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10 followers · 11 following
  • Earle A. Chiles Research Institute
  • Portland, OR

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Achievement: Pull Sharkx2Achievement: Arctic Code Vault Contributor

Achievements

Achievement: Pull Sharkx2Achievement: Arctic Code Vault Contributor

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amcrabtree/README.md

Hello, I'm Ange! 👋

I am a bioinformatics scientist in the field of cancer research


  • 🤖 Current focus: studying machine learning and other AI techniques for cancer research applications
  • 🔬 Previous lab's research project: characterizing new double-stranded RNA viruses and satellites in budding yeast
  • 📸 Current research project: building machine learning models from biopsy slide images to study the tumor microenvironment (TME)

  • 🏃‍♀️ Past research areas: anti-aging drug development (C. elegans), anti-viral drug development, SARS2/HIV/EBOV viral entry (mammalian tissue culture), viral pseudotyping, virus discovery, killer yeast (esp. Saccharomyces spp.), dsRNA sequencing method development, plasmid biology, multi-drug-resistant bacteria, gut microbiome (Zebrafish)

  • 💻 Computational skills: transcriptome analysis (C. elegans), de novo assembly of viral genomes, NGS pipeline development, variant calling (viruses)


Connect with me:

Angela Crabtree


Primary Languages and Tools:

bash r rstudio python jupyter vscode


Familiar Languages and Tools:

cplusplus perl


Statistical Data :

amcrabtree


amcrabtree


 amcrabtree


amcrabtree


Trophies :

amcrabtree

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  1. pub-rag pub-rag Public

    PubRAG uses your own collection of scientific articles to answer your niche questions and cite sources.

    Python 2

  2. tumor-finder tumor-finder Public

    A framework for training ML models for tumor recognition on H&E WSIs

    Python 2

  3. killer-denovo killer-denovo Public

    Assembles de novo contigs from raw Illumina sequence reads. Optimized for dsRNA elements in yeast.

    Shell 1 1

  4. killer-align killer-align Public

    Aligns raw Illumina reads to various reference sequences, calls variants, and creates consensus sequence. Optimized for dsRNA elements in yeast.

    Shell 1 1

  5. INdigestion INdigestion Public

    This app calculates possible restriction digests, given a plasmid sequence and the lab's enzyme inventory.

    Python

  6. ebov_project ebov_project Public

    Output, hosted by shinyapps.io, displays data from a small molecule inhibitor screening against various pseudoviruses.

    R