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Claude Skills by NVlabs
github.com/NVlabs1,342 skills6 installs400 views
- A B Test DesignDesign rigorous A/B tests with hypotheses, variants, metrics, and sample size calculations.Votes: 0GitHub stars: 158
- Ab TestingWhen the user wants to plan, design, or implement an A/B test or experiment, or build a growth experimentation program. Also use when the user mentions "A/B test," "split test," "experiment," "test this change," "variant copy," "multivariate test," "hypothesis," "should I test this," "which version is better," "test two versions," "statistical significance," "how long should I run this test," "growth experiments," "experiment velocity," "experiment backlog," "ICE score," "experimentation prog...Votes: 0GitHub stars: 158
- Academic Cv BuilderFormat CVs for academic positions with publications, grants, and teachingVotes: 0GitHub stars: 158
- Accessibility AuditConduct a comprehensive accessibility audit against WCAG guidelines with severity ratings and remediation steps.Votes: 0GitHub stars: 158
- Accessibility Test PlanCreate accessibility testing plans covering assistive technologies and WCAG criteria.Votes: 0GitHub stars: 158
- Aesthetic UsabilityApply the Aesthetic-Usability Effect — visually consistent, polished interfaces are perceived as more usable.Votes: 0GitHub stars: 158
- Affinity DiagramOrganize qualitative research data into an affinity diagram with themes, clusters, and insight statements. Use when synthesizing large amounts of qualitative data from interviews, observations, or surveys.Votes: 0GitHub stars: 158
- Alterlab Abm MesaBuilds agent-based models of social systems with Mesa 3 — the current AgentSet API (model.agents.shuffle_do('step'), auto-assigned unique_id, mandatory super().__init__(seed=...)), cell spaces (mesa.discrete_space OrthogonalMooreGrid / classic mesa.space grids), the DataCollector, batch_run parameter sweeps, and SolaraViz — for emergence, segregation, diffusion, opinion dynamics, and cooperation models. It uses the Mesa 3.x API (the old mesa.time schedulers like RandomActivation are removed) ...Votes: 0GitHub stars: 158
- Alterlab Accreditation AolScaffolds program-level Assurance-of-Learning (AoL) documentation for AACSB (2020 Standard 5) and ABET (Criterion 3 Student Outcomes, Criterion 4 Continuous Improvement) accreditation — program learning outcomes / competency goals, curriculum-to-outcome mapping matrices, direct- and indirect-assessment plans, rubric design, and closing-the-loop continuous-improvement narratives — and validates the structure of an outcome-mapping matrix with scripts/aol_matrix.py. Use when the user needs AACSB...Votes: 0GitHub stars: 158
- Alterlab Akademik TesvikComputes the annual Turkish academic-incentive (akademik teşvik) score for Devlet (state) university öğretim elemanı (academic staff) from a classified activity list, applying the verified Akademik Teşvik Ödeneği Yönetmeliği (2018/11834) Faaliyet Hesaplama Tablosu headline puanları (Proje 20, Araştırma 15, Yayın 30, Patent 30, Atıf 30, Tebliğ 20, Ödül 20) with the k (author-count), p (Q1 1/Q2 0.8/Q3 0.5/Q4 0.25), and r (project-role) coefficients via türü puanı = Σ(faaliyet oranları) × headli...Votes: 0GitHub stars: 158
- Alterlab AlphafoldPredict protein 3D structures with AlphaFold2 via ColabFold — MMseqs2-accelerated MSAs, monomer and AlphaFold2-Multimer complex folding, and confidence-based validation (pLDDT, pTM/ipTM, PAE). Use when folding a protein sequence or complex from FASTA, generating a predicted structure with confidence metrics, ranking models, or checking self-consistency of a design. For co-folding a protein WITH a small-molecule ligand or predicting binding affinity prefer alterlab-boltz; for antibody–antigen ...Votes: 0GitHub stars: 158
- Alterlab ApertaDrives TÜBİTAK Açık Bilim Politikası (Open Science Policy) compliance and deposition into Aperta — TÜBİTAK ULAKBİM's national open archive at aperta.ulakbim.gov.tr — encoding the binding mandates (green-road deposit of the accepted manuscript on acceptance; open access within 6 months for fen/mühendislik (STEM) and 12 months for sosyal/beşeri (SSH); İlke-6 documentation when data must stay closed for KVKK/privacy reasons) and scaffolding a TÜBİTAK Veri Yönetim Planı / VYP (data management pla...Votes: 0GitHub stars: 158
