–‘β–‘β–‘β–‘β–‘β–‘β–‘β–‘β–‘β–‘β–‘  scikit-learn, sequence models
Pipeline Dev          β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–‘β–‘β–‘β–‘  Nextflow, Snakemake, HPC/SLURM

πŸ’» Languages


🧬 Bioinformatics & Analysis Stack

πŸ”­ NGS & Variant Analysis

GATK BWA STAR HISAT2 SAMtools BCFtools Trimmomatic FastQC MultiQC VEP

πŸ”¬ Single-cell & Transcriptomics

Seurat Scanpy DESeq2 edgeR Monocle3 STAR-Fusion

🧫 CRISPR & Functional Genomics

MAGeCK CRISPResso2 Bowtie2

🐍 Python Ecosystem

Biopython Pandas NumPy scikit-learn Matplotlib Seaborn PyTorch

πŸ“Š R / Bioconductor

Bioconductor ggplot2 limma clusterProfiler ComplexHeatmap GSEA


βš™οΈ Dev Tools & Infrastructure


πŸ—„οΈ Databases & Resources


πŸŽ“ Education

Degree Institution Years
πŸŽ“ M.Sc. Biotechnology Bezmialem VakΔ±f University 2024 – 2026
πŸ”¬ B.Sc. Genetics & Bioinformatics Kadir Has University 2019 – 2023

πŸ“Š GitHub Stats

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