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Get Started Free →Grounded question-answering with citations and entity extraction.
This skill works best with `web_search` + `web_fetch`, but **`web_search` is optional**. If your environment does not have `web_search` available (e.g., no API key configured), the skill will automatically degrade to use built-in Bing scraping scripts instead.
Problem-solving strategies for boundary value problems in odes pdes
End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon, featureCounts), assembles a gene-level counts matrix, then hands off to differential expression (pydeseq2), pathway/GSEA enrichment (pathway-enrichment), and publication figures (scientific-visualization). Use whenever the user has bulk RNA-seq reads or quant output and wants a complete, reproducible differential-expression workflow — e.g.
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.
Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.
Search NCBI databases using Biopython Bio.Entrez. Use when finding records by keyword, building complex search queries, discovering database structure, or getting global query counts across databases.
Draft scientific introductions: argument logic, framing, multi-experiment coherence.
Calculates statistical power and minimum sample sizes for RNA-seq, ATAC-seq, and other sequencing experiments. Use when planning experiments, determining how many replicates are needed, or assessing whether a study is adequately powered to detect expected effect sizes.
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.
Unified agent for leveraging single-cell foundation models (scGPT, scBERT, Geneformer, scFoundation) for cross-species annotation, perturbation prediction, and gene network inference.
End-to-end RNA-seq workflow from FASTQ files to differential expression results. Covers QC, quantification (Salmon or STAR+featureCounts), and DESeq2 analysis with visualization. Use when running RNA-seq from FASTQ to DE results.
End-to-end multi-omics integration workflow. Orchestrates data harmonization, MOFA/mixOmics integration, factor interpretation, and downstream analysis across transcriptomics, proteomics, metabolomics, and other modalities. Use when integrating multiple omics datasets.
Check if medicinal chemistry papers are in ChEMBL database to access curated bioactivity data
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.
Metagenome assembly from long reads using metaFlye and metaSPAdes with binning strategies. Use when reconstructing genomes from microbial communities, recovering metagenome-assembled genomes (MAGs), or resolving strain-level variation in complex samples.
Retrieve records from NCBI databases using Biopython Bio.Entrez. Use when downloading sequences, fetching GenBank records, getting document summaries, or parsing NCBI data into Biopython objects.
Programmatic access to biological web services and databases
Modify phylogenetic tree structure using Biopython Bio.Phylo. Use when rooting trees with outgroups or midpoint, pruning taxa, collapsing clades, ladderizing branches, or extracting subtrees.
Calculate linkage disequilibrium statistics (r², D'), perform LD pruning for population structure analysis, identify haplotype blocks, and visualize LD patterns using PLINK, scikit-allel, and LDBlockShow. Use when calculating LD or pruning variants.
Download, prepare, and manage reference panels for phasing and imputation. Covers 1000 Genomes, HRC, and TOPMed panels. Use when setting up imputation infrastructure or selecting appropriate reference panels for target populations.
Find free legal full-text versions of scholarly articles via Unpaywall
gget CLI and Python workflow for quick genomic database queries, sequence lookup, BLAST-style searches, enrichment checks, and reproducible bioinformatics evidence logs.
Bioinformatics / Phylogenetics: apply the codified rules and ground precise facts at runtime instead of recalling them.
An advanced agent for de novo antibody design and optimization using state-of-the-art protein language models (MAGE, RFdiffusion).
End-to-end TCR/BCR repertoire analysis from FASTQ to clonotype diversity metrics. Use when analyzing immune repertoire sequencing data from bulk or single-cell experiments.
AI-powered analysis of patient-derived xenograft (PDX) models for drug response prediction, translational research, and personalized treatment selection.
scRNA-seq Explorer
Research pipeline for PubMed and arXiv. Quick search and structured literature reviews using pure Python standard library.
Polish genome assemblies to reduce errors using short reads (Pilon), long reads (Racon), or ONT-specific tools (medaka). Essential for improving long-read assembly accuracy. Use when improving assembly accuracy with polishing tools.
Calculate sequence properties like GC content, molecular weight, isoelectric point, and GC skew using Biopython. Use when analyzing sequence composition, computing physical properties, or comparing sequences.
Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks.
AI-powered academic paper search and retrieval
Problem-solving strategies for analytic functions in complex analysis
专业深度研究与报告生成技能。支持企业竞争分析、产品竞争分析、行业分析、市场规模/竞争格局、AI大模型厂商、AI工具学习指南等领域。整合17个搜索引擎，三阶段工作流（主题确认→框架生成→报告输出），运用PESTEL、SWOT、波特五力、商业模式画布等经典咨询研究模型，输出精美的深蓝色政务风格HTML与Markdown双格式咨询级报告。
Search and retrieve preprints from the arXiv repository
Multi-phase literature-review exemplar with phase-aware retrieval, filtering, provenance, and cross-phase validation.
Designs experiments to minimize and account for batch effects using balanced layouts and blocking strategies. Use when planning multi-batch experiments, assigning samples to sequencing lanes, or designing studies where technical variation could confound biological signals.
High-quality genome assembly from PacBio HiFi reads using hifiasm with phasing support. Use when building reference-quality diploid assemblies from HiFi data, especially with trio or Hi-C phasing for fully resolved haplotypes.
Impute missing genotypes using reference panels with Beagle or Minimac4. Use when increasing variant density for GWAS, harmonizing data across genotyping platforms, or inferring variants not directly typed in array data.
Econometrics skill for Difference-in-Differences (DID) analysis. Activates when the user asks about: "difference in differences", "DID", "DiD", "diff-in-diff", "parallel trends", "treatment group", "control group", "pre-treatment", "post-treatment", "policy evaluation", "natural experiment", "staggered DID", "event study regression", "two-way fixed effects DID", "callaway santanna", "sun and abraham", "双重差分", "倍差法", "平行趋势", "处理组", "对照组", "政策评估", "事件研究", "交错DID", "渐进处理"
Query NCBI Gene Expression Omnibus (GEO) for expression datasets using Biopython Bio.Entrez. Use when finding microarray/RNA-seq datasets, downloading expression data, or linking GEO series to SRA runs.
Gene regulatory network inference using tree-based ensemble methods
Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData. Read Space Ranger outputs, convert formats, and access spatial coordinates. Use when loading Visium, Xenium, MERFISH, or other spatial data.
Call SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting variants from BAM files or generating VCF from alignments.
Problem-solving strategies for source coding in information theory
Detect signatures of natural selection using Fst, Tajima's D, iHS, XP-EHH, and other selection statistics. Calculate population differentiation, test for departures from neutrality, and identify selective sweeps with scikit-allel and vcftools. Use when computing selection signatures like Fst or Tajima's D.
Systematic review response workflow from comment analysis to professional rebuttal writing. Use when the user asks to "write rebuttal", "respond to reviewers", "draft review response", or "analyze review comments". Improves paper acceptance rates.
Generate reverse complements and complements of DNA/RNA sequences using Biopython. Use when working with opposite strands, primer design, or converting between template and coding strands.
Detect contamination and assess genome quality using CheckM, CheckM2, GTDB-Tk, and GUNC for metagenome-assembled genomes and isolate assemblies. Use when checking assemblies for contamination.
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
This skill should be used when the user asks to "search for academic papers", "find working papers on SSRN", "look up a DOI", "download paper PDF", "check open access availability", "search NBER papers", "find arXiv preprints", or "search CrossRef". Provides unified search, metadata retrieval, and PDF download across arXiv, NBER, SSRN, CrossRef, OpenAlex, Unpaywall, and Semantic Scholar. Covers economics, finance, social science, CS/AI, and all academic disciplines.
Problem-solving strategies for constrained optimization in optimization
Direct PubMed and NCBI E-utilities search workflows for biomedical literature, MeSH queries, PMID lookup, citation retrieval, and API-backed literature monitoring.
AI-powered analysis of long-read sequencing data (PacBio, ONT) for structural variant detection, isoform discovery, epigenetic modifications, and de novo assembly.
Generate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, indexing references, or creating sequence dictionaries.