- Alterlab BoltzCo-fold biomolecular complexes with Boltz-2, an open AlphaFold3-style model — predict protein + ligand (SMILES/CCD), protein + nucleic-acid, and multi-chain structures in one pass, with binding-affinity prediction. Use when folding a protein together with a small-molecule ligand, predicting a holo (ligand-bound) complex or its binding affinity, or co-folding protein–DNA/RNA assemblies. For protein-only or protein–protein folding without ligands prefer alterlab-alphafold; for antibody–antigen ...Votes: 0GitHub stars: 158
- Alterlab BorzoiPredict genome-wide functional genomics tracks from DNA sequence with Borzoi (Linder 2025) — a sequence-to-function model outputting RNA-seq, CAGE, ATAC, and ChIP coverage across long context, used to score non-coding and regulatory variant effects. Use when predicting functional tracks from a DNA sequence, scoring a non-coding/regulatory variant's effect on expression or chromatin, or doing in-silico mutagenesis of a locus. To LOOK UP a variant's population frequency prefer alterlab-gnomad; ...Votes: 0GitHub stars: 158
- Alterlab Causal InferenceEstimates causal effects from observational and quasi-experimental data — difference-in-differences, instrumental variables, regression discontinuity, panel fixed effects, propensity-score / doubly-robust methods, and heterogeneous treatment effects (CATE) — using the verified Python stack: statsmodels and linearmodels (PanelOLS, IV2SLS), pyfixest (feols, event studies, Sun-Abraham, did2s), DoWhy (identify -> estimate -> refute), EconML (LinearDML, CausalForestDML, DRLearner), and rdrobust fo...Votes: 0GitHub stars: 158
- Alterlab ChaiPredict biomolecular complexes with Chai-1, an open AlphaFold3-style model that folds multi-entity assemblies (proteins, ligands, nucleic acids) from a single typed FASTA — strong on antibody–antigen and protein–ligand complexes, with optional MSA and restraint inputs. Use when predicting an antibody–antigen complex, folding a mixed protein/ligand/nucleic-acid assembly described in one FASTA, or generating a complex with experimental restraints. For binding-affinity prediction or a ligand-foc...Votes: 0GitHub stars: 158
- Alterlab Citation VerifierVerifies that every entry in a bibliography ACTUALLY EXISTS by cross-checking it against four keyless public scholarly APIs (Crossref, OpenAlex, Semantic Scholar, arXiv) with a polite mailto identifier, resolving DOI/arXiv IDs, fuzzy-matching title and authors (difflib SequenceMatcher ratio >=0.70), flagging retractions marked in Crossref (update-to) or OpenAlex (is_retracted), and emitting per-entry JSON verdicts mapped to the AlterLab citation-hallucination taxonomy (TF/PAC/IH/PH/SH). Accep...Votes: 0GitHub stars: 158
- Alterlab DergiparkHarvests article metadata, abstracts, and full-text PDFs from DergiPark (TÜBİTAK ULAKBİM's national journal-hosting platform, ~2,537 journals) via its verified platform-wide OAI-PMH endpoint (https://dergipark.org.tr/api/public/oai/; verbs Identify/ListSets/ListRecords/GetRecord; prefixes oai_dc/oai_mods/oai_marc/oai_etdms; setSpec=journal-slug), parses Highwire citation_* and DC.* meta tags on /pub/{slug}/article/{id} pages, pulls PDFs from the citation_pdf_url path, and emits BibTeX/RIS loc...Votes: 0GitHub stars: 158
- Alterlab Docentlik EligibilityRuns a PARTIAL pre-screen of a Turkish associate-professorship (doçentlik) publication list against the ÜAK (Üniversitelerarası Kurul) Sağlık Bilimleri TABLO 10 criteria, applying the author-share rule (full; 0.8 + 0.5; lead-author half-the-rest split) and pass-fail checking the four computable minimums (≥100 total, ≥90 post-doctorate, ≥40 SCIE/SSCI article points, ≥3 lead-author Q1–Q4 articles). It deliberately does NOT emit an ELIGIBLE verdict — it lists the unmodelled mandatory minimums (T...Votes: 0GitHub stars: 158
- Alterlab Figure QaVerify publication figures with a render-then-check QA pass — data-fidelity against every underlying row, axis/label floor-and-ceiling legibility, bounding-box collision detection for overlapping text/markers, and 300-dpi print-readiness. Use when proofing or auditing a finished figure for correctness and print quality, catching mislabeled or overlapping elements, or confirming a plot faithfully represents its data before submission. For CREATING the plot prefer alterlab-matplotlib (or alterl...Votes: 0GitHub stars: 158
