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Claude Skills by zongtingwei
github.com/zongtingwei66 skills0 installs83 views
- Alignment And MappingWorkflow for read alignment, sorting, indexing, mapping statistics, and downstream-ready alignment artifacts.Votes: 0GitHub stars: 26
- Database AccessWorkflow for retrieving public omics datasets, sequences, annotations, and literature-linked biological resources.Votes: 0GitHub stars: 26
- Read QcWorkflow for sequencing read QC, trimming, contamination screening, and pre-alignment cleanup.Votes: 0GitHub stars: 26
- Reporting And Figure ExportWorkflow for packaging analysis outputs into reproducible reports, clean tables, and publication-ready figure exports.Votes: 0GitHub stars: 26
- Sequence And Format IoWorkflow for foundational sequence parsing, conversion, compression handling, and interval-aware file validation.Votes: 0GitHub stars: 26
- Workflow ManagementWorkflow for orchestrating reproducible omics pipelines with workflow engines and clear execution provenance.Votes: 0GitHub stars: 26
- Ehr AnalysisEnd-to-end EHR predictive modeling pipeline with PyHealth, covering dataset loading, task definition, model training, evaluation, calibration, and clinical interpretation.Votes: 0GitHub stars: 26
- Atac SeqATAC-seq processing with assay QC, MACS3 peak calling, consensus peak matrices, differential accessibility, and motif or footprint follow-up.Votes: 0GitHub stars: 26
- Chip SeqChIP-seq peak calling and downstream interpretation with MACS3, signal track export, annotation, motif analysis, and differential binding review.Votes: 0GitHub stars: 26
- EpitranscriptomicsWorkflow for RNA modification analysis such as m6A peak calling, differential modification, and transcript-level visualization.Votes: 0GitHub stars: 26
- Gene Regulatory NetworksWorkflow for regulatory network inference, regulon scoring, perturbation-aware comparison, and network visualization.Votes: 0GitHub stars: 26
- Hi C 3d GenomicsWorkflow for Hi-C and related 3D genomics analyses including compartments, loops, TADs, differential contacts, and visualization.Votes: 0GitHub stars: 26
- Methylation AnalysisWorkflow for methylation alignment or calling, DMR analysis, methylation QC, and locus-level interpretation.Votes: 0GitHub stars: 26
- Comparative GenomicsWorkflow for orthology, synteny, ancestral reconstruction, and evolutionary comparison across genomes.Votes: 0GitHub stars: 26
- Copy NumberWorkflow for copy-number estimation, segmentation, annotation, and visualization in sequencing-based assays.Votes: 0GitHub stars: 26
- Genome AssemblyWorkflow for de novo assembly, scaffolding, polishing, contamination review, and assembly QC.Votes: 0GitHub stars: 26
- Long Read GenomicsWorkflow for nanopore or PacBio long-read QC, alignment, polishing, methylation-aware analysis, and structural variant discovery.Votes: 0GitHub stars: 26
- Phasing ImputationWorkflow for haplotype phasing, genotype imputation, reference-panel matching, and imputation QC.Votes: 0GitHub stars: 26
- Variant CallingWorkflow for small-variant and structural-variant discovery, filtering, annotation, and interpretation from sequencing data.Votes: 0GitHub stars: 26
- MetagenomicsShotgun metagenomics workflow with host-depletion-aware QC, taxonomic profiling, functional profiling, AMR follow-up, and reproducible community output tables.Votes: 0GitHub stars: 26
- Microbiome AmpliconWorkflow for amplicon microbiome analysis including denoising, taxonomy assignment, diversity analysis, and differential abundance.Votes: 0GitHub stars: 26
- Pathogen Epi GenomicsWorkflow for outbreak-style pathogen genomics, surveillance, lineage assignment, and transmission-oriented comparative analysis.Votes: 0GitHub stars: 26
- PhylogeneticsWorkflow for multiple sequence alignment, tree inference, annotated tree visualization, and distance-based evolutionary comparison.Votes: 0GitHub stars: 26
- Causal GenomicsWorkflow for fine-mapping, colocalization, mediation, pleiotropy analysis, and Mendelian randomization.Votes: 0GitHub stars: 26
- Machine Learning For OmicsWorkflow for predictive modeling, biomarker discovery, survival modeling, and explainability over omics-derived features.Votes: 0GitHub stars: 26
- Multi Omics IntegrationWorkflow for integrating matched or partially matched omics layers into shared latent structure and cross-modal interpretation.Votes: 0GitHub stars: 26
- Pathway AnalysisWorkflow for enrichment testing, ranked-gene analysis, pathway scoring, and pathway-focused visualization across omics outputs.Votes: 0GitHub stars: 26
- Systems BiologyWorkflow for constraint-based metabolic modeling, context-specific models, gene essentiality, and systems-level interpretation.Votes: 0GitHub stars: 26
