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Achievement: Arctic Code Vault Contributor

Achievements

Achievement: Arctic Code Vault Contributor

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@GenomelyBio

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JLSteenwyk/README.md

🧬 Bay Area | 🌿 Omics / AI / Evo | 🌐 jlsteenwyk.com

Python R Bash Linux

Active Projects

🧬 Bio

  • ✂️ ClipKIT - a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
  • 🌿 PhyKIT - a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
  • 🧰 BioKIT - a versatile toolkit for processing and analyzing diverse types of sequence data
  • 🏷️ GOKIT - a command-line toolkit for Gene Ontology enrichment analysis
  • 🎣 orthofisher - a broadly applicable tool for automated gene identification and retrieval
  • 🪚 orthosnap - a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

✨ AI

  • 🤹 agent-skills - a collection of skills for agents
  • 🦬 plmtogo - a small protein language model for GO-conditioned protein sequence generation

🤖 (Semi)Automations

  • 📰 biotech_business_weekly - automated newsletter scraping for biotech business news
  • 🧠 bioai_newsletter - automated weekly newsletter at the intersection of biology and AI, with AI-powered summaries

🎨 Colorblind-friendly Data Visualization

  • 🌈 ggpubfigs - colorblind-friendly color palettes and ggplot2 extensions for publication-quality scientific figures
  • 📊 pypubfigs - publication-quality themes and colorblind-friendly palettes for seaborn and matplotlib

👻 For fun

Connect

📬 jlsteenwyk@gmail.com · 🦋 @jlsteenwyk.bsky.social · 📡 @JLSteenwyk · 📝 genomely.substack.com

Pinned Loading

  1. ClipKIT ClipKIT Public

    a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

    Python 88 5

  2. PhyKIT PhyKIT Public

    a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies

    Python 82 9

  3. orthofisher orthofisher Public

    a broadly applicable tool for automated gene identification and retrieval

    Python 41 1

  4. orthosnap orthosnap Public

    a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

    Python 29 1

  5. ggpubfigs ggpubfigs Public

    colorblind friendly color palettes and ggplot2 graphic system extensions for publication-quality scientific figures

    R 125 8

  6. BioKIT BioKIT Public

    a versatile toolkit for processing and analyzing diverse types of sequence data

    Python 22 10