Claude Code Skills · page 33

Search arXiv physics, math, and computer science preprints using natural language queries. Powered by Valyu semantic search.

Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.

Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions. Use for literature reviews, evidence synthesis, and finding experimental details not available in abstracts alone.

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Query BindingDB for measured drug-target binding affinities (Ki, Kd, IC50, EC50). Search by target (UniProt ID), compound (SMILES/name), or pathogen. Essential for drug discovery, lead optimization, polypharmacology analysis, and structure-activity relationship (SAR) studies.

Predicts ADMET properties using ADMETlab 3.0 API or DeepChem models. Estimates bioavailability, CYP inhibition, hERG liability, and 119 toxicity endpoints with uncertainty quantification. Filters for PAINS and other structural alerts. Use when filtering compounds for drug-likeness or prioritizing leads by predicted safety.

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.

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.

Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use when comparing two sequences, finding optimal alignments, scoring similarity, and identifying local or global matches between DNA, RNA, or protein sequences.

Call accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-specific parameters. Use when identifying open chromatin regions from aligned ATAC-seq BAM files, different from ChIP-seq peak calling.

Quality control metrics for ATAC-seq data including fragment size distribution, TSS enrichment, FRiP, and library complexity. Use when assessing ATAC-seq library quality before or after peak calling to identify problematic samples.

Find differentially accessible chromatin regions between conditions using DiffBind or DESeq2. Use when comparing chromatin accessibility between treatment groups, cell types, or developmental stages in ATAC-seq experiments.

Detect transcription factor binding sites through footprinting analysis in ATAC-seq data using TOBIAS. Use when identifying TF occupancy patterns within accessible regions, as TF binding protects DNA from Tn5 cutting.

Analyze transcription factor motif accessibility variability using chromVAR. Use when identifying which TF motifs show variable accessibility across samples or conditions in ATAC-seq data.

Extract nucleosome positions from ATAC-seq data using NucleoATAC, ATACseqQC, and fragment analysis. Use when analyzing chromatin organization, identifying nucleosome-free regions at promoters, or characterizing nucleosome occupancy patterns from ATAC-seq fragment size distributions.

Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller. Covers model selection, GPU acceleration, modified base detection, and quality filtering. Use when processing raw Nanopore data before alignment. Guppy is deprecated; use Dorado for all new analyses.

Process multiple sequence files in batch using Biopython. Use when working with many files, merging/splitting sequences, or automating file operations across directories.

Test whether two traits share a causal variant at a genomic locus using Bayesian colocalization with coloc. Computes posterior probabilities for shared vs distinct causal variants between GWAS and eQTL signals. Use when determining if a GWAS signal and an eQTL share the same causal variant.

Identify likely causal variants within GWAS loci using SuSiE for sum of single effects regression and FINEMAP for shotgun stochastic search. Computes posterior inclusion probabilities and credible sets to prioritize variants for functional follow-up. Use when narrowing GWAS association signals to candidate causal variants or building credible sets for functional validation.

Decompose genetic effects into direct and indirect paths through mediating variables using the mediation R package. Tests whether gene expression, methylation, or other molecular phenotypes mediate the effect of genetic variants on disease. Use when testing whether a molecular phenotype mediates the genotype-to-phenotype relationship.

Estimate causal effects between exposures and outcomes using genetic variants as instrumental variables with TwoSampleMR. Implements IVW, MR-Egger, weighted median, and MR-PRESSO methods for robust causal inference from GWAS summary statistics. Use when testing whether an exposure causally affects an outcome using genetic instruments.

Detect and correct for horizontal pleiotropy in Mendelian randomization analyses using MR-PRESSO for outlier removal, MR-Egger regression for directional pleiotropy, and Steiger filtering for variant directionality. Use when validating MR results, detecting pleiotropic instruments, or running sensitivity analyses for causal inference.

Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate removal using fgbio. Applies cfDNA-specific quality thresholds and fragment length filtering. Use when processing plasma cfDNA sequencing data before downstream analysis.

Differential binding analysis using DiffBind. Compare ChIP-seq peaks between conditions with statistical rigor. Requires replicate samples. Outputs differentially bound regions with fold changes and p-values. Use when comparing ChIP-seq binding between conditions.

De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP. Identify transcription factor binding motifs in ChIP-seq, ATAC-seq, or other genomic peak data. Use when finding enriched DNA motifs in peak sequences.

Annotate ChIP-seq peaks to genomic features and genes using ChIPseeker. Assign peaks to promoters, exons, introns, and intergenic regions. Find nearest genes and calculate distance to TSS. Generate annotation plots and statistics. Use when annotating ChIP-seq peaks to genomic features.

ChIP-seq peak calling using MACS3 (or MACS2). Call narrow peaks for transcription factors or broad peaks for histone modifications. Supports input control, fragment size modeling, and various output formats including narrowPeak and broadPeak BED files. Use when calling peaks from ChIP-seq alignments.

ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), library complexity, and IDR (Irreproducibility Discovery Rate) for replicate concordance. Use to assess experiment quality before downstream analysis. Use when assessing ChIP-seq data quality metrics.

Identifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools. Use when studying cell identity genes, cancer-associated regulatory elements, or master transcription factor binding regions that cluster into large enhancer domains.

Visualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. Create heatmaps, profile plots, and genome browser tracks. Visualize signal around peaks, TSS, or custom regions. Use when visualizing ChIP-seq signal and peaks.

Query ClinVar for variant pathogenicity classifications, review status, and disease associations via REST API or local VCF. Use when determining clinical significance of variants for diagnostic or research purposes.

Query dbSNP for rsID lookups, variant annotations, and cross-references to other databases. Use when mapping between rsIDs and genomic coordinates or retrieving basic variant information.

Query gnomAD for population allele frequencies to assess variant rarity. Use when filtering variants by population frequency for rare disease analysis or determining if a variant is common in the general population.

Call HLA alleles from NGS data using OptiType, HLA-HD, or arcasHLA for immunogenomics applications. Use when determining HLA genotype for transplant matching, neoantigen prediction, or pharmacogenomic screening.

Query myvariant.info API for aggregated variant annotations from multiple databases (ClinVar, gnomAD, dbSNP, COSMIC, etc.) in a single request. Use when annotating variants with clinical and population data from multiple sources simultaneously.

Query PharmGKB and CPIC for drug-gene interactions, pharmacogenomic annotations, and dosing guidelines. Use when predicting drug response from genetic variants or implementing clinical pharmacogenomics.

Calculate polygenic risk scores using PRSice-2, LDpred2, or PRS-CS from GWAS summary statistics. Use when predicting disease risk from genome-wide genetic variants.

Extract and analyze mutational signatures from somatic variants using SigProfiler or MutationalPatterns to characterize mutagenic processes. Use when identifying DNA damage mechanisms or etiology in cancer genomes.

Calculate tumor mutational burden from panel or WES data with proper normalization and clinical thresholds. Use when assessing immunotherapy eligibility or characterizing tumor immunogenicity.

Filter and prioritize variants by pathogenicity, population frequency, and clinical evidence for rare disease analysis. Use when identifying candidate disease-causing variants from exome or genome sequencing.

Read and write compressed sequence files (gzip, bzip2, BGZF) using Biopython. Use when working with .gz or .bz2 sequence files. Use BGZF for indexable compressed files.

Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific reference sequences or reconstructing haplotypes.

Manage AI coding agent sessions via Agent of Empires (aoe)

Generate demo assets (GIF/MP4) from real tmux E2E runs and viewer screenshots using asciinema and Playwright

Test JS logic embedded in HTML using two-layer strategy - Python unit tests + Playwright browser integration tests

Validate maintainer docs structure, standards freshness, manifest paths, and plan state. Run this after modifying any file under .agents/docs/standards/, .agents/docs/plans/, .agents/docs/architecture/, or AGENTS.md — it catches stale metadata, broken manifest paths, and plan state drift before CI does.

Record browser test videos with Playwright for PR review and bug fix verification

Full pre-PR merge-readiness check. Run this before opening or merging a pull request — it validates local gates (lint, format, tests), CI status, screenshot evidence, and PR metadata in one pass. Also useful for reviewing an existing PR's readiness.

Push to GitHub and optionally bump version to trigger PyPI release

Validate screenshot and viewer HTML quality for PR evidence. Run this after adding or modifying images under .agents/evidence/pr/ or .agents/recordings/, or after generating a new viewer HTML file. Combines image quality checks (resolution, blankness, file size) with Playwright-based viewer rendering verification.

Fill missing i18n translations in the viewer source JSON. Run this after adding or modifying English or Chinese UI strings in claude_tap/viewer_i18n.json — it auto-translates to ja, ko, fr, ar, de, ru via OpenRouter.

Provides AI and machine learning techniques for CTF challenges. Use when attacking ML models, crafting adversarial examples, performing model extraction, prompt injection, membership inference, training data poisoning, fine-tuning manipulation, neural network analysis, LoRA adapter exploitation, LLM jailbreaking, or solving AI-related puzzles.

Provides cryptography attack techniques for CTF challenges. Use when attacking encryption, hashing, signatures, ZKP, PRNG, or mathematical crypto problems involving RSA, AES, ECC, lattices, LWE, CVP, number theory, Coppersmith, Pollard, Wiener, padding oracle, GCM, key derivation, or stream/block cipher weaknesses.

Provides digital forensics and signal analysis techniques for CTF challenges. Use when analyzing disk images, memory dumps, event logs, network captures, cryptocurrency transactions, steganography, PDF analysis, Windows registry, Volatility, PCAP, Docker images, coredumps, side-channel power traces, DTMF audio spectrograms, packet timing analysis, CD audio disc images, or recovering deleted files and credentials.

