Claude Skills by FridrichMethod

Master monorepo management with Turborepo, Nx, and pnpm workspaces to build efficient, scalable multi-package repositories with optimized builds and dependency management. Use when setting up monorepos, optimizing builds, or managing shared dependencies.

"Multi-objective, gradient-based protein binder design with Mosaic. Use this skill when: (1) Composing several structure or sequence models into one design objective, (2) Optimizing binders against a custom loss rather than a fixed pipeline, (3) Wanting gradient descent over sequence space in the style of ColabDesign, RSO, or BindCraft but with interchangeable predictors, (4) Letting the optimizer choose the epitope instead of fixing hotspots.

Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER, MEME-ChIP (STREME, CentriMo, TOMTOM, FIMO), monaLisa, and AME. Handles background selection (GC-matched, dinucleotide-shuffled, Markov order-2, peak-flanks), motif databases (JASPAR 2024 CORE PWMs, JASPAR 2026 deep-learning collection, HOCOMOCO v12, HOMER built-in), centrally-enriched motif testing, and differential motif analysis. Use when identifying TF binding motifs in pea...

Analyze TF motif accessibility variability across samples or single cells using chromVAR. Use when identifying TF motifs whose accessibility correlates with conditions, computing per-sample motif z-scores after matched background correction, comparing to ArchR / Signac equivalents, or distinguishing motif-accessibility signal from per-site footprinting.

AI-powered myeloproliferative neoplasm monitoring for disease progression prediction, treatment response tracking, and transformation risk assessment in PV, ET, and myelofibrosis.

Myeloproliferative neoplasm (MPN) research expertise including JAK2/CALR/MPL mutations, myelofibrosis, polycythemia vera, essential thrombocythemia. Use for MPN literature search, driver mutation analysis, PPM1D pathway analysis, fibrosis markers, megakaryocyte biology, clinical trial data interpretation, and translational research.

Ultra-sensitive AI-powered molecular residual disease detection using MRD-EDGE deep learning for sub-0.001% VAF ctDNA detection and early relapse prediction.

Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.

Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when comparing alignment quality, measuring sequence divergence, and analyzing evolutionary patterns.

Configure mutual TLS (mTLS) for zero-trust service-to-service communication. Use when implementing zero-trust networking, certificate management, or securing internal service communication.

AI-powered multi-ancestry polygenic risk score calculation and optimization for equitable disease risk prediction across diverse global populations.

Design multi-cloud architectures using a decision framework to select and integrate services across AWS, Azure, GCP, and OCI. Use when building multi-cloud systems, avoiding vendor lock-in, or leveraging best-of-breed services from multiple providers.

Analyzes medical images (X-ray, MRI, CT) using multimodal LLMs to identify anomalies and generate reports.

AI-powered multimodal diagnostic fusion integrating radiology imaging (CT/MRI/PET), digital pathology (WSI), genomics, and clinical data for comprehensive cancer diagnosis and treatment planning.

Assemble multiple plots into ONE publication-ready multi-panel journal figure (e.g. Figure 1 with panels A, B, C). Use whenever the user asks to combine, compose, or lay out several plots as a single composite figure — newly plotted from data or from already-rendered panels the user supplies (PNG/PDF). Ask the user to pick one of two approaches: (1) redraw every panel into one unified figure using independent, tightly packed `subfigures` (each sized to its own labels, so axes need NOT align),...

Multi-modal single-cell analysis with muon/MuData. Joint RNA+ATAC (10x Multiome), CITE-seq (RNA+protein), other multi-omics. MuData holds per-modality AnnData with shared obs. WNN joint embedding, per-modality preprocessing, MOFA factor analysis. Use scanpy-scrna-seq for single-modality RNA; use muon when combining 2+ omics from the same cells.

AI-powered minimal residual disease (MRD) analysis for multiple myeloma using next-generation flow cytometry, NGS, and mass spectrometry approaches.

Queries myvariant.info BioThings aggregator for ClinVar, gnomAD, dbSNP, dbNSFP, COSMIC, CADD, and CIViC annotations in batched, version-tracked requests. Use when annotating variant lists from multiple databases simultaneously without managing per-source APIs, and when reproducibility-grade analyses require recording source data versions via _meta.

Search literature across sources, verify or manage citations, and build MeSH strategies or citation-impact audits. Use for 文献检索、引文核对、参考文献管理、严格他引 and evidence-backed citer profiles; not for translating a paper or drafting manuscript prose.

Find and verify Nature/CNS-family literature supporting manuscript claims, with claim-to-source mapping and reference-manager export. Use for Nature系列引用、CNS支撑文献、分段补引用 when this journal scope is requested; use broader literature search for unrestricted sources.

Draft or audit manuscript Data/Code Availability statements, dataset access routes, repository plans, and FAIR metadata. Use for 数据可用性声明、数据共享、数据仓库选择 and dataset citations; not general data cleaning or statistical analysis.

Create, revise, audit, and export manuscript scientific figures in Python or R. Use for 论文配图、科研绘图、多面板图 and submission-ready plots, or explicitly requested AI-generated graphical abstracts and mechanism schematics. Not for interactive dashboards, data cleaning, or statistics-only analysis.

Reconstruct slide images, screenshots, scanned PDFs, or image-only PPTX files as object-level editable PowerPoint. Use for 图片转可编辑PPT、截图还原PPT and diagram reconstruction; not authoring a new deck from research notes.

