awesome-skills

Performs ML-based protein-ligand pose prediction and scoring using DiffDock-L (diffusion-based), Boltz-1 / Boltz-2 (foundation model with affinity), Chai-1, AlphaFold3 ligand, EquiBind, TANKBind, NeuralPLexer, and hybrid workflows (DiffDock pose + GNINA rescore + PoseBusters QC). Explicit handling of when ML beats classical docking, when classical beats ML, the PB-invalid pose problem, and rescoring as the standard production hybrid. Use when modern docking is needed: foundation-model ligand-pose prediction, AI rescoring of classical poses, or scaffold-hopping in cross-docking scenarios.

Multi-source literature search, citation verification, strict independent other-citation audits, article-level citation metric tables, influential citer profiling with citation-context extraction, MeSH search strategy, citation file management (.nbib/.ris/.bib conversion), and reference management (BibTeX, related articles, ID conversion) via MCP tools (PubMed, CrossRef, arXiv, Scopus, ScienceDirect). Use for coordinated literature workflows beyond one MCP call, including 文献检索、 查文献、找文献、文献综述检索、查论文、引文核对、参考文献管理、文献去重、 严格他引、他引判定、排除自引、谁引用了我的文章、引用我的文章的人有没有大牛、 院士引用、校长引用、院长引用、杰青引用、长江学者引用、Fellow引用、文章引用表、 指定文章引用数、严格他引数、整理成表格.

Add strict Nature/CNS citations to manuscript text by splitting long passages into citable segments, searching only accepted flagship and subjournal titles from Nature Portfolio, the AAAS Science family, and Cell Press, filtering by publication time range, and exporting one reference-manager-ready output by default. Use this skill whenever the user asks to input text and automatically get references, add citations to a paragraph/manuscript, find Nature-series or CNS support for statements, create text-to-reference correspondence, "分段引用", "自动给出引用", "Nature系列引用", "CNS及子刊", "支撑文献", "补引用", "找引用", or export EndNote/RIS/ENW/Zotero RDF. Also trigger on general academic-writing citation needs even without the word "Nature", such as adding references while writing a paper, finding sources/literature for a claim, building a reference list, citation/referencing for academic writing, and Chinese phrasings like 学术写作引用、写论文加引用、写paper找文献、加参考文献、配文献、引用文献、文献支撑.

Prepare, audit, or revise Nature-ready Data Availability statements, data repository plans, dataset citations, and FAIR metadata checklists for manuscripts. Use when the user asks about Nature data availability, research data sharing, repository selection, accession numbers, restricted or sensitive data, source data, supplementary datasets, DataCite-style dataset references, FAIR metadata for academic publication, or Chinese-to-English data availability wording for Chinese-speaking authors preparing Nature-family submissions. Also trigger on general academic-writing data needs even without the word "Nature", such as writing a data availability statement for any journal, code/data sharing sections, repository selection while writing a paper, and Chinese phrasings like 数据可用性声明、数据可用性、 数据共享、代码可用性、学术写作数据声明、写数据声明、数据存放、数据仓库选择.

Create, revise, audit, and export submission-grade scientific figures for Nature-family and other high-impact venues in Python (matplotlib/seaborn) or R (ggplot2/patchwork/ComplexHeatmap), including multi-panel plots, figures4papers-style work, and journal-ready SVG/PDF/TIFF outputs. Use for paper or scientific plots, manuscript data visualization, 论文配图、学术写作配图、科研绘图、科研作图、画图、作图、出图、论文图表、可视化. Define the conclusion, evidence logic, data integrity, template compatibility, export needs, and reviewer risks before plotting; honor or persist the Python/R backend choice. Also use the separate OpenRouter GPT Image 2 route for explicit AI-generated graphical abstracts, mechanism diagrams, concept schematics, 论文示意图、机制示意图、图形摘要; this route skips backend choice and treats outputs as drafts. Do not use for interactive dashboards, statistics-only analysis, data cleaning, literature review, code debugging, pure photo editing, or Illustrator/Figma-first infographics without manuscript-figure intent.

Complete automated literature discovery pipeline: multi-source search → six-dimension scoring → fine reading → formatted delivery → archival. Combines a configurable engine with daily cron-driven application layer. Works with Feishu, Telegram, or any messaging platform.

Proposal-first scientific writing pipeline. Three modes (compose/revise/hybrid) with four-layer QA pipeline. Enforces evidence-before-prose, argument-before-sections, and contracts-before-paragraphs.

