编码规范、框架、重构、代码审查（1.7万 个）
Call protein-RNA binding sites from CLIP-seq BAM with CLIPper, PureCLIP, Skipper, Piranha, omniCLIP, CTK, CLAM, or Paraclu. Use when choosing between coverage-based, HMM-based, beta-binomial window-based, and crosslink-site-based peak callers; applying ENCODE eCLIP thresholds (log2 IP/SMInput >= 3, -log10 p >= 3); deciding when SMInput is mandatory; or reconciling peak-set discordance between callers for the same RBP.
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Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, population frequencies, and clinical-variant content. Covers bedtools/pybedtools interval intersection, AnnotSV comprehensive annotation and ranking, ClinGen haploinsufficiency/triplosensitivity scoring, gnomAD-SV/DGV frequency filtering, COSMIC Cancer Gene Census, and ClinVar overlap. Use when interpreting which genes a CNV affects, distinguishing the driver gene of a focal event from passengers, filtering against population CNVs, separating whole-gene from partial-gene overlap, or preparing CNVs for clinical classification.
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Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, simulate gel electrophoresis patterns, and perform double digests. Use when analyzing restriction digest fragment patterns.
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ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds. Use when assessing whether an ATAC-seq library passes ENCODE acceptance criteria, diagnosing transposition artefacts, comparing Omni-ATAC vs standard prep quality, or selecting which replicates to drop before peak calling.
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Detect and track antimicrobial resistance genes using AMRFinderPlus and ResFinder with epidemiological context. Monitor resistance trends and identify emerging resistance patterns. Use when screening genomes for AMR genes or tracking resistance in surveillance programs.
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Call accessible chromatin regions from ATAC-seq BAM files using MACS3, MACS2, Genrich, or HMMRATAC. Use when identifying open chromatin from aligned ATAC-seq, choosing between point-source vs HMM peak callers, applying ENCODE-style pseudoreplicate IDR, removing blacklist regions, or fixing 501bp consensus peaks for downstream differential analysis.
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Process multiple sequence files in batch using Biopython. Use when working with many files, merging/splitting sequences, or automating file operations across directories.
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Pull pre-computed ortholog calls from public databases (OrthoDB, Ensembl Compara, OMA browser, eggNOG, PANTHER, KEGG Orthology, HomoloGene) via their REST APIs. Use when orthologs are already curated upstream, when the question is "what is the X ortholog of Y" rather than "how to infer orthology de novo", when batch-mapping gene IDs across species, or when comparing the resources for consensus calls. Encodes confidence-level semantics, 1:1 vs 1:many vs many:many, HomoloGene deprecation, and when to defect to de novo computation.
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Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.
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Query Reactome for biological pathways and reactions. Use when user asks about signaling cascades, biological processes, pathway diagrams, or reaction details. Triggers on "reactome", "signaling cascade", "biological pathway", "pathway diagram", "reaction mechanism".
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Applies ACMG/AMP 2015 framework with ClinGen SVI specifications, Tavtigian 2018/2020 Bayesian point system, Abou Tayoun 2018 PVS1 decision tree, Pejaver 2022 calibrated PP3/BP4 thresholds for REVEL/BayesDel/AlphaMissense, Brnich 2020 PS3/BS3 OddsPath, Walker 2023 SpliceAI splicing framework, and AMP/ASCO/CAP 2017 tumor tiers. Use when classifying germline variants P / LP / VUS / LB / B, applying VCEP-specific CSpec rules, computing Whiffin BS1, or assigning cancer Tier I-IV per Li 2017.
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Query UniProt protein database. Use when user asks about protein sequences, functions, annotations, domains, or protein identifiers. Triggers on "uniprot", "protein function", "protein sequence", "gene product", "protein info".
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Structure similarity search with Foldseek. Use this skill when: (1) Finding similar structures in PDB/AFDB databases, (2) Structural homology search, (3) Database queries by 3D structure, (4) Finding remote homologs not detected by sequence, (5) Clustering structures by similarity. For sequence similarity, use uniprot BLAST. For structure prediction, use chai or boltz.
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Workflow for retrieving public omics datasets, sequences, annotations, and literature-linked biological resources.
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麦当劳省钱体检：不看你想吃什么，先看你已经亏在哪。输入你实际的点法或历史订单，枚举所有可行买法（单点/套餐/券/满减），用麦当劳MCP的calculate-price逐个复算，报出差额、归因与凑单临界点。支持批量核价、HTML交互报告和离线恢复。触发词：省钱、体检、比价、买贵、凑单、满减、优惠券、套餐、差价、审计、复盘。
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麦当劳省钱体检：不看你想吃什么，先看你已经亏在哪。输入你实际的点法或历史订单，枚举所有可行买法（单点/套餐/券/满减），用麦当劳 MCP 的 calculate-price 逐个复算，报出差额、归因与凑单临界点。适用于：想知道自己常点的组合有没有更便宜的买法、犹豫要不要为满减凑单、想复盘最近订单买贵了多少。不适用于：代替用户下单、承诺长期价格、营养或医疗建议。
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Save a contact someone shared with you (a Contact card) as a local peer. agent-talk does NOT auto-import — review staged cards and import only ones from a peer you trust. `<user>` is this session's user directory (absolute path; from init).
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Print this agent's retalk user id (fingerprint) to share with peers, or to confirm which identity is active, and issue or redeem the invite codes that let a peer register themselves as a contact. Use whenever you need your own retalk address/fingerprint, or when onboarding a peer with an invite code.
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Hold every response to the ISO 24495 plain-language rules, and route to the sector skills. Codex has no output style, so these rules are a skill.
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Plain language applied to source code (ISO 24495-1:2023 principles). Governs the parts of code a person reads: the order units appear in, their names, comments, and error messages. Applied when writing or restructuring code, not when explaining it.
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Internal publisher module for /codeck. Exports deck to PDF or PPTX with post-export QA. User-facing export requests should enter through /codeck; this skill defines the export behavior.
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Editor role. Reads local materials, asks narrative questions, plans story arc. Outputs $DECK_DIR/deck.md as the sole content source. Use whenever the user says "outline", "plan slides", "organize materials", "structure", "table of contents", "narrative", or wants to structure content into a presentation.
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Internal speech module for /codeck. Reads deck content, asks about style and duration only when missing, generates a verbatim speech transcript with stage directions. Outputs $DECK_DIR/speech.md.
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codeck entry point. Scans local files for materials, shows pipeline dashboard with diagnostic intelligence, guides user to the next step. Use when the user says "codeck", "new deck", "make a presentation", "make a deck", "new slides", "build a presentation", "export", "speech", "script", or wants to start or continue a presentation project. /codeck is the user-facing entry; legacy sub-skills are internal modules.
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