「agent-skill」の検索結果

Workflow for copy-number estimation, segmentation, annotation, and visualization in sequencing-based assays.

日本語の概要は準備中です。原文の説明を表示しています。

Workflow for ligand-receptor communication inference in single-cell or spatial data with sender-receiver summaries and cautious interpretation.

日本語の概要は準備中です。原文の説明を表示しています。

Workflow for orthology, synteny, ancestral reconstruction, and evolutionary comparison across genomes.

日本語の概要は準備中です。原文の説明を表示しています。

Workflow for event-level and isoform-level splicing analysis with sashimi-ready outputs and splice QC.

日本語の概要は準備中です。原文の説明を表示しています。

Validate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer. For faster single-chain prediction, use esm. For QC thresholds, use protein-qc.

日本語の概要は準備中です。原文の説明を表示しています。

Quality control metrics and filtering thresholds for protein design. Use this skill when: (1) Evaluating design quality for binding, expression, or structure, (2) Setting filtering thresholds for pLDDT, ipTM, PAE, (3) Checking sequence liabilities (cysteines, deamidation, polybasic clusters), (4) Creating multi-stage filtering pipelines, (5) Computing PyRosetta interface metrics (dG, SC, dSASA), (6) Checking biophysical properties (instability, GRAVY, pI), (7) Ranking designs with composite scoring. This skill provides research-backed thresholds from binder design competitions and published benchmarks.

日本語の概要は準備中です。原文の説明を表示しています。

Goal-oriented binder design campaign planning and health assessment. Use this skill when: (1) Planning a complete binder design campaign, (2) Converting high-level goals into runnable pipelines, (3) Assessing campaign health and pass rates, (4) Diagnosing why designs are failing QC, (5) Estimating time, cost, and expected yields, (6) Selecting between design tools for a specific target. This skill orchestrates the other protein design tools. For individual tool parameters, use the specific tool skills.

日本語の概要は準備中です。原文の説明を表示しています。

First-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 "modal: command not found", (3) Modal authentication errors occur, (4) User asks how to get started or set up the environment, (5) biomodals directory is missing or tools aren't working.

日本語の概要は準備中です。原文の説明を表示しています。

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. For structure retrieval, use pdb. For sequence design, use proteinmpnn.

日本語の概要は準備中です。原文の説明を表示しています。

Structure similarity search with Foldseek. Use this skill when: (1) Finding similar structures in PDB/AFDB databases, (2) Structural homology search, (3) Database queries by 3D structure, (4) Finding remote homologs not detected by sequence, (5) Clustering structures by similarity. For sequence similarity, use uniprot BLAST. For structure prediction, use chai or boltz.

日本語の概要は準備中です。原文の説明を表示しています。

Workflow for integrating matched or partially matched omics layers into shared latent structure and cross-modal interpretation.

日本語の概要は準備中です。原文の説明を表示しています。

Ligand-aware protein sequence design using LigandMPNN. Use this skill when: (1) Designing sequences around small molecules, (2) Enzyme active site design, (3) Ligand binding pocket optimization, (4) Metal coordination site design, (5) Cofactor binding proteins. For standard protein design, use proteinmpnn. For solubility optimization, use solublempnn.

日本語の概要は準備中です。原文の説明を表示しています。

Design protein sequences using ProteinMPNN inverse folding. Use this skill when: (1) Designing sequences for RFdiffusion backbones, (2) Redesigning existing protein sequences, (3) Fixing specific residues while designing others, (4) Optimizing sequences for expression or stability, (5) Multi-state or negative design. For backbone generation, use rfdiffusion or bindcraft. For ligand-aware design, use ligandmpnn. For solubility optimization, use solublempnn.

日本語の概要は準備中です。原文の説明を表示しています。

Boltz-1 / Boltz-2 structure prediction for proteins, complexes, and ligand-aware validation. Use this skill when: (1) Predicting protein complex structures, (2) Validating designed binders, (3) Need open-source alternative to AF2, (4) Predicting protein-ligand complexes, (5) Using local GPU resources. For QC thresholds, use protein-design-qc. For AlphaFold2 prediction, use alphafold2-multimer. For Chai prediction, use chai1-structure-prediction.

日本語の概要は準備中です。原文の説明を表示しています。

Workflow for de novo assembly, scaffolding, polishing, contamination review, and assembly QC.

日本語の概要は準備中です。原文の説明を表示しています。

Python-first workflow for bulk RNA-seq expression intake, normalization, sample QC, and downstream-ready matrices.

日本語の概要は準備中です。原文の説明を表示しています。

End-to-end protein design pipeline guide across preparation, generation, validation, and filtering. Use this skill when: (1) Starting a new protein design project, (2) Need step-by-step workflow guidance, (3) Understanding the full design pipeline, (4) Planning compute resources and timelines, (5) Integrating multiple design tools. For tool selection, use binder-design-tool-selection. For QC thresholds, use protein-design-qc.

日本語の概要は準備中です。原文の説明を表示しています。

Binder design campaign planning, monitoring, and troubleshooting. Use this skill when: (1) Planning a complete binder design campaign, (2) Converting high-level goals into runnable pipelines, (3) Assessing campaign health and pass rates, (4) Diagnosing why designs are failing QC, (5) Estimating time, cost, and expected yields, (6) Selecting between design tools for a specific target. This skill orchestrates the other protein design tools. For individual tool parameters, use the specific tool skills.

日本語の概要は準備中です。原文の説明を表示しています。

Solubility-optimized protein sequence design using SolubleMPNN. Use this skill when: (1) Designing for E. coli expression, (2) Optimizing solubility of designed proteins, (3) Reducing aggregation propensity, (4) Need high-yield expression, (5) Avoiding inclusion body formation. For standard design, use proteinmpnn. For ligand-aware design, use ligandmpnn.

日本語の概要は準備中です。原文の説明を表示しています。

Workflow for RNA modification analysis such as m6A peak calling, differential modification, and transcript-level visualization.

日本語の概要は準備中です。原文の説明を表示しています。

Workflow for retrieving public omics datasets, sequences, annotations, and literature-linked biological resources.

日本語の概要は準備中です。原文の説明を表示しています。

Workflow for fine-mapping, colocalization, mediation, pleiotropy analysis, and Mendelian randomization.

日本語の概要は準備中です。原文の説明を表示しています。

Workflow for methylation alignment or calling, DMR analysis, methylation QC, and locus-level interpretation.

日本語の概要は準備中です。原文の説明を表示しています。

Binder design tool selection and workflow routing guidance. Use this skill when: (1) Deciding between BoltzGen, BindCraft, or RFdiffusion, (2) Planning a binder design campaign, (3) Understanding trade-offs between different approaches, (4) Selecting tools for specific target types. For specific tool parameters, use the individual tool skills (boltzgen, bindcraft, rfdiffusion, etc.).

日本語の概要は準備中です。原文の説明を表示しています。