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Claude Skills by mims-harvard
github.com/mims-harvard331 skills1 installs379 views
- Tooluniverse Vaccine DesignComputational vaccine candidate design: peptide/subunit vaccines via MHC-I/MHC-II epitope prediction (IEDB), population HLA coverage optimization, B-cell epitope identification, and cross-strain conservation analysis. Use for vaccine epitope prediction, HLA allele coverage, multi-epitope construct design, and immunogenicity assessment. Combines predicted MHC binding with experimentally validated IEDB epitopes for higher-confidence designs.Votes: 0GitHub stars: 1,719
- Tooluniverse Variant AnalysisVCF and variant analysis — parsing, annotation, classification (synonymous, missense, frameshift, stop_gained), VAF filtering, coding vs non-coding categorization, multi-condition variant comparison. Use for VCF parsing, variant fraction calculations (denominator = coding subset only, NOT all variants), and per-sample mutation profiling.Votes: 0GitHub stars: 1,719
- Tooluniverse Variant Functional AnnotationFunctional annotation of protein variants — ProtVar structural/functional context, ClinVar clinical classifications, gnomAD population frequencies, CADD deleteriousness, ClinGen gene-disease validity, plus FAVOR one-call comprehensive GRCh38 annotation. Use for variant annotation pipelines, missense effect prediction, and protein-level variant interpretation with functional context.Votes: 0GitHub stars: 1,719
- Tooluniverse Variant InterpretationClinical variant interpretation from raw variant calls to ACMG-classified recommendations with structural impact analysis. Use for VUS classification, pathogenicity assessment with cited criteria, structure-based variant impact (AlphaFold/PDB), non-coding/regulatory variant effect prediction with sequence deep-learning models (AlphaGenome, Enformer, Borzoi, ChromBPNet, Evo 2), and producing clinical-grade variant reports for return of results or molecular tumor boards. Use this whenever a use...Votes: 0GitHub stars: 1,719
- Tooluniverse Variant Predictor Dms ValidationValidate a variant-effect predictor (AlphaMissense, ESM-C SAE, ESM logits, EVE, conservation scores, or any per-variant numeric score) against experimental deep mutational scanning (DMS) data. Computes per-variant predictor scores, splits variants into neutral vs disruptive groups by DMS effect, runs a Mann-Whitney U test on the predictor scores, and sweeps the stratification thresholds for robustness. Use when you need to know whether a predictor's scores track real functional disruption on ...Votes: 0GitHub stars: 1,719
- Tooluniverse Variant To MechanismEnd-to-end variant-to-mechanism analysis — trace a variant (rsID/coordinates) through regulatory context, target gene(s), molecular pathway(s), and phenotypic consequences. Integrates 7+ databases across 3 evidence layers (regulatory, molecular, disease) for a mechanistic model. Use for GWAS-hit-to-mechanism, eQTL-causal-gene tracing, and full causal-chain reports.Votes: 0GitHub stars: 1,719
- TooluniverseToolUniverse plugin router. STEP 1 BEFORE ANY ANALYSIS: if the data folder contains `*_executed.ipynb`, run `tu run read_executed_notebook '{\"data_folder\":\"<path>\",\"search\":\"<keyword>\"}'` to extract its cell outputs and apply EVERY filter/sample-exclusion the notebook used — even when the question says 'Using DESeq2/Run X/Compute Y' (this describes the METHOD the notebook used, not a request to rerun). The notebook's cell outputs are the only published authoritative answers; reimpleme...Votes: 0GitHub stars: 1,719
- Host And Share Remote ToolHost, validate, and privately share a user's own model, Python function, workflow, or existing Streamable HTTP MCP endpoint through ToolUniverse Platform. Use when turning a local CPU/GPU workload or lab endpoint into a stable TU remote tool, diagnosing its setup, or preparing it for controlled sharing.Votes: 0GitHub stars: 1,719