- Alterlab Grant ReportingDrafts post-award grant deliverables across funder formats — NIH RPPR (Annual/Interim/Final via eRA Commons), NSF annual/final project reports and the public Project Outcomes Report (Research.gov), and Horizon Europe / ERC periodic and final reports (technical Part A/B + financial statements on the EU Funding & Tenders Portal) — plus milestone and deliverable tracking, budget-vs-actual variance narratives, no-cost-extension and rebudgeting justifications, and effort/closeout reporting. Comput...Votes: 0GitHub stars: 158
- Alterlab Kvkk DmpProduces KVKK-compliant (Law 6698, as amended by Law 7499 — published in the Official Gazette 12 Mar 2024, KVKK provisions effective 1 Jun 2024) data management plans for Turkish research, encoding the açık rıza (explicit consent) default basis, the Art. 28(1)(b) anonymization exemption as the primary compliance lever, the Art. 6 special-category regime for health/genetic/biometric data, Art. 7 deletion/destruction/anonymization at purpose-end, the Art. 13 thirty-day data-subject response win...Votes: 0GitHub stars: 158
- Alterlab LigandmpnnDesign protein sequences around bound ligands, metals, and nucleic acids with LigandMPNN (Dauparas 2023) — inverse folding that conditions on non-protein context, so binding-pocket and metal-site residues are chosen to fit the actual ligand. Use when designing a small-molecule or metal binding pocket, redesigning residues that contact a ligand/ion/nucleic acid, or doing enzyme active-site design where the substrate matters. For backbone sequence design with NO ligand/metal context prefer alte...Votes: 0GitHub stars: 158
- Alterlab Meta AnalysisRuns quantitative meta-analysis — computes effect sizes (Hedges' g / standardized mean difference, log odds/risk ratios) with their variances, pools them under fixed-effect and random-effects models, quantifies heterogeneity (I-squared, tau-squared, Cochran's Q), draws forest and funnel plots, and tests publication bias (Egger's regression, trim-and-fill) — using statsmodels.stats.meta_analysis in Python or the field-standard R metafor via Rscript. It enforces PRISMA reporting and the random-...Votes: 0GitHub stars: 158
- Alterlab Missing DataHandles missing data with principled methods — forces an explicit MCAR / MAR / MNAR mechanism statement, then applies multiple imputation by chained equations (MICE) with Rubin's-rules pooling of estimates and standard errors, or full-information maximum likelihood (FIML) where a likelihood/SEM model applies. Uses statsmodels MICE / MICEData in Python or the field-standard R mice via Rscript, and warns that single (mean/regression) imputation and scikit-learn's IterativeImputer return one com...Votes: 0GitHub stars: 158
- Alterlab Multilevel ModelsFits and reports mixed-effects / multilevel / hierarchical models for clustered, nested, longitudinal, and repeated-measures data — random intercepts and slopes, variance components and the ICC, cross-level interactions, and GLMMs (logistic/Poisson) — using statsmodels MixedLM and bambi (Bayesian on PyMC) in Python, or the field-standard R lme4 / glmmTMB / brms via Rscript. It enforces the reporting items reviews find under-reported: full fixed + random specification, centering, variance comp...Votes: 0GitHub stars: 158
- Alterlab Nf Core SarekRuns FASTQ-to-VCF germline and somatic variant calling via the Nextflow nf-core/sarek pipeline pinned to -r 3.8.1 — builds the samplesheet.csv (patient, sex, status, sample, lane, fastq_1, fastq_2), runs bwa-mem/bwa-mem2/dragmap alignment plus GATK4 MarkDuplicates and BQSR against the GATK GRCh38 resource bundle (dbSNP, Mills/1000G indels), and selects callers — explicitly correcting that sarek defaults to Strelka when --tools is unset (pass haplotypecaller for GATK best practice or deepvaria...Votes: 0GitHub stars: 158