对学术文献逐条执行多源交叉验证，逐字段对比作者、标题、年份、卷期、页码， 标记卷年/DOI年冲突、作者顺序异常、页码偏差等问题，输出结构化验证报告。 可批量处理整篇论文/开题报告的参考文献列表，也可单条校验，支持与 Zotero 同步修正。

Draft, audit, or revise Nature-style revision correspondence packages: point-by-point reviewer response letters, rebuttal letters, revision cover letters, LaTeX cover/response templates, and red-marked revised-manuscript excerpts. Use for reviewer comments, editor decision letters, pasted editorial emails, response drafts, cover letters, response to reviewers, rebuttal, 修回信, 返修邮件, 编辑邮件, 返修 cover letter, 审稿意见回复, 逐点回复, 大修回复, 小修回复, 回复审稿人, 修改稿回复, 写rebuttal, 回应审稿意见, 标红修改, or LaTeX 模板.

Simulate a Nature-style reviewer assessment from the referee perspective rather than an author rebuttal. Use when the user wants a pre-submission review, reviewer report, peer-review style critique, novelty/significance/technical soundness assessment, reviewer-style manuscript evaluation, 审稿人视角评估, 预审稿意见, or Nature reviewer report. Return 3 reviewer reports plus a cross-review synthesis, grounded only in the local Nature reviewer source basis. Also trigger on general pre-submission review requests during academic writing even without the word "Nature", such as getting a mock peer review for any journal, critiquing a draft as a reviewer would, assessing novelty/rigor before submission, and Chinese phrasings like 审稿人视角、模拟审稿、预审、帮我审一下论文、投稿前自审、审稿意见模拟、找论文问题.

Audit, revise, or draft manuscript statistical reporting for Nature / high-impact journal submissions. Use when the user asks to check statistical analysis sections, p values, confidence intervals, sample size, biological versus technical replicates, randomization, blinding, multiple-comparison correction, model assumptions, figure legends, Results statistics wording, reviewer comments about statistics, or Chinese academic drafts needing publication-ready Statistical analysis text. Also trigger on general paper-statistics requests such as 统计审查、统计分析小节、统计方法、p值、样本量、重复数、多重比较、置信区间、效应量、图注统计、审稿人统计意见.

Scaffold a new Open Knowledge Format (OKF) knowledge base and populate it from existing material: a tree of small markdown concept files with YAML frontmatter, a spec, a validator, and session-start hooks that orient Claude on the knowledge base before it works. Use when the user wants to start an OKF atlas/wiki/knowledge base, build one from existing docs, plans, notes, or a repo, structure docs as one-concept-per-file with provenance, or initialize OKF in a repo (optionally into its GitHub wiki).

Query the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants. Use when a question is about individuals or variants in the 1000 Genomes Project cohort: which individuals carry variants matching specific criteria in a gene or region, which individuals are homozygous-reference at a position, which variants exist in the dataset or carried by specified individuals in a gene or region, the relatedness between two specified individuals. Variants are returned with 1000 Genomes allele frequencies (AF), gnomAD v4.1 exome and genome AF, AlphaMissense score, and HGVSp annotations.

MCP bio bridge

Pipeline maestro

Trial shortlist

Improve the clarity and voice of AI-assisted academic writing (papers, theses, rebuttals) and funding proposals (NSF Project Summary/Description, NIH Specific Aims): preserve scholarly conventions, match claims to evidence (and, for proposals, claims to feasibility), and match the author's own voice. It never changes a number, result, or citation, and it is not for evading AI-use disclosure. Use when editing AI-assisted academic prose or grant proposals.

Use after generating code, after accepting AI suggestions, or when reviewing AI-written modules. Also use when code works but feels brittle, when error handling seems thin, when orphaned resources or missing cleanup are suspected, or when the agent claims done but hidden debt may exist. Catches the specific failure patterns AI agents produce that humans would not.

Single-variant common-variant GWAS with plink2 --glm (linear/logistic, Firth) and the linear mixed models GEMMA, BOLT-LMM, SAIGE, regenie (SPA). A GWAS statistic is valid only when genotype is independent of unmodeled phenotype drivers after the chosen covariates and random effects, so the engine follows sample structure and case:control imbalance, not taste: PC covariates absorb continuous ancestry but cannot remove relatedness (a covariance structure needing an LMM), genomic inflation above 1 is mostly true polygenic signal not confounding (the LDSC intercept is the diagnostic), LOCO prevents proximal contamination, and SPA/Firth keep the tail calibrated at extreme imbalance and low MAC. Use when running single-variant GWAS, choosing between a GLM and a mixed model, or controlling stratification, relatedness, and case:control imbalance. For rare-variant aggregation (burden, SKAT, SKAT-O, ACAT) see rare-variant-association; fine-mapping and MR see causal-genomics; PRS see clinical-databases/polygenic-risk.