- Alphafold2 MultimerAlphaFold2 / AlphaFold-Multimer structure prediction for validation and confidence scoring. 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 esm2-sequence-scoring. For QC thresholds, use protein-design-qc.Votes: 0GitHub stars: 26
- BindcraftEnd-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built-in AF2 validation, (2) Running production-quality binder campaigns, (3) Using different design protocols (fast, default, slow), (4) Need joint backbone and sequence optimization, (5) Want high experimental success rate. For backbone-only generation, use rfdiffusion. For QC thresholds, use protein-design-qc. For tool selection guidance, use binder-design-tool-selection.Votes: 0GitHub stars: 26
- Binder Design Campaign ManagerBinder 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...Votes: 0GitHub stars: 26
- Binder Design Tool SelectionBinder 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.).Votes: 0GitHub stars: 26
- Boltz Structure PredictionBoltz-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.Votes: 0GitHub stars: 26
- 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 molecules or ligands, (3) Want all-atom diffusion (not just backbone), (4) Require precise binding geometries, (5) Using YAML-based configuration. For backbone-only generation, use rfdiffusion. For sequence-only design, use proteinmpnn. For structure validation, use boltz-structure-prediction.Votes: 0GitHub stars: 26
- Cell Free Protein ExpressionCell-free protein synthesis (CFPS) planning and optimization guidance. Use when: (1) Planning CFPS experiments, (2) Troubleshooting low yield or aggregation, (3) Optimizing DNA template design for CFPS, (4) Expressing difficult proteins (disulfide-rich, toxic, membrane).Votes: 0GitHub stars: 26
- Chai1 Structure PredictionChai-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.Votes: 0GitHub stars: 26
- End To End Protein Design WorkflowEnd-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.Votes: 0GitHub stars: 26
- Esm2 Sequence ScoringESM2 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.Votes: 0GitHub stars: 26
- FoldseekStructure 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 chai1-structure-prediction or boltz-structure-prediction.Votes: 0GitHub stars: 26
- IpsaeBinder design ranking using ipSAE (interprotein Score from Aligned Errors). Use this skill when: (1) Ranking binder designs for experimental testing, (2) Filtering BindCraft or RFdiffusion outputs, (3) Comparing AF2/AF3/Boltz predictions, (4) Predicting binding success rates, (5) Need better ranking than ipTM or iPAE. For structure prediction, use chai1-structure-prediction or alphafold2-multimer. For QC thresholds, use protein-design-qc.Votes: 0GitHub stars: 26
- LigandmpnnLigand-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.Votes: 0GitHub stars: 26
- PdbFetch and analyze protein structures from RCSB PDB. Use this skill when: (1) Need to download a structure by PDB ID, (2) Search for similar structures, (3) Prepare target for binder design, (4) Extract specific chains or domains, (5) Get structure metadata. For sequence lookup, use uniprot. For binder design workflow, use binder-design-tool-selection.Votes: 0GitHub stars: 26
- Protein Design QcProtein design quality control, filtering thresholds, and ranking guidance. 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 comp...Votes: 0GitHub stars: 26
- Proteina ComplexaProteina-Complexa flow-based protein backbone generation with fold-conditioned sampling guidance. Use this skill when: (1) Generating de novo protein backbones with hierarchical fold conditioning, (2) Exploring long-chain backbone generation beyond standard diffusion baselines, (3) Using NVIDIA Proteina-style flow matching workflows for controllable backbone design, (4) Comparing flow-based backbone generation against RFdiffusion or BoltzGen, (5) Prototyping fold-guided backbone campaigns bef...Votes: 0GitHub stars: 26
- ProteinmpnnDesign 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.Votes: 0GitHub stars: 26
- RfdiffusionGenerate 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 alphafold2-...Votes: 0GitHub stars: 26
- 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 "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.Votes: 0GitHub stars: 26
- SolublempnnSolubility-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.Votes: 0GitHub stars: 26
- Spr Bli Binding CharacterizationSPR and BLI assay planning, kinetic interpretation, and troubleshooting guidance. Use when: (1) Planning binding kinetics experiments, (2) Troubleshooting poor/no binding signal, (3) Interpreting kinetic data artifacts, (4) Choosing between SPR vs BLI platforms.Votes: 0GitHub stars: 26
- UniprotAccess 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.Votes: 0GitHub stars: 26