Provides malware analysis and network traffic techniques for CTF challenges. Use when analyzing obfuscated scripts, malicious packages, custom crypto protocols, C2 traffic, PE/.NET binaries, RC4/AES encrypted communications, YARA rules, shellcode analysis, memory forensics for malware (Volatility malfind, process injection detection), anti-analysis techniques (VM/sandbox detection, timing evasion, API hashing, process injection, environment checks), or extracting malware configurations and indicators of compromise.

Provides miscellaneous CTF challenge techniques for problems that do not cleanly fit the main categories. Use for encoding puzzles, pyjails, bash jails, RF/SDR, DNS oddities, unicode tricks, esoteric languages, QR or audio puzzles, constraint solving, game theory, unusual sandbox escapes, and hybrid logic puzzles. Prefer a more specific skill first when the challenge is mainly web, pwn, reverse, forensics, malware, OSINT, or crypto. Treat this as the fallback skill for genuine cross-category or edge-case challenges, not the default starting point.

Provides open source intelligence techniques for CTF challenges. Use when gathering information from public sources, social media, geolocation, DNS records, username enumeration, reverse image search, Google dorking, Wayback Machine, Tor relays, FEC filings, or identifying unknown data like hashes and coordinates.

Provides binary exploitation techniques for CTF challenges. Use when you already have a vulnerable native target or service and need to turn memory corruption or low-level primitives into code execution or privilege escalation, such as buffer overflows, format strings, heap bugs, ROP, ret2libc, shellcode, kernel exploitation, seccomp bypass, sandbox escape, or Windows/Linux exploit chains. Do not use it when the main blocker is understanding what the binary does; use reverse engineering first. Do not use it for pure web bugs, disk or packet forensics, or standalone crypto/math challenges.

Provides reverse engineering techniques for CTF challenges. Use when the main job is to understand how a compiled, obfuscated, packed, or virtualized target works before exploiting or solving it, including binaries, APKs, WASM, firmware, custom VMs, bytecode, game clients, malware-like loaders, and anti-debug or anti-analysis logic. Do not use it when the vulnerability is already understood and the remaining task is exploitation; use pwn instead. Do not use it for pure web workflows, log or disk forensics, or standalone crypto problems unless reversing the implementation is the real blocker.

Provides web exploitation techniques for CTF challenges. Use when the target is primarily an HTTP application, API, browser client, template engine, identity flow, or smart-contract frontend/backend surface, including XSS, SQLi, SSTI, SSRF, XXE, JWT, auth bypass, file upload, request smuggling, OAuth/OIDC, SAML, prototype pollution, and similar web bugs. Do not use it for native binary memory corruption, reverse engineering of standalone executables, disk or memory forensics, or pure cryptanalysis unless the web flaw is still the main path to the flag.

Generates a single standardized submission-style CTF writeup for competition handoff and organizer review. Use after solving a CTF challenge to document the solution steps, tools used, and lessons learned in a structured format.

Solves CTF challenges by performing first-pass triage, identifying the dominant category, and routing execution to the right specialized ctf-* skill. Use when the user gives you a challenge bundle, a remote service, a suspicious file, or only a vague challenge description and you must determine where to start. Do not use it when the category is already clear and a specialized skill can be invoked directly; this is the dispatcher and recon entrypoint, not the deepest reference for category-specific techniques.

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Fetches articles from 92 Karpathy-curated RSS feeds, scores them with an LLM, selects the top 3, and delivers a formatted digest to Telegram every morning.

Use ONLY for abstract DataChain SDK questions — API usage, method signatures, or code patterns — when no specific dataset or bucket is referenced. If the request mentions creating, saving, listing, exploring datasets or buckets, use datachain-knowledge instead.

Use when asked about Studio job analytics — compute hours, user spend, failure rates, cost estimation, cluster usage. Generates and maintains dc-knowledge/jobs/index.md.

Use whenever datasets, cloud storage buckets, or data pipelines are mentioned — creating, saving, querying, listing, exploring, deleting, or processing data in S3, GCS, Azure Blob, or local storage. Also use when running any script that may create datasets as a side effect. Maintains a knowledge base at dc-knowledge/ (JSON + markdown). ALWAYS use this skill when the user creates a dataset, saves pipeline output, runs a data script, or references any storage bucket.

Manage Apple Notes via the memo CLI on macOS (create, view, search, edit).

Manage Apple Reminders via remindctl CLI (list, add, complete, delete).

Track Apple devices and AirTags via FindMy.app on macOS using AppleScript and screen capture.

Send and receive iMessages/SMS via the imsg CLI on macOS.

Transcribe audio via OpenAI Audio Transcriptions API (Whisper).

Local speech-to-text with the Whisper CLI (no API key).

ElevenLabs text-to-speech with mac-style say UX.

Local text-to-speech via sherpa-onnx (offline, no cloud)