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danangcrysnanto/README.md

Hi there 👋

I am Danang and I have extensive experiences working on the bioinformatics of whole genome sequencing data. Currently I am working to apply graph analytic in order to integrate diverse genetic variations into a unified graph-based pangenome. With this, I extended functional genomics analysis to the genomic regions inaccessible with current standard of a linear genome and facilitate integrative multi-omics data analysis and vizualisation.

Skills

  • Professional experiences in bioinformatics data analyses, including (but not limited to) Next generation sequencing, transcriptomic, graph-based genomics, genetic variant discovery, and basic genome assembly
  • Main programming languages: Bash (Unix/Linux), R/Bioconductor [Statistical analysis], Python [Extensive use], C++ for bioinformatics
  • Data science: Tidyverse, Python Data Science (Numpy, Pandas, Jupyter)
  • Application development: Shiny, Flask, Plotly
  • Computational pipelines: Snakemake
  • Reproducible data: Git, Docker
  • High Performance Computing (HPC IBM LSF)
  • Others: Affinity Designer, Affinity Photo, Ms. Office, VIM, Latex, vscode, Sublime Text

Pinned

  1. bovine-graphs bovine-graphs Public

    Forked from AnimalGenomicsETH/bovine-graphs

    Integrate multiple genome assemblies into a pangenome graph

    Python

  2. bovine-graphs-mapping bovine-graphs-mapping Public

    Comparison of sequencing read mapping to pangenome graphs

    Jupyter Notebook 5 2

  3. Graph-genotyping-paper-pipelines Graph-genotyping-paper-pipelines Public

    Variant discovery and genotyping pipelines from pangenome graphs

    Python 4 5

  4. phdthesis phdthesis Public

    My PhD dissertation on bovine pangenome graph

    TeX