Use when finalizing the main exhibits of a Quarterly Journal of Economics (QJE) manuscript — making the paper figure-forward, with clean tables and self-contained notes that read well in QJE's single-PDF, author-date format. Designs exhibits; it does not run new analysis.
End-to-end multiome workflow for joint scRNA-seq + scATAC-seq analysis. Covers data loading, separate modality processing, and WNN integration with Seurat/Signac. Use when analyzing joint scRNA+scATAC data.
Assess genome assembly quality using QUAST for contiguity metrics and BUSCO for completeness. Essential for evaluating assembly success and comparing assemblers. Use when evaluating assembly completeness and quality.
Econometrics skill for Synthetic Control Method (SCM). Activates when the user asks about: "synthetic control", "SCM", "synthetic counterfactual", "donor pool", "placebo test", "in-space placebo", "in-time placebo", "MSPE ratio", "Abadie Diamond Hainmueller", "augmented synthetic control", "penalized SCM", "synthetic DID", "合成控制", "合成控制法", "捐助池", "安慰剂检验", "合成反事实", "合成DID", "政策评估"
Protein engineering and directed evolution analysis using Adaptyv Bio platform
Research uncertain questions with an explicit, user-approved web search or ChatGPT consultation, then present options and wait for implementation approval.
Convert between gene identifier systems including Ensembl, Entrez, HGNC symbols, and UniProt. Use when mapping IDs for pathway analysis or matching different data sources.
Quantify transcript expression using pseudo-alignment with Salmon or kallisto. Use when quantifying transcripts with Salmon or kallisto.
Align RNA-seq reads with HISAT2, a memory-efficient splice-aware aligner. Use when STAR's memory requirements are too high or for general RNA-seq alignment.
Analyzes spatial proteomics data from CODEX, IMC, and MIBI platforms including cell segmentation and protein colocalization. Use when working with multiplexed imaging data, analyzing protein spatial patterns, or integrating spatial proteomics with transcriptomics.
Problem-solving strategies for integration theory in measure theory
Variant calling with GATK HaplotypeCaller following best practices. Covers germline SNP/indel calling, GVCF workflow for cohorts, joint genotyping, and variant quality score recalibration (VQSR). Use when calling variants with GATK HaplotypeCaller.
Monitor topics of interest and proactively alert when important developments occur. Use when user wants automated monitoring of specific subjects (e.g., product releases, price changes, news topics, technology updates). Supports scheduled web searches, AI-powered importance scoring, smart alerts vs weekly digests, and memory-aware contextual summaries.
Problem-solving strategies for modular arithmetic in graph number theory
Problem-solving strategies for gradient methods in optimization
Find restriction enzyme cut sites in DNA sequences using Biopython Bio.Restriction. Search with single enzymes, batches of enzymes, or commercially available enzyme sets. Returns cut positions for linear or circular DNA. Use when finding restriction enzyme cut sites in sequences.
Problem-solving strategies for entropy in information theory
Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICOM to BIDS, writing metadata sidecars, or creating BIDS derivatives.
End-to-end metagenomics workflow from FASTQ to taxonomic and functional profiles. Covers Kraken2 classification, Bracken abundance estimation, and HUMAnN functional profiling. Use when profiling metagenomic samples.
End-to-end genome assembly workflow from reads to polished assembly with QC. Supports short reads (SPAdes), long reads (Flye), and hybrid approaches. Use when assembling genomes from raw reads.
Protein-protein interaction (PPI) network analysis — STRING (predicted + experimental), BioGRID (curated), SASBDB (small-angle scattering). Distinguishes physical interactions (binding) from functional associations (co-expression, co-regulation). Use for interactome queries, complex partner identification, and pathway-level interaction analysis.
Count reads per gene from aligned BAM files using Subread featureCounts. Use when processing BAM files from STAR/HISAT2 to generate gene-level counts for DESeq2/edgeR.