- Setup Boltz Remote ToolSet up, launch, validate, and troubleshoot the Boltz-2 ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Borzoi Remote ToolSet up, launch, validate, and troubleshoot the Borzoi ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Cell2location Remote ToolSet up, launch, validate, and troubleshoot the cell2location ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Cellrank Remote ToolSet up, launch, validate, and troubleshoot the CellRank ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Celltypist Remote ToolSet up, launch, validate, and troubleshoot the CellTypist ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Chrombpnet Remote ToolSet up, launch, validate, and troubleshoot the ChromBPNet ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Depmap 24q2 Remote ToolSet up, launch, validate, and troubleshoot the DepMap 24Q2 ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Enformer Remote ToolSet up, launch, validate, and troubleshoot the Enformer ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Esm Remote ToolSet up, launch, validate, and troubleshoot the ESM ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Expert Feedback Remote ToolSet up, launch, validate, and troubleshoot the Human expert feedback ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Harmony Remote ToolSet up, launch, validate, and troubleshoot the Harmony ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Immune Compass Remote ToolSet up, launch, validate, and troubleshoot the immune COMPASS ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Ldsc Remote ToolSet up, launch, validate, and troubleshoot the LDSC ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Liana Remote ToolSet up, launch, validate, and troubleshoot the LIANA ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Macs3 Remote ToolSet up, launch, validate, and troubleshoot the MACS3 ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Milo Remote ToolSet up, launch, validate, and troubleshoot the Milo ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Mofa Remote ToolSet up, launch, validate, and troubleshoot the MOFA+ ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Monocle3 Remote ToolSet up, launch, validate, and troubleshoot the Monocle 3 ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Paga Remote ToolSet up, launch, validate, and troubleshoot the PAGA ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Pinnacle Remote ToolSet up, launch, validate, and troubleshoot the PINNACLE ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Scanvi Remote ToolSet up, launch, validate, and troubleshoot the scANVI ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Scrublet Remote ToolSet up, launch, validate, and troubleshoot the Scrublet ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Scvelo Remote ToolSet up, launch, validate, and troubleshoot the scVelo ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Scvi Remote ToolSet up, launch, validate, and troubleshoot the scVI ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Singler Remote ToolSet up, launch, validate, and troubleshoot the SingleR ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Slingshot Remote ToolSet up, launch, validate, and troubleshoot the Slingshot ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Squidpy Remote ToolSet up, launch, validate, and troubleshoot the Squidpy ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Tangram Remote ToolSet up, launch, validate, and troubleshoot the Tangram ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Transcriptformer Remote ToolSet up, launch, validate, and troubleshoot the TranscriptFormer ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Setup Uspto Downloader Remote ToolSet up, launch, validate, and troubleshoot the USPTO downloader ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.Votes: 0GitHub stars: 1,719
- Tooluniverse Biomedical Fact LookupAnswer biomedical FACTUAL / recall / multiple-choice questions by querying ToolUniverse database tools instead of answering from memory. Triggers on any 'which gene/drug/variant/disease/pathway/miRNA/TF...' lookup, any question phrased 'according to <database>' (DisGeNet, OMIM, MSigDB, miRDB, GTRD, MGI, Ensembl, ClinVar, ChEMBL, OpenTargets, Reactome, GtoPdb, UniProt...), and multiple-choice biology/medicine knowledge questions where one option must be verified against an authoritative source...Votes: 0GitHub stars: 1,719
- Tooluniverse Molecular CloningMolecular cloning, in both directions. DESIGN — Gibson Assembly (overlap design for seamless multi-fragment joining) and Golden Gate Assembly (Type IIS / BsaI / BbsI / Esp3I / BsmBI / SapI design with unique 4-bp fusion overhangs). ANALYSIS — work out what an existing reaction produces: given input plasmid sequences and an enzyme, digest them, join the fragments by their overhangs, and identify features of the product (expressed ORF, gRNA spacer and its target gene). Use when you need to plan...Votes: 0GitHub stars: 1,719
- Tooluniverse Nih Funding LandscapeAnalyze NIH grant portfolios and funding history using the OpenNIH FY1985-present corpus, then connect grants to investigators, institutions, publications, clinical trials, patents, targets, or drugs with ToolUniverse. Use for NIH grant discovery, topic or Institute/Center trends, PI and institution profiles, activity-code or mechanism analysis, funding growth and concentration, grant-writing landscape research, SBIR/STTR landscapes, research-policy analysis, expert discovery, funding-to-outp...Votes: 0GitHub stars: 1,719
