285건(BioTender-max의 저장소) · 인기순
End-to-end EHR predictive modeling pipeline with PyHealth, covering dataset loading, task definition, model training, evaluation, calibration, and clinical interpretation.
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Workflow for copy-number estimation, segmentation, annotation, and visualization in sequencing-based assays.
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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.
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Workflow for nanopore or PacBio long-read QC, alignment, polishing, methylation-aware analysis, and structural variant discovery.
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Workflow for fine-mapping, colocalization, mediation, pleiotropy analysis, and Mendelian randomization.
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Workflow for integrating matched or partially matched omics layers into shared latent structure and cross-modal interpretation.
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Workflow for untargeted or targeted metabolomics including preprocessing, normalization, annotation, statistics, and pathway mapping.
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Workflow for predictive modeling, biomarker discovery, survival modeling, and explainability over omics-derived features.
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Workflow for multiplexed imaging or IMC segmentation, phenotyping, and spatial summarization.
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Workflow for regulatory network inference, regulon scoring, perturbation-aware comparison, and network visualization.
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ESM2 protein language model for sequence scoring, embeddings, and plausibility checks. Use this skill when: (1) Computing pseudo-log-likelihood (PLL) scores, (2) Getting protein embeddings for clustering, (3) Filtering designs by sequence plausibility, (4) Zero-shot variant effect prediction, (5) Analyzing sequence-function relationships. For structure prediction, use chai1-structure-prediction or boltz-structure-prediction. For QC thresholds, use protein-design-qc.
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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.
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Workflow for retrieving public omics datasets, sequences, annotations, and literature-linked biological resources.
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Chai-1 structure prediction for protein complexes and design validation. Use this skill when: (1) Predicting protein-protein complex structures, (2) Validating designed binders, (3) Predicting protein-ligand complexes, (4) Using the Chai API for high-throughput prediction, (5) Need an alternative to AlphaFold2. For QC thresholds, use protein-design-qc. For AlphaFold2 prediction, use alphafold2-multimer. For ESM-based analysis, use esm2-sequence-scoring.
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Workflow for ligand-receptor communication inference in single-cell or spatial data with sender-receiver summaries and cautious interpretation.
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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.
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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.).
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Workflow for event-level and isoform-level splicing analysis with sashimi-ready outputs and splice QC.
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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.
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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.
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Generate protein backbones using RFdiffusion, a diffusion-based generative model for de novo protein structure generation. Use this skill when: (1) Designing binder scaffolds for a target protein, (2) Generating novel protein backbones from scratch, (3) Scaffolding functional motifs into new proteins, (4) Specifying hotspot residues for interface design, (5) Creating symmetric oligomers. For sequence design after backbone generation, use proteinmpnn. For structure validation, use alphafold or chai. For QC thresholds, use protein-qc.
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