"Complete automated literature discovery pipeline: multi-source search → six-dimension scoring → fine reading → formatted delivery → archival.

Turn research papers or inventor materials into evidence-grounded Chinese invention patent drafts and technical disclosures. Use for 技术交底书、专利撰写、现有技术对比 and Chinese DOCX patent packages; not general manuscript writing.

Create or improve a Chinese academic PPTX from a scientific paper or research reading notes, with source figures and speaker notes. Use for 论文做PPT、文献汇报、组会PPT and paper-based conference or defense presentations.

Polish, translate, or tighten existing academic prose while preserving facts, terminology, and evidence boundaries. Use for 论文润色、学术翻译、正文精简, or manuscript LaTeX layout fixes. Use nature-writing when the main task is drafting new sections or rebuilding the manuscript argument.

Compose, revise, or audit research proposals, opening reports, and research plans from supporting evidence. Use for 研究计划、开题报告、科研项目申请书. Invoked as researchwrite for compatibility; use nature-writing for general manuscript sections.

Create source-grounded Chinese-English paper readers with aligned text, figures, tables, and equations. Use for 全文翻译、中英文对照、论文精读 or source-linked questions about a paper; respect a requested excerpt or question without generating a full reader.

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 responses to peer review, revision cover letters, and marked-manuscript or LaTeX revision packages. Use for 审稿意见回复、逐点回复、返修信、 rebuttals and edits to existing response drafts. Initial-submission materials belong to nature-writing; simulated peer review belongs to nature-reviewer.

Provide evidence-grounded mock peer review of scientific manuscripts or excerpts, covering significance, validity, and major/minor concerns. Use for 模拟审稿、投稿前自审、审稿人视角评估; not author rebuttal drafting.

Internal shared-reference support package for installed Nature Skills, including nature-writing, nature-polishing, nature-response, nature-reader, and nature-paper2ppt. Do not invoke it as a standalone user workflow. Load only the specific core or journal-format file requested by another Nature skill.

Audit or improve manuscript statistical reporting, including experimental units, replication, uncertainty, tests, and figure statistics. Use for 统计审查、统计方法小节、图注统计 and reviewer concerns; compute new analyses only when requested with data.

Draft or restructure scientific manuscript arguments, sections, and initial-submission materials from author-provided evidence. Use for 论文写作、章节起草、论证重构、正文压缩、首次投稿材料. Use nature-polishing for language-only edits to existing prose and nature-response for post-decision correspondence.

Retrieve protein and nucleotide sequences from NCBI databases using E-utilities. Supports direct accession lookup, CDS translation, gene+organism search, locus lookup, PubMed-linked sequences, patent protein extraction, and organism+length fallback search. Use when you need to fetch biological sequences by accession, gene name, locus tag, PubMed ID, or patent number.

Email newsletter workflows. Use when creating newsletters, building subscriber lists, designing templates, or tracking engagement.

Enforces AP Style and newsroom conventions. Use when writing news, editing drafts, creating headlines, or tightening copy.

Master Next.js 14+ App Router with Server Components, streaming, parallel routes, and advanced data fetching. Use when building Next.js applications, implementing SSR/SSG, or optimizing React Server Components.

Implement NFT standards (ERC-721, ERC-1155) with proper metadata handling, minting strategies, and marketplace integration. Use when creating NFT contracts, building NFT marketplaces, or implementing digital asset systems.

Next-generation sequencing data analysis pipelines including bulk RNA-seq, scRNA-seq preprocessing, variant calling, and quality control. Use when working with FASTQ files, alignment (STAR, BWA), quantification (featureCounts, Salmon), DESeq2/edgeR analysis, or building NGS pipelines. Supports GEO/SRA data retrieval.

Foundation model-powered spatial transcriptomics analysis leveraging 53M+ spatially resolved cells for cellular architecture modeling and tissue niche discovery.

AI-powered NK cell therapy design for cancer immunotherapy including CAR-NK engineering, memory-like NK generation, and KIR/HLA matching optimization.

Build production-ready Node.js backend services with Express/Fastify, implementing middleware patterns, error handling, authentication, database integration, and API design best practices. Use when creating Node.js servers, REST APIs, GraphQL backends, or microservices architectures.

Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC, ATACseqQC, DANPOS3, or scprinter. Use when characterizing nucleosome organization at promoters and enhancers, calling +1/-1 nucleosomes flanking NFRs, generating V-plots for chromatin structure visualization, or comparing nucleosome positioning between conditions.

Three-tiered approach to omics data analysis (transcriptomics, proteomics) covering validated pipelines, standard workflows, and custom methods

omics-plotting: publication-style figure authoring for omics / bioinformatics results with matplotlib / seaborn. Read this before writing any plotting or figure code in any omics analysis — RNA-seq, proteomics, single-cell, variant, or database results — not only when a plot is explicitly requested: whenever an analysis will produce a figure, load this first and follow its recipes. Covers volcano, MA, expression / correlation heatmap, GSEA bar / dot plot, box / violin / bar / ridgeline, PCA /...

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 individ...

Query, search, and download data from the openFDA API for drugs, devices, foods, tobacco, cosmetics, animal and veterinary products, substances, and transparency data. Use for FDA adverse events, recalls, labeling, approvals, shortages, 510(k) clearances, NDC lookups, and any FDA safety or regulatory data query across all 28 API endpoints.

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