- Tooluniverse PhylogeneticsPhylogenetic analysis — de novo multiple sequence alignment (Clustal Omega/MUSCLE/MAFFT via EBI_msa_align) and neighbour-joining/UPGMA tree building (EBI_build_phylogenetic_tree) from your own sequences, plus tree analysis, treeness, saturation (PhyKIT), parsimony-informative sites, alignment gap analysis, DVMC, long-branch detection, BUSCO orthologs. Uses PhyKIT, Biopython, DendroPy. Use to align a set of sequences, build a tree from sequences or an alignment, or for phylogenetic tree QC, mu...Votes: 0GitHub stars: 1,719
- TooluniverseToolUniverse plugin router. STEP 1 BEFORE ANY ANALYSIS: if the data folder contains `*_executed.ipynb`, run `tu run read_executed_notebook '{\"data_folder\":\"<path>\",\"search\":\"<keyword>\"}'` to extract its cell outputs and apply EVERY filter/sample-exclusion the notebook used — even when the question says 'Using DESeq2/Run X/Compute Y' (this describes the METHOD the notebook used, not a request to rerun). The notebook's cell outputs are the only published authoritative answers; reimpleme...Votes: 0GitHub stars: 1,719
- Tooluniverse Acmg Variant ClassificationSystematic ACMG/AMP germline variant classification with all 28 criteria (PVS1, PS1-4, PM1-6, PP1-5, BA1, BS1-4, BP1-7) for clinical significance. Produces 5-tier verdict (Pathogenic / Likely Pathogenic / VUS / Likely Benign / Benign) with cited evidence per criterion. Use for variant interpretation, VUS resolution, and pathogenicity assessment. Combines ClinVar, gnomAD, computational predictors, and gene-mechanism context.Votes: 0GitHub stars: 1,719
- Tooluniverse Adverse Event DetectionDetect and analyze adverse drug event signals using FDA FAERS reports, drug labels, and disproportionality statistics (PRR, ROR, IC). Generates quantitative safety signal scores (0-100) with evidence grading. Use for post-market surveillance, pharmacovigilance, drug safety assessment, regulatory submissions, and detecting rare AE signals not visible in clinical trials.Votes: 0GitHub stars: 1,719
- Tooluniverse Adverse Outcome PathwayMap environmental and industrial chemicals to adverse outcome pathways (AOPs) — molecular initiating event to organ-level toxicity. Uses AOPWiki, GHS classification, IARC carcinogen status, and LD50 data. Use for environmental/industrial chemical risk assessment, regulatory-grade hazard characterization, and AOP stressor mapping. Distinct from drug-safety analysis (use tooluniverse-pharmacovigilance for drugs).Votes: 0GitHub stars: 1,719
- Tooluniverse Aging SenescenceAging biology, cellular senescence, and longevity research. Covers senescence markers (p16/CDKN2A, SASP, SA-beta-gal), aging hallmarks, senolytic drug discovery (dasatinib+quercetin, fisetin, navitoclax), epigenetic clocks, telomere biology, and longevity GWAS. Use for senescence-pathway analysis, age-related disease genetics, senolytic-target discovery, and centenarian-genetics queries. Distinguishes correlative vs causal evidence (knockout, intervention).Votes: 0GitHub stars: 1,719
- Tooluniverse Antibody EngineeringTherapeutic antibody engineering and optimization, lead-to-clinical-candidate. Covers sequence humanization (germline alignment, framework retention), affinity maturation, developability (aggregation, stability, PTMs), structure modeling (AlphaFold/PDB CDR analysis), immunogenicity prediction, and manufacturing feasibility. Use for biologic-drug optimization, mAb design review, biosimilar engineering, and clinical-precedent comparison.Votes: 0GitHub stars: 1,719
- Tooluniverse Binder DiscoveryDiscover novel small-molecule binders for protein targets using structure-based and ligand-based screening. Covers druggability assessment, known-ligand mining (ChEMBL, BindingDB), similarity expansion, ADMET filtering, and synthesis feasibility. Use for hit identification, virtual screening, target-to-compounds workflows, and lead-finding before commit-to-medchem.Votes: 0GitHub stars: 1,719
- Tooluniverse Cancer ClassificationTranslate free-text tumor descriptions to OncoTree codes and resolve cancer subtypes/tissue hierarchy. Cross-references UMLS/NCI vocabularies. Use for standardizing cancer-type nomenclature in EHR free-text, building cohorts in OncoKB or GDC, mapping tumor-board notes to ontology codes, and ensuring consistent terminology across cancer-genomics pipelines.Votes: 0GitHub stars: 1,719