YuukiAS
@YuukiAS
Public Skills
etetoolkit
by YuukiAS
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
deeptools
by YuukiAS
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
skill-installer
by YuukiAS
Install external Codex skills from curated lists or GitHub repo paths. Use for third-party skill downloads; for AI_Skills_Collection installs prefer ai-skills repo/user targets and treat codex-home as explicit legacy compatibility.
lamindb
by YuukiAS
This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR.
phylogenetics
by YuukiAS
Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.
esm
by YuukiAS
Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations).
scikit-bio
by YuukiAS
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
pymc
by YuukiAS
Bayesian modeling with PyMC: model specification, priors, NUTS/VI fitting, diagnostics, posterior predictive checks, LOO/WAIC comparison, prediction, and code review.
gwas-database
by YuukiAS
Archived provider note for GWAS Catalog lookup. Use bioinformatics-database-retrieval for active project routing and GWAS summary-stat database selection.
scientific-slides
by YuukiAS
Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design templates, timing guidance, and visual validation. Works with PowerPoint and LaTeX Beamer.
ai-ml-imaging
by YuukiAS
AI/ML support for imaging workflows with PyTorch Lightning and Transformers.
bioinformatics-workflows
by YuukiAS
Common bioinformatics workflows across databases, single-cell analysis, genomics I/O, and omics analysis.
pptx
by YuukiAS
Use this skill any time a .pptx file is involved in any way — as input, output, or both. Trigger whenever the user mentions \"deck,\" \"slides,\" \"presentation,\" or references a .pptx filename, regardless of what they plan to do with the content afterward.
medical-imaging-workflows
by YuukiAS
Medical imaging workflows for CMR, DICOM/NIfTI, classical features, deep learning, and pathology imaging.
database-query
by YuukiAS
Query a Notion database by name or ID and return structured, readable results with optional filters and sorting.
gnomad-database
by YuukiAS
Archived provider note for gnomAD variant lookup. Use bioinformatics-database-retrieval for active project routing.
kegg-database
by YuukiAS
Archived provider note for KEGG pathway lookup. Use bioinformatics-database-retrieval for active project routing.
gtex-database
by YuukiAS
Archived provider note for GTEx expression lookup. Use bioinformatics-database-retrieval for active project routing.
jaspar-database
by YuukiAS
Archived provider note for JASPAR motif lookup. Use bioinformatics-database-retrieval for active project routing.
meeting-intelligence
by YuukiAS
Prepare meeting materials by gathering context from Notion, enriching with research, and creating both an internal pre-read and external agenda saved to Notion.
find
by YuukiAS
Quickly find pages or databases in Notion by title keywords. Returns precise matches rather than comprehensive results.
research-documentation
by YuukiAS
Search across your Notion workspace, synthesize findings from multiple pages, and create comprehensive research documentation with proper citations and actionable insights.
tasks-build
by YuukiAS
Build a task from a Notion page URL. Fetches task details, marks it in progress, implements the work, and updates status in Notion.
search
by YuukiAS
Search the user's Notion workspace using the Notion MCP server. Use for finding pages, databases, and content by keywords or natural-language queries.