End-to-end CLIP-seq pipeline from FASTQ to ENCODE-compliant binding sites, single-nucleotide crosslink maps, annotation, motifs, and (optionally) differential binding. Use when running the full Yeo lab eCLIP / iCLIP / iCLIP2 / iCLIP3 / irCLIP / PAR-CLIP analysis with SMInput control, protocol-specific UMI extraction, ENCODE STAR parameters, CLIPper or Skipper peak calling with stringent log2 FC and -log10 p thresholds, IDR rescue and self-consistency QC, and downstream motif registration with mCross or PEKA.

Orchestrates the copy-number pipeline from BAM to segmented, integer-called, annotated CNVs, forking on germline-vs-somatic - CNVkit (somatic exome/panel: coverage -> assay-matched reference/PoN -> fix -> segment -> purity/ploidy-aware call), GATK gCNV (germline rare-CNV cohort), and allele-specific callers (ASCAT/FACETS/PURPLE) for purity/ploidy. Use when committing the build + target/access BED + PoN once (assay-matched), building the reference from normals BEFORE segmenting, fitting purity/ploidy BEFORE integer calls in tumors, centering on the true (non-diploid) mode before GISTIC2 recurrence, or routing cfDNA to ichorCNA. Hands mechanism to the copy-number component skills; not a re-teach of any single step.

End-to-end pooled and single-cell CRISPR screen analysis from FASTQ to hit genes. Orchestrates library design QC, guide counting, six-stage screen QC (plasmid Gini, replicate Pearson, CEGv2 PR-AUC, copy-number artifact), method-appropriate hit calling across MAGeCK RRA/MLE, BAGEL2, drugZ, JACKS, and Chronos, cancer-cell-line copy-number correction (CRISPRcleanR / Chronos), batch correction for multi-batch screens, and the specialized branches for combinatorial paralog screens, single-cell Perturb-seq, base-editor variant-function screens, prime-editor screens, and in vivo bottleneck-aware screens. Use when analyzing any pooled CRISPR screen end-to-end, matching the hit-calling method to the experimental design, integrating copy-number correction into the pipeline, or branching the workflow for single-cell, combinatorial, base-editor, prime-editor, or in vivo variants.

Install and operate Hermes Tweet, a Hermes Agent plugin for X/Twitter research, timeline reading, tweet analysis, and approval-gated tweet actions. Use this skill when installing Hermes Tweet, researching X/Twitter accounts, monitoring launch signals, investigating mentions, auditing giveaways, or preparing guarded tweet actions. Use proactively when a Hermes Agent workflow needs current X/Twitter context. Requires XQUIK_API_KEY for read and action tools.

Analyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct RNA, R10.4.1+) long-read RNA-seq with full-isoform resolution. Tools include FLAIR (correct/collapse/quantify/diffSplice for PacBio + ONT), IsoQuant (de-novo or annotation-guided isoform discovery 2024 SOTA), Bambu (annotation-aware Bayesian discovery + quantification with Novel Discovery Rate), SQANTI3 (isoform classification: FSM/ISM/NIC/NNC + artifact flags), rMATS-long (event calling on long-read isoforms), and minimap2 (-ax splice:hq for HiFi; -ax splice -k14 for ONT cDNA; add -uf only for direct RNA or stranded cDNA preps). Solves microexon detection, recursive splicing, complex multi-exon isoforms, and DTU without transcript-quantification uncertainty. Use when short-read AS limitations (anchor length, complex isoforms, microexons, recursive splicing, transcript ambiguity) demand full-isoform resolution.

Imports Bismark coverage or cytosine-report files into the methylKit object model, then runs the import-to-results spine - filterByCoverage, normalizeCoverage, unite/destrand, calculateDiffMeth, getMethylDiff - for both per-CpG (DMC) and fixed-tile (DMR) differential methylation, plus tileMethylCounts, PCA/correlation/clustering QC, and assocComp/removeComp batch handling. Covers the silent default traps that shape the false-positive rate: overdispersion='none' does no correction while 'MN' forces the F-test (ignoring test='Chisq'), adjust defaults to SLIM not BH, getMethylDiff defaults difference=25/qvalue=0.01, cov.bases=0 admits single-CpG tiles, and pool destroys biological replication. Use when importing bisulfite count tables, filtering/normalizing/uniting methylation samples, running methylKit differential testing, or QC-ing methylomes. For per-site test-choice (count vs continuous) see differential-cpg-testing; for selection-aware region FDR (dmrseq/DSS) see dmr-detection.

Orchestrates neoantigen discovery from somatic variants to ranked vaccine candidates, chaining HLA typing (OptiType/arcasHLA + LOHHLA), VEP annotation (Wildtype+Frameshift plugins) + expression/readcount annotation, proximal-variant phasing, pVACseq MHC-I/II binding, CCF/clonality, and immunogenicity/quality ranking. Use when recognizing that binding is single-digit PPV and the critical steps are downstream (full-resolution HLA + LOH gating, proximal-variant phasing, clonality from purity+CN not raw VAF, expression), sequencing normalize+annotate -> phase -> HLA -> binding -> quality in the defensible order, dropping candidates on LOH-lost alleles, supplying --phased-proximal-variants-vcf so the mutant peptide is real, or ranking WITHIN patient rather than a fixed IC50 threshold. Hands mechanism to the immunoinformatics component skills; not a re-teach of any single step.

Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.

Ancient text restoration, attribution, dating, contextualization, and embedding via Aeneas (Latin) / Ithaca (Ancient Greek). Use when asked to "restore", "attribute", "date", "contextualize", "find parallels", "where was it written", "when was it written", "embed", or "analyze" an ancient text, inscription, or epigraphic document, or when the user mentions "Aeneas", or "Ithaca".

This skill should be used when the user asks to "optimize a prompt", "improve prompt performance", "design a prompt template", "write better prompts", "debug prompt issues", "use chain-of-thought", "structured prompting", "few-shot prompting", or wants to apply advanced prompt engineering patterns for production LLM applications.

Use when working on complex multi-step tasks, when a session is getting long (40+ tool calls), when the agent starts ignoring rules it followed earlier, when conventions drift, when output quality seems to degrade, or after any context compaction event. Prevents long-session corruption AND context compaction amnesia through behavioral self-enforcement.

Chains a somatic (tumor-normal) SNV/indel and structural-variant pipeline end to end with GATK Mutect2 (or Strelka2), wiring the somatic-specific machinery - panel-of-normals and gnomAD germline-resource priors, GetPileupSummaries/CalculateContamination, and LearnReadOrientationModel FFPE/oxoG orientation-bias filtering fed into FilterMutectCalls. Use when calling somatic mutations from a tumor-normal pair (or tumor-only with PoN caveats), deciding which artifact filter removes which class of false positive, reasoning about VAF/purity/ploidy and clonal-vs-subclonal detection, adding somatic SV/CNV or TMB/MSI/signatures, or routing variants to AMP/ASCO/CAP tier and oncogenicity interpretation (never germline ACMG).

Checks whether the uv Python package manager is installed and installs it if missing. Ensures uv is on PATH. Use when another skill requires uv as a prerequisite.

Use when making UI/frontend changes guided by visual context, when the user selects elements visually, draws annotations, or provides screenshots alongside change requests. Also use when editing components where spatial context (element identity, DOM references, layout data) supplements text instructions.

Retrieve and analyze AlphaFold predicted structures for a protein. Use when the user provides a specific UniProt Accession ID and wants structural confidence metrics (pLDDT), domain boundary analysis, or disorder assessment. Do not use if the user only has a protein name, gene name, or amino acid sequence — ask for a UniProt ID first.

Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API. Use when the user asks about non-coding variant effects, pathogenicity, clinical significance, disease associations, functional effects, gene expression changes, splicing disruption, or regulatory effects in promoters and enhancers. Also use for resolving biological terms to tissue/cell-type ontologies (UBERON/CL) or analyzing variants in chr:pos:ref>alt format.

Query the ChEMBL database for bioactive molecules, drug targets, bioactivity data, approved drugs, and chemical structures. Use when the user asks about compounds, targets, IC50/Ki values, drug mechanisms, or structure searches.

Reference for the Claude API / Anthropic SDK — model ids, pricing, params, streaming, tool use, MCP, agents, caching, token counting, model migration. TRIGGER — read BEFORE opening the target file; don't skip because it "looks like a one-liner" — whenever: the prompt names Claude/Anthropic in any form (Claude, Anthropic, Fable, Opus, Sonnet, Haiku, `anthropic`, `@anthropic-ai`, `claude-*`, `us.anthropic.*`, `[1m]`); the user asks about an LLM (pricing/model choice/limits/caching) — never answer from memory; OR the task is LLM-shaped with provider unstated (agent/MCP/tool-definition/multi-agent/RAG/LLM-judge/computer-use; generate/summarize/extract/classify/rewrite/converse over NL; debugging refusals/cutoffs/streaming/tool-calls/tokens). SKIP only when another provider is being worked on (overrides all triggers): OpenAI/GPT/Gemini/Llama/Mistral/Cohere/Ollama named in the query; OR `grep -rE 'openai|langchain_openai|google.generativeai|genai|mistralai|cohere|ollama'` over the project hits (run this grep...

Query ClinicalTrials.gov via APIv2. Use when you want to search for trials by condition, drug, location, status, or phase; retrieve trial details by NCT ID; check eligibility/inclusion criteria; count trials across conditions or time periods; identify a sponsor's trial portfolio; find recruiting trials for patient matching.

Use when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls for human genomic variants.

Instructions for handling API keys and credentials safely, verifying their presence, and prompting the user to add them if missing using a safe protocol.