Econometrics skill for creating publication-quality LaTeX regression and summary tables. Activates when the user asks about: "regression table", "LaTeX table", "esttab", "stargazer", "modelsummary", "publication table", "format results", "multi-panel table", "journal table", "export regression results", "table formatting", "回归表格", "LaTeX表格", "结果导出", "论文表格", "回归结果格式化", "多模型表格"
Preprocess CLIP-seq data including adapter trimming, UMI extraction, and PCR duplicate removal. Use when preparing raw CLIP, iCLIP, or eCLIP reads for peak calling.
Design PCR primers for a target sequence using primer3-py. Specify target regions, product size, melting temperature, and other constraints. Returns ranked primer pairs with quality metrics. Use when designing standard PCR primers.
Humanize murine antibody sequences using CDR grafting and framework optimization to reduce immunogenicity while preserving antigen binding. Predicts optimal human germline frameworks and identifies critical back-mutations for therapeutic antibody development.
Align short reads using Bowtie2 with local or end-to-end modes. Supports gapped alignment. Use when aligning ChIP-seq, ATAC-seq, or when flexible alignment modes are needed.
BED file format fundamentals, creation, validation, and basic operations. Covers BED3 through BED12 formats, coordinate systems, sorting, and format conversion using bedtools and pybedtools. Use when working with genomic coordinates or preparing interval files for downstream tools.
Align RNA-seq reads with STAR (Spliced Transcripts Alignment to a Reference). Supports two-pass mode for novel splice junction discovery. Use when aligning RNA-seq data requiring splice-aware alignment.
Astronomical computations, coordinate transforms, and celestial data analysis
Web search with optional content scraping. Returns search results as JSON, optionally with full page content.
End-to-end workflow for detecting structural variants from long-read sequencing data. Covers ONT/PacBio alignment with minimap2 and SV calling with Sniffles or cuteSV. Use when detecting structural variants from long reads.
End-to-end copy number variant detection workflow from BAM files. Covers CNVkit analysis for exome/targeted sequencing with visualization and annotation. Use when detecting copy number alterations from sequencing data.
End-to-end outbreak investigation from pathogen isolates to transmission networks. Orchestrates MLST typing, AMR surveillance, phylodynamic dating, and transmission inference with TransPhylo. Use when investigating disease outbreaks or tracking pathogen transmission chains.
Problem-solving strategies for predicate logic in mathematical logic
Paper Retrieval Agent - Multi-database paper fetching from Semantic Scholar, OpenAlex, arXiv Handles rate limiting, deduplication, and PDF URL extraction Use when: fetching papers, searching databases, paper retrieval Triggers: fetch papers, retrieve papers, database search, Semantic Scholar, OpenAlex, arXiv
Fast miRNA quantification with isomiR detection and A-to-I editing analysis using miRge3. Use when quantifying known miRNAs quickly or analyzing isomiR variants and RNA editing.
FAIR data descriptor exemplar for schema, provenance, license, and dataset release-readiness validation.
End-to-end bisulfite sequencing workflow from FASTQ to differentially methylated regions. Covers Bismark alignment, methylation calling, and DMR detection with methylKit. Use when analyzing bisulfite sequencing data.
Variant Scorer
Compare claims from one or more AI answers, verify their citations against public primary sources, and produce an evidence-linked fact-check report without installing a bundled browser runtime.
Expert in historical analysis, periodization, material culture, and historiography — validates historical coherence and enriches settings with authentic period detail grounded in primary and secondary sources
Brave Search API integration with managed authentication. Search the web, images, news, and videos with privacy-focused search. Use this skill when users want to search the web, find images, get news, or search videos using Brave Search. For other third party apps, use the api-gateway skill (https://clawhub.ai/byungkyu/api-gateway).
Use when the user explicitly invokes CrossFrame or 跨尺度结构诊断 for Chinese-canonical structural diagnosis of complex relationships, organizations, institutions, public disputes, or long-term evolution.
L0 foundation for all medical market-sizing tasks. Use this skill whenever a task involves MECE department/age/region/indication slicing, evidence grading, drug-target three-state activity matrix, or cross-department patient-flow sizing. Trigger phrases: "市场多大", "market sizing", "用药占比", "竞品格局", "患者流". Disease-specific L1 skills (ifi-market-sizing-skill, etc.) must reference this first.