- Alterlab Pdf ExploreExplore a single PDF in depth — parse it once, then answer questions across its sections, figures, tables, and appendices — comparing methods across sections, extracting every instance of a pattern within the document, and reading values off its charts and tables. Use when interrogating one paper or report end-to-end, pulling every occurrence of something inside a document, or reading data from a figure/table in a PDF, serving the literature-review and paper-review pipeline. To build a compar...Votes: 0GitHub stars: 158
- Alterlab Preprint DepositionDrives preprint deposition across servers (arXiv, bioRxiv, medRxiv, SSRN, OSF Preprints): picks the right server by field, prepares submission metadata, sets the license (arXiv offers CC BY/BY-SA/BY-NC-SA/BY-NC-ND 4.0, the arXiv non-exclusive license, or CC0; bioRxiv/medRxiv offer CC BY/BY-NC/BY-ND/BY-NC-ND/CC0 or No-reuse), maps arXiv category taxonomy, handles immutable versioning and preprint DOIs, checks a journal's preprint/self-archiving policy via the Sherpa Romeo v2 API, and links the...Votes: 0GitHub stars: 158
- Alterlab Preregistration DisciplineEnforces pre-registration discipline with the Iron Law NO DATA ANALYSIS WITHOUT A PRE-REGISTERED ANALYSIS PLAN FIRST, a spirit-vs-letter line, an Excuse-vs-Reality rationalization table, and a Red-Flags-STOP list (HARKing, optional stopping, post-hoc covariates, outlier-dropping, test-shopping). Runs a PLAN/COLLECT/CONFIRM/EXPLORE workflow that freezes hypotheses, tests, exclusions, and stopping rules before data, then forces unplanned findings to be labeled exploratory (their p-values lose c...Votes: 0GitHub stars: 158
- Alterlab ProteinmpnnDesign protein sequences for a fixed backbone with ProteinMPNN (Dauparas 2022) — message-passing inverse folding that outputs sequences predicted to fold to a given structure, with fixed positions, tied/symmetric chains, amino-acid bias, and a soluble-model variant. Use when inverse-folding a backbone PDB into sequences, redesigning selected positions, imposing symmetry across chains, or generating the sequence step of a design→fold→score loop. For pocket/interface design WITH a bound ligand,...Votes: 0GitHub stars: 158
- Alterlab QcaRuns Qualitative Comparative Analysis — crisp-set (csQCA), multi-value (mvQCA), and fuzzy-set (fsQCA) — for small-to-medium-N configurational research: calibrating raw data into set membership, building and refining a truth table, and Boolean minimization into conservative / parsimonious / intermediate solutions with consistency and coverage. Because there is no maintained Python QCA library, it shells out to R's QCA package (calibrate, truthTable, minimize) via Rscript and documents that dep...Votes: 0GitHub stars: 158
- Alterlab Qiime2 AmpliconRuns 16S/ITS amplicon (microbiome) analysis with the QIIME 2 amplicon distribution (2026.1; renamed to "qiime2" in 2026.4) in the correct order: manifest import, cutadapt trim-paired primer removal BEFORE dada2 denoise-paired (trunc-len chosen from the demux quality .qzv), feature-classifier classify-sklearn against a version-matched SILVA 138 or Greengenes2 classifier, and diversity core-metrics-phylogenetic — teaching the .qza/.qzv artifact-and-provenance model and the 2026.1 feature-table ...Votes: 0GitHub stars: 158
- Alterlab Qualitative AnalysisAnalyzes qualitative data as a dispatched pipeline module — codebook development, thematic / framework / content analysis, and inter-coder reliability computed correctly (Krippendorff's alpha as primary via the krippendorff package or a bundled stdlib nominal calculator with bootstrap CIs; Cohen's / Fleiss' kappa via statsmodels) with 95% CIs and thresholds (alpha >= .80 reliable, .667-.80 tentative). It BRANCHES by design: coefficient-based ICR for codebook / content-analytic coding, versus ...Votes: 0GitHub stars: 158
- Alterlab Recommendation LettersDrafts evidence-anchored academic reference and recommendation letters across types — graduate admission, faculty hiring, tenure/promotion external review, fellowship, and award nomination — from a structured prompt of candidate accomplishments, role context, evaluator relationship, and audience, calibrating specificity and register to the letter type and running a no-fabrication guard that flags unsupported superlatives, unanchored rankings, and claims with no evidence in the supplied dossie...Votes: 0GitHub stars: 158
- Alterlab Results TransparencyEnforces results-reporting transparency as a discipline gate built on the Iron Law "NO RESULTS CLAIM WITHOUