YuukiAS
@YuukiAS
Public Skills
publication-figures
by YuukiAS
Publication figure orchestration with contextual palette discovery, Matplotlib, Seaborn, Plotly, and export-ready layout.
pysam
by YuukiAS
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
gtars
by YuukiAS
High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.
polars-bio
by YuukiAS
High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merge, coverage, complement, subtract for BED/VCF/BAM/GFF intervals. Streaming, cloud-native, faster bioframe alternative.
skill-creator
by YuukiAS
Guide for creating effective skills. This skill should be used when users want to create a new skill (or update an existing skill) that extends Codex's capabilities with specialized knowledge, workflows, or tool integrations.
flowio
by YuukiAS
Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.
statistical-analysis
by YuukiAS
Plan and report statistical analyses: estimand framing, test/model choice, assumption checks, power/sensitivity notes, effect sizes, uncertainty, and reproducible reporting.
mcp-builder
by YuukiAS
Guide for creating high-quality MCP (Model Context Protocol) servers that enable LLMs to interact with external services through well-designed tools. Use when building MCP servers to integrate external APIs or services, whether in Python (FastMCP) or Node/TypeScript (MCP SDK).
plugin-creator
by YuukiAS
Create and scaffold plugin directories for Codex with a required .codex-plugin/plugin.json, optional plugin folders/files, and baseline placeholders you can edit before publishing or testing.
openai-docs
by YuukiAS
Use for openai docs workflows when the task directly names this tool or domain. Prefer narrower project skills or umbrella retrieval skills when the task is only a lookup.
pydeseq2
by YuukiAS
Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.
bioinformatics-database-retrieval
by YuukiAS
Use for gene, protein, pathway, variant, expression, disease, and structure database lookups. Prefer workflow-specific skills for scanpy, scvi-tools, pysam, or DICOM work.
skill-library-analysis
by YuukiAS
Analyze, deduplicate, cluster, and select skills from a large skill library or cloned upstream sources. Use when maintaining AI_Skills_Collection, comparing external skill repos, or deciding whether to merge, add, archive, or ignore skills.
arboreto
by YuukiAS
Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.
zarr-python
by YuukiAS
Chunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS integration, NumPy/Dask/Xarray compatible, for large-scale scientific computing pipelines.
imagegen
by YuukiAS
Generate or edit raster images when the task benefits from AI-created bitmap visuals such as photos, illustrations, textures, sprites, mockups, or transparent-background cutouts.
simpy
by YuukiAS
Build and validate process-based discrete-event simulations in Python with SimPy: entities, resources, queues, event timing, replications, sensitivity analysis, and reporting.
dnanexus-integration
by YuukiAS
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
bayesian-ppl-diagnostics
by YuukiAS
Executable guidance for Bayesian workflows using Stan/CmdStanPy, brms, PyMC, and ArviZ, with legacy JAGS/OpenBUGS paths and Rcpp acceleration patterns.
latchbio-integration
by YuukiAS
Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.
tiledbvcf
by YuukiAS
Efficient storage and retrieval of genomic variant data using TileDB. Scalable VCF/BCF ingestion, incremental sample addition, compressed storage, parallel queries, and export capabilities for population genomics.
biopython
by YuukiAS
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.
geniml
by YuukiAS
This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic feature learning.
statsmodels
by YuukiAS
Implement and review statsmodels analyses: OLS/GLM/mixed models, time series, robust covariance, diagnostics, coefficient tables, and reproducible inference workflows.