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概要と使いどころ
All-in-one FASTQ QC and adapter trimming. Auto-detects Illumina adapters, filters low-quality reads, corrects paired-end overlaps, emits HTML+JSON QC in one pass. 3-10x faster than Trim Galore/Trimmomatic. First step before STAR, BWA-MEM2, or Salmon.
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Query ReMap 2022 TF ChIP-seq peak database via REST API and BED downloads. Retrieve TF peaks overlapping a region (chr:start-end), peaks near a gene, TFs by species, peaks filtered by biotype (promoter, enhancer), and BED files for a TF-cell type pair. Use for TF co-occupancy, regulatory annotation, and TF binding atlases. Use jaspar-database for PWM motifs; encode-database for ENCODE tracks.
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Query the ClinPGx (formerly PharmGKB) REST API plus the CPIC PostgREST companion API for pharmacogenomic clinical annotations, CPIC/DPWG dosing guidelines, gene-drug pairs, variant-drug associations, FDA/EMA drug labels, and PGx pathways. Two-host architecture: api.clinpgx.org for annotation records, api.cpicpgx.org for genotype→recommendation lookups. No auth. For germline pathogenicity use clinvar-database; for somatic cancer PGx use cosmic-database or opentargets-database; for drug bioactivity use chembl-database-bioactivity.
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Read, write, and edit ChemDraw CDX/CDXML files with RDKit's rdkit.Chem.rdChemDraw plus direct XML editing, always paired with a rendered PNG. Parse molecules and reactions from .cdxml/.cdx, write structures with good 2D depiction, and hand-build or modify the parts RDKit cannot write: reaction arrows, plus signs, schemes/steps, and text/labels. Use for reaction schemes, synthesis routes, mechanisms, retrosynthesis, or SI figures. Critical: RDKit writes structures only — round-tripping a reaction through a Mol silently drops arrows and text; this skill shows the XML layer that preserves them. For pure molecular analysis (descriptors, fingerprints, SMARTS) use rdkit-cheminformatics; for multi-format 3D conversion use openbabel.
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Infer and visualize intercellular communication from scRNA-seq with CellChat (R). Build CellChat from Seurat/counts → subset CellChatDB ligand-receptor pairs → over-expressed genes per group → communication probabilities → pathway signaling → network centrality (senders/receivers/influencers) → chord/heatmap/bubble plots → cross-condition compare. Human, mouse. Use liana for pure-Python.
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Per-feature NaN-safe Spearman/Pearson correlation across many features (genes, proteins, variants) with missing values. Covers why bulk matrix shortcuts fail, correct pairwise deletion, degenerate input filtering, and large-dataset performance. Use statistical-analysis for test choice; shap-model-explainability for interpretability.
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Python library for biology: sequence manipulation (DNA/RNA/protein), pairwise/multiple alignment, phylogenetic trees (NJ, UPGMA), diversity (Shannon, Faith PD, Bray-Curtis, UniFrac), ordination (PCoA, CCA, RDA), stats (PERMANOVA, ANOSIM, Mantel), file I/O (FASTA, FASTQ, Newick, BIOM). Use for microbiome, community ecology, or phylogenetics.
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Open-source bio-image data management. Use the omero-py client to connect to an OMERO server, retrieve images as numpy arrays, annotate with tags and key-value pairs, manage ROIs, and feed image data into Python analysis pipelines — programmatically, no GUI.
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Statistical visualization on matplotlib with native pandas support. Auto aggregation, CIs, grouping for distributions (histplot, kdeplot), categorical (boxplot, violinplot), relational (scatterplot, lineplot), regression (regplot, lmplot), matrix (heatmap, clustermap), grids (pairplot, FacetGrid). Use for quick statistical summaries; matplotlib for fine control; plotly for interactive HTML.
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protocols.io REST API: search and fetch wet-lab, bioinformatics, and clinical protocols by keyword, DOI, or category, with steps, reagents, materials, equipment, timing. Public access free; auth needed for private or publishing. Pair with opentrons-protocol-api or benchling-integration to execute.
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Molecular biology toolkit: sequence manipulation, FASTA/GenBank/PDB I/O, NCBI Entrez, BLAST automation, pairwise/MSA alignment, Bio.PDB, phylogenetic trees. Use for batch processing, custom pipelines, format conversion, PubMed/GenBank queries. For quick gene lookups use gget; for multi-service REST APIs use bioservices.
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Find and compare current FF&E candidates from a design brief, with sourced purchasing facts and optional CSV-library save. Use to research or source products; not to match from an image or pair coordinating items.
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Create an HTML color palette from a mood, description, or image, with swatches, color codes, pairings, and contrast checks. Use for color schemes or brand colors.
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Audit a product, selection or FF&E schedule against sourced evidence and flag discrepancies, unknowns and stale specifications. Use to check product data; not to repair records, certify compliance or generate cut sheets.
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Project memory workflow for init/upgrade, profile-aware setup, end session, normal/full close, file organization, document archiving, language switching, versioned update logs, rule review, status, wiki sync, and context recovery. Use for /project-butler, setup/初始化, foundation setup, profile setup, end session/收工, normal close, full close, foundation repair, organize files/整理文件, change language/切换语言, continue/接着上次, continue full context/全面回顾, review claude, sync wiki, status. Maintains project memory files. Runs version freshness check before trigger routing.
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Build RAG / unstructured-document evaluation datasets and demo documents (e.g. for Knowledge Assistant) on Databricks: generate synthetic PDFs locally, upload to Unity Catalog volumes, and pair each document with test questions for retrieval evaluation.
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Build, modify, debug, and cloud-validate VeADK Agents from an accepted product intent. Use for VeADK architecture, tools, workflows, memory, knowledge, executable AgentKit projects, local tests, and AgentKit build/deploy/invoke/log repair loops. Do not use for unrelated user requests, other Agent frameworks, standalone cloud administration, or production Runtime operations.
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Recommend font combinations for different use cases. Provide Google Fonts alternatives to premium fonts with hierarchy examples.
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Point Cowork at a folder of resumes plus a job description -- screens every candidate against the actual requirements, produces a ranked shortlist with evidence, drafts advance/decline emails, and builds interview kits for the top picks. Pairs with hiring-scorecard for the interview stage.
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Use when one validated cohort analysis must be repeated across many exposure/outcome pairs. Generates one R/Python script per combination from a single methodology template, changing only the variables, and aggregates the results into a summary matrix.
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Capture a Burp Suite Repeater request/response as a PoC image (targets/<eng>/poc/) by driving the Burp MCP + the Kali GUI. Replays a request in a Repeater tab, sends it, and grabs the request+response panes - a Burp-native PoC (client report / CTF writeup). Use when you want the evidence to come from Burp rather than a curl/terminal card, or whenever you drive a target through Burp and need the images. Pairs with hunt-burp.
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Build, install, pair, and operate the Life Recorder iPhone-to-Mac local transcription system. Use when a user asks to reproduce or troubleshoot this project.
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Repair a failing WooCommerce Android Maestro flow by reproducing it against the store it runs on, inspecting Maestro selectors, patching the smallest selector/wait/setup issue, and rerunning with repeat evidence. Human-triggered only.
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Check that this machine's agent team can work and say what is wrong in plain lines: tools installed, core skills installed, skill commands runnable, hooks configured, Reach seat live, a heartbeat running, both vendors' quota readable, temp space free. Checks only, never repairs. Use on a new machine, when agents stop reaching each other or a long run fails to start, or when the owner asks whether everything is healthy.
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