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codebiogenomics/README.md

I work at Instytut Chemii Bioorganicznej Polskiej Akademii Nauk, Poznań Poland as a part of a very good team. I work as area expert and responsible for genomic analysis and software development from illumina and long read sequencing. I work using Python, R, RUST, Typescript at I provide bio-software development, algorithms, bioinformatics, machine learning as an Area Expert area for Illumina and LongRead sequencing technologies across all domains of life covering plant, bacterial, fungal and humans. I use Python and R (data analysis and web), RUST (system programming and bio-software) and Typescript and React (Web and Mobile SDK).

Scientific and Bio-Computing Areas of Interest: ▶️ I am specific to the genomics area such as RNA-seq, single cell genomics, and any genomics or protein language models and biological deep bio ML 🧬 and bio-software. ❌ I don't do protein structural modelling, and ML on the same.

Sequencing specifics:
2010-2021: Plant, Bacterial, Fungi 🧬 RNASeq, GenomSeq, Phylogenomics, PacBio Sequencing, Single Cell Analysis, Bio-software. 👨‍💻
2021:2023: Machine Learning, Bio-software. 👨‍💻
2024: PanGenome, Bio-software👨‍💻.
2025: Human Genomics 🧬and Bio-software, Mobile SDK 👨‍💻

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  1. panscape panscape Public

    reads to genome, pangenome graphs, summarize and analyze

    Rust 2

  2. eVaiutilities eVaiutilities Public

    eVaiutilities for post-eVai human genomics

    Rust 1

  3. ensemblcov ensemblcov Public

    genomics utilities for human genomics

    Rust

  4. vcfilter vcfilter Public

    population scale variant filter

    Rust 1

  5. varlinker varlinker Public

    exact point variant annotation

    Rust

  6. repgenerate repgenerate Public

    repgenerate for illumina sequencing reports

    Rust