biotender-max/awesome-bio-agent-skills
53 skills
$npx skills add biotender-max/awesome-bio-agent-skillsSkillInstalls
alphafoldValidate protein designs using AlphaFold2 structure prediction.atac-seqATAC-seq processing with assay QC, MACS3 peak calling, consensus peak matrices, differential accessibility, and motif or footprint follow-up.bindcraftEnd-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built-in AF2 validation, (2) Running…binder-designGuidance for choosing the right protein binder design tool. Use this skill when: (1) Deciding between BoltzGen, BindCraft, or RFdiffusion, (2) Planning a…binding-characterizationGuidance for SPR and BLI binding characterization experiments.bio-agent-skills-hubDiscover and invoke 1,676 deduplicated biomedical AI agent skills from the Awesome Bio Agent Skills repository (20 source repos, 15 categories).bio-analysis-systemStep 5: Analysis system design (分析方法体系构建)bio-dataset-searchStep 3: Dataset search and task matching (数据集搜索与匹配)bio-human-feedbackPhase 2.6: Human review checkpoint (人类反馈验证)bio-manuscript-pipelineEnd-to-end pipeline from structured research input to a full manuscript plan (一条龙 Pipeline)bio-manuscript-refineRefine loop: three-reviewer iterative refinement (三审稿人迭代优化)bio-toolsBiology research tools reference. Always available inside agent containers.blast-searchRun BLAST sequence similarity searches. Use when the user asks to BLAST a sequence, find similar sequences, identify a gene/protein, or do homology search.boltzStructure prediction using Boltz-1/Boltz-2, an open biomolecular structure predictor.boltzgenAll-atom protein design using BoltzGen diffusion model. Use this skill when: (1) Need side-chain aware design from the start, (2) Designing around small…campaign-managerGoal-oriented binder design campaign planning and health assessment.cell-annotationAutomated and marker-guided single-cell cell type annotation using CellTypist, marker review, reference transfer, and confidence-aware label curation.cell-free-expressionchaiStructure prediction using Chai-1, a foundation model for molecular structure.chip-seqChIP-seq peak calling and downstream interpretation with MACS3, signal track export, annotation, motif analysis, and differential binding review.differential-expressionBulk transcriptomics differential expression with count-aware modeling, design validation, contrast handling, thresholded exports, and publication-ready DE…esmESM2 protein language model for embeddings and sequence scoring.foldseekStructure similarity search with Foldseek. Use this skill when: (1) Finding similar structures in PDB/AFDB databases, (2) Structural homology search, (3)…ipsaeBinder design ranking using ipSAE (interprotein Score from Aligned Errors).ligandmpnnLigand-aware protein sequence design using LigandMPNN. Use this skill when: (1) Designing sequences around small molecules, (2) Enzyme active site design, (3)…metagenomicsShotgun metagenomics workflow with host-depletion-aware QC, taxonomic profiling, functional profiling, AMR follow-up, and reproducible community output tables.pdbprotein-design-workflowEnd-to-end guidance for protein design pipelines. Use this skill when: (1) Starting a new protein design project, (2) Need step-by-step workflow guidance, (3)…protein-qcQuality control metrics and filtering thresholds for protein design.proteinmpnnDesign protein sequences using ProteinMPNN inverse folding. Use this skill when: (1) Designing sequences for RFdiffusion backbones, (2) Redesigning existing…proteomicsMass spectrometry proteomics QC, quantification, comparative analysis, and export for DDA, DIA, and protein-level result tables.query-alphafoldQuery AlphaFold protein structure predictions. Use when user asks about protein structure, 3D structure, protein folding, or structure prediction.query-clinvarQuery ClinVar for clinical variant significance. Use when user asks about variant pathogenicity, genetic variants, clinical significance, or disease-causing…query-ensemblQuery Ensembl for genomic data. Use when user asks about gene coordinates, genomic sequences, variants, gene structure, exons, transcripts, or species…query-geoQuery NCBI GEO for gene expression datasets. Use when user asks about RNA-seq datasets, microarray data, expression data, GEO accessions, or finding public…query-interproQuery InterPro for protein domains and families. Use when user asks about protein domains, functional sites, protein families, domain architecture, or motifs.query-keggQuery KEGG for biological pathways and gene info. Use when user asks about metabolic pathways, signaling pathways, pathway genes, or KEGG IDs.query-opentargetQuery OpenTargets for drug targets, disease associations, and therapeutic evidence.query-pdbQuery RCSB PDB for experimental protein structures. Use when user asks about crystal structures, X-ray, cryo-EM, NMR structures, or PDB IDs.query-reactomeQuery Reactome for biological pathways and reactions. Use when user asks about signaling cascades, biological processes, pathway diagrams, or reaction details.query-stringdbQuery STRING for protein-protein interactions. Use when user asks about protein interactions, interaction networks, binding partners, or interactome.query-uniprotQuery UniProt protein database. Use when user asks about protein sequences, functions, annotations, domains, or protein identifiers.report-templatePublication-quality PDF report generation using Typst templates.rfdiffusionGenerate protein backbones using RFdiffusion, a diffusion-based generative model for de novo protein structure generation.scrna-preprocessing-clusteringStandard scRNA-seq preprocessing and clustering with Scanpy. Use for QC, normalization, HVG selection, PCA, neighbor graph construction, UMAP, Leiden…sds-gel-reviewReview SDS-PAGE or protein purification gel images using DNA sequence, protein sequence, base-pair length, expected protein size, and lane labels.sec-reportSEC (size-exclusion chromatography) analysis with peak detection, oligomer classification, and publication-quality PDF report generation via Typst templates.sequence-analysisAnalyze DNA/RNA/protein sequences. Use when the user provides a sequence and asks for analysis, translation, GC content, ORFs, motifs, restriction sites, or…setupFirst-time setup for protein design tools. Use this skill when: (1) User is new and hasn't run any tools yet, (2) Commands fail with "file not found" or…skills-hubBrowse and install community skills from the BioClaw Skills Hub.solublempnnSolubility-optimized protein sequence design using SolubleMPNN. Use this skill when: (1) Designing for E.structural-biologyStructure retrieval, confidence-aware AlphaFold DB usage, coordinate download, PAE and pLDDT interpretation, and structure-guided biological annotation.uniprotAccess UniProt for protein sequence and annotation retrieval. Use this skill when: (1) Looking up protein sequences by accession, (2) Finding functional…