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  • Penn State University
  • State College, PA

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Achievement: Pull SharkAchievement: Arctic Code Vault Contributor
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Achievements

Achievement: Pull SharkAchievement: Arctic Code Vault Contributor
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ShaopengLiu1/README.md

Hi there, welcome to my GitHub 👋

🐵 About me

  • Ph.D. candidate in Dr. David Koslicki's lab, Penn State University
  • Domain: Bioinformatics, Metagenomics, Genomics data science
  • Email: spliu@psu.edu
  • Resume

🐝 Currently working on

  • Metagenomic analysis and method development
  • Knowledge graph and graph learning

🏆 Selected projects:

  • Knowledge graph and graph-based genomic data science:
    1. MetagenomicKG: construction of a metagenomic-specific knowledge graph and how it can be used for metagenomic data mining.
    2. ARAX: a knowledge-graph-based computational reasoning tool for translational biomedicine.
  • Metagenomic analysis and algorithm development:
    1. CMash: a modified containment MinHash algorithm for multi-resolution k-mer-based similarity estimation.
    2. FracMinHash vs Syncmer: bridging the FracMinHash algorithm with syncmers for metagenomic analysis.
    3. FracMinHash for functional profiling: utilization of the FracMinHash algorithm for metagenomic functional profiles.
  • Genomic data analysis
    1. AIAP: an integrative pipeline for comprehensive analysis of ATAC-seq dataset implemented in Docker and Singularity.

⚒️ Tech stack

python R bash
git Github
Markdown YAML neo4j
mysql jekyll HTML5

Pinned

  1. ATAC-seq_QC_analysis ATAC-seq_QC_analysis Public

    Forked from Zhang-lab/ATAC-seq_QC_analysis

    Atac-seq QC matrix

    Shell 1

  2. Koslicki_lab_metagenomic_analysis Koslicki_lab_metagenomic_analysis Public

    Metagenomic-related analysis pipeline and resources

    Python

  3. KoslickiLab/CMASH-reproducibles KoslickiLab/CMASH-reproducibles Public

    Python 1

  4. KoslickiLab/Koslicki-lab-PSU KoslickiLab/Koslicki-lab-PSU Public

    Website for Koslicki Lab.

    HTML 1

  5. KoslickiLab/useful_tools KoslickiLab/useful_tools Public

    Lab forum to share scripts, software, and technical issues

    Shell 2