Skip to content
View codebiogenomics's full-sized avatar
3 followers · 304 following

Highlights

Block or report codebiogenomics

Block user

Prevent this user from interacting with your repositories and sending you notifications. Learn more about blocking users.

You must be logged in to block users.

Please don't include any personal information such as legal names or email addresses. Maximum 100 characters, markdown supported. This note will be visible to only you.
Report abuse

Contact GitHub support about this user’s behavior. Learn more about reporting abuse.

Report abuse
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 and 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.

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. ❌ What i don't code anymore: C++ since 2021 (2010-2021), dropped DevOPS and Golang (2024).

🧬 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 Bio-software 🧬 , Blockchain Healthcare 🧬

🧬 Language stack: I am very specific and oritented toward taking typed languages over the others. My language stack has been dominated by the typed languages and you can find below:
Software Development: C++ (2010-2021) and now I use RUST.
Web Mobile Development: RUST, Typescript and React and React Native/Expo.
Bioinformatics Data Analysis: Python, R.
Blockchain Healthcare: RUST,Javascript and Python.

🧬 Language categorization:
I have categorized every language for specific purposes, so that i can use the maximum use of the same. I dont do web programming in Python such as Django and other web frameworks in Python. Similarly in R, i dont do Shiny and hence only used Python and R for deep learning and machine learning purposes.This catgorial distincttion for each language allows me to use the maximum benefit of what language has to offer and in-demand according to the latest development in those respective languages.

My Skills

Pinned Loading

  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