Claude Skills by FridrichMethod

Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audit (library prep, read length, depth, replicates), STAR 2-pass cohort-style alignment, junction saturation curves and discovery plateau detection, novel-vs-known junction ratio diagnostics, junction-overhang distribution, splice-site strength scoring (MaxEntScan intrinsic + SpliceAI context-aware), strandedness verification, GENCODE basic vs comprehensive choice, and rRNA con...

Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter (annotation-free intron clusters), VAST-TOOLS (cross-species with microexon support), Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage), or IRFinder-S (intron retention coverage-aware). Distinguishes the five canonical event classes (SE, A5SS, A3SS, MXE, RI), special classes (microexons, exitrons, AFE/AL...

Master SQL query optimization, indexing strategies, and EXPLAIN analysis to dramatically improve database performance and eliminate slow queries. Use when debugging slow queries, designing database schemas, or optimizing application performance.

Track, calculate, and optimize key performance metrics for SaaS, marketplace, consumer, and B2B startups from seed through Series A, including unit economics, growth efficiency, and cash management. Use this skill when defining a metrics framework, calculating CAC/LTV/burn multiple, benchmarking business health, or preparing metrics dashboards for investors or board reporting.

Guided statistical analysis: test choice, assumption checks, effect sizes, power, APA reporting. Pick tests, verify assumptions, or format results for publication. Covers frequentist (t-test, ANOVA, chi-square, regression, correlation, survival, count, reliability) and Bayesian. Use statsmodels or pymc-bayesian-modeling to fit.

Crafts story pitches for different outlets. Use when pitching editors, writing query letters, or shaping feature or op-ed angles.

Systematic strategic planning framework for philosophy and interdisciplinary academic papers targeting preprint platforms (PhilArchive, arXiv, PhilSci-Archive). Use when users want to: (1) plan a paper on a specific topic, (2) identify research gaps and assess originality, (3) develop optimized paper outlines, (4) prepare for preprint submission, or (5) understand platform requirements and writing standards. Triggered by phrases like 'plan a paper on,' 'help me design a paper about,' 'identif...

Apply STRIDE methodology to systematically identify threats. Use when analyzing system security, conducting threat modeling sessions, or creating security documentation.

Query the STRING database for protein-protein interactions (PPIs), functional enrichment, and homology. Use when the user asks about interactions between specific proteins, interaction evidence, confidence scores, protein interaction partners, or pathway enrichments.

Implement Stripe payment processing for robust, PCI-compliant payment flows including checkout, subscriptions, and webhooks. Use when integrating Stripe payments, building subscription systems, or implementing secure checkout flows.

Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticity dialect, vector binding, atom map indices, and reactive/PAINS/REOS/Brenk filter catalogs. Use when filtering compounds by pharmacophore features, functional groups, scaffold matches, or screening for assay-interference / structural alerts.

Identifies super-enhancers from H3K27ac, MED1, or BRD4 ChIP-seq using ROSE, ROSE2, LILY, HOMER -style super, and ENCODE dELS cross-referencing. Handles peak stitching parameters, ranking choices, hockey-stick inflection, marker choice (H3K27ac vs MED1/BRD4), and cross-condition comparison with spike-in normalization. Constructs core regulatory circuitry (Saint-Andre 2016) from SE-encoded TFs. Use when identifying cell-identity / cancer-associated regulatory domains, comparing super-enhancers ...

Install-time cooldowns for npm/bun plus a sandboxed pre-install scan for bypasses. Use for supply-chain attacks or npm security.

Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting...

Build scalable design systems with Tailwind CSS v4, design tokens, component libraries, and responsive patterns. Use when creating component libraries, implementing design systems, or standardizing UI patterns.

AI-powered analysis of T-cell exhaustion states, epigenetic scarring, stem-like T-cell populations, and checkpoint blockade response prediction in cancer immunotherapy.

AI-powered TCR-peptide-MHC interaction prediction using AlphaFold3 and deep learning for therapeutic TCR discovery, neoantigen validation, and T cell immunogenicity assessment.

AI-powered T-cell receptor repertoire analysis for cancer diagnosis, immunotherapy response prediction, and therapeutic TCR selection using deep learning and multi-layer ML approaches.

Structured messaging protocols for agent team communication including message type selection, plan approval, shutdown procedures, and anti-patterns to avoid. Use this skill when establishing communication norms for a newly spawned team, when deciding whether to send a direct message or a broadcast, when a team-lead needs to review and approve an implementer's plan before work begins, when orchestrating a graceful team shutdown after all tasks are complete, or when debugging why teammates are ...

Design optimal team structures, hiring plans, compensation strategies, and equity allocation for early-stage startups from pre-seed through Series A. Use this skill when planning headcount, determining which roles to hire next, setting compensation or equity ranges, designing org structure, or building a hiring budget aligned to funding milestones.

Design optimal agent team compositions with sizing heuristics, preset configurations, and agent type selection. Use this skill when deciding how many agents to spawn for a task, when choosing between a review team versus a feature team versus a debug team, when selecting the correct subagent_type for each role to ensure agents have the tools they need, when configuring display modes (tmux, iTerm2, in-process) for a CI or local environment, or when building a custom team composition for a non-...

Selects the correct CLAUDE.md or LESSONS.md template via decision trees. Use when starting a project or unsure which fits.

Build reusable Terraform modules for AWS, Azure, GCP, and OCI infrastructure following infrastructure-as-code best practices. Use when creating infrastructure modules, standardizing cloud provisioning, or implementing reusable IaC components.

Enforces a test-driven bug-fixing workflow. Use when a user reports a bug, failing code, an error, or asks to fix something.

Map identified threats to appropriate security controls and mitigations. Use when prioritizing security investments, creating remediation plans, or validating control effectiveness.

AI-powered time-resolved cryo-EM analysis for capturing protein dynamics, drug-binding kinetics, and conformational transitions for dynamics-based drug discovery.

Analyzes time-series and longitudinal RNA-seq for differential expression and trajectory structure. Covers DESeq2 LRT with reduced models, time as factor vs continuous vs natural splines, maSigPro (Nueda 2014 for RNA-seq), ImpulseDE2 with explicit impulse-model failure modes, DREAM for repeated measures via linear mixed models, pseudoreplication avoidance, conditional vs marginal modeling, and trajectory clustering with DPGP, Mfuzz (with Schwämmle 2010 fuzzifier estimation), and splines+k-mea...

Comprehensive AI-powered tumor microenvironment immune profiling integrating bulk deconvolution, single-cell analysis, and spatial transcriptomics for immunotherapy biomarker discovery.

Offers the user an informed choice about how much response depth to consume before answering. Use this skill when the user explicitly wants to control response length, depth, or token budget. TRIGGER when: \"token budget\", \"token count\", \"token usage\", \"token limit\", \"response length\", \"answer depth\", \"short version\", \"brief answer\", \"detailed answer\", \"exhaustive answer\", \"respuesta corta vs larga\", \"cuántos tokens\", \"ahorrar tokens\", \"responde al 50%\", \"dame la v...

Production-ready single-cell and expression matrix analysis using scanpy, anndata, and scipy. Performs scRNA-seq QC, normalization, PCA, UMAP, Leiden/Louvain clustering, differential expression (Wilcoxon, t-test, DESeq2), cell type annotation, per-cell-type statistical analysis, gene-expression correlation, batch correction (Harmony), trajectory inference, and cell-cell communication analysis. NEW: Analyzes ligand-receptor interactions between cell types using OmniPath (CellPhoneDB, CellChatD...

Production-ready VCF processing, variant annotation, mutation analysis, and structural variant (SV/CNV) interpretation for bioinformatics questions. Parses VCF files (streaming, large files), classifies mutation types (missense, nonsense, synonymous, frameshift, splice, intronic, intergenic) and structural variants (deletions, duplications, inversions, translocations), applies VAF/depth/quality/consequence filters, annotates with ClinVar/dbSNP/gnomAD/CADD via ToolUniverse, interprets SV/CNV c...

AI-powered ternary complex prediction for targeted protein degradation, modeling POI-degrader-E3 ligase assemblies to optimize PROTAC and molecular glue efficacy.

Use this skill when creating, managing, or working with Conductor tracks - the logical work units for features, bugs, and refactors. Applies to spec.md, plan.md, and track lifecycle operations.

Models continuous temporal trajectories from BULK or time-resolved omics where the x-axis is measured experimental time: penalized GAMs (mgcv) for smooth trends and changepoint detection (segmented, ruptures) for abrupt regime shifts. Use when deciding between a smooth GAM and a changepoint model; choosing the GAM distribution (nb() plus a library-size offset for raw counts vs Gaussian on vst/log-CPM); setting the basis-dimension ceiling k below the number of timepoints and letting REML pick ...

Infers person-to-person transmission from pathogen genomes using outbreaker2, TransPhylo, phybreak, BadTrIP, SCOTTI, BEASTLIER, and SNP-distance / cluster-picker approaches (HIV-TRACE for HIV; transcluster). Defines outbreak clusters using pathogen-specific SNP thresholds (NOT a universal cutoff -- TB <=12 SNPs; MRSA <=15; C. difficile <=2; Klebsiella <=21), models within-host diversity and transmission bottlenecks, integrates contact-tracing data, distinguishes generation from serial interva...

Parse trial protocols and patient data to produce criterion-level MET/NOT/UNKNOWN determinations with evidence and gaps for clinical trial screening tasks.

Trial shortlist

AI-powered analysis of tumor clonal architecture, subclonal dynamics, and evolutionary trajectories from multi-region sequencing and longitudinal liquid biopsy data.

Estimates tumor fraction (the genome-wide proportion of cfDNA molecules that are tumor-derived, the cfDNA analogue of bulk-tumor purity) from shallow whole-genome sequencing with ichorCNA, an HMM over 1 Mb bins that jointly EM-estimates tumor fraction, ploidy, and subclonal prevalence over a normal/ploidy grid. Encodes the load-bearing reframes: tumor fraction is the quantity that travels across assays and is NOT mutation VAF (clonal-het VAF approximately TF/2), CNA-based estimation has a har...

AI-powered intratumor heterogeneity analysis for clonal architecture reconstruction, subclonal evolution tracking, and therapy resistance prediction using multi-region and longitudinal sequencing.

Calculates and harmonizes Tumor Mutational Burden (TMB) across platforms to predict immunotherapy response.

Calculates tumor mutational burden from WES/WGS/panel data with Friends of Cancer Research harmonization equations, per-assay calibration (FDA 10/Mb = 7.8 TSO500 = 8.4 OncomineTML), synonymous/indel/germline filtering, hypermutator tiering, blood TMB, and integration with HLA-LOH and neoantigen quality (Luksza 2017 fitness). Use when assessing ICI eligibility under tumor-specific cutoffs (McGrail 2021), comparing tissue vs bTMB, or auditing TMB-H reporting against ESMO 2024 and FDA pembrolizu...

Configure Turborepo for efficient monorepo builds with local and remote caching. Use when setting up Turborepo, optimizing build pipelines, or implementing distributed caching.

Master TypeScript's advanced type system including generics, conditional types, mapped types, template literals, and utility types for building type-safe applications. Use when implementing complex type logic, creating reusable type utilities, or ensuring compile-time type safety in TypeScript projects.

Fetch Evolutionary Conservation scores (phyloP, phastCons) and Transcription Factor Binding Sites (TFBS) from the UCSC Genome Browser. Use when analyzing whether genomic variants or regions are evolutionarily conserved, functionally important, or bounded by TF regulators across major projects (ENCODE, JASPAR, ReMap).

Semantic search across UK Biobank's 12,000+ data fields and publications — find the right variables for your research question.

UMAP dimensionality reduction for visualization, clustering prep, and feature engineering. Fast nonlinear manifold learning preserving local and global structure. Standard UMAP (fit/transform, sklearn-compatible), supervised/semi-supervised, Parametric UMAP (NN encoder/decoder, TensorFlow), DensMAP (density), AlignedUMAP (temporal/batch). 15+ distance metrics, custom Numba metrics, precomputed distances. For linear reduction use PCA; for neighborhood graphs use sklearn NearestNeighbors.

Queries the UniBind database for experimentally validated transcription factor (TF) binding sites. Use when retrieving direct TF-DNA interaction datasets, downloading binding site coordinates (BED/FASTA) for local analysis, or listing available datasets by species, cell line, or TF name. Don't use to query specific intervals, locations, genes, motif models or expression data.

Query UniProt's REST API (post-2022 endpoint at rest.uniprot.org) for protein sequences, annotations, GO terms, cross-references, ID mappings, and proteomes. Use when fetching UniProtKB entries, navigating the JSON schema, choosing between UniProtKB/UniRef/UniParc/Proteomes resources, deciding stream vs search endpoint for batch retrieval, running ID-mapping jobs with the async pattern, handling isoform suffixes, or filtering reviewed Swiss-Prot vs auto-annotated TrEMBL. Encodes the legacy UR...

"Access UniProt for protein sequence and annotation retrieval. Use this skill when: (1) Looking up protein sequences by accession, (2) Finding functional annotations, (3) Getting domain boundaries, (4) Finding homologs and variants, (5) Cross-referencing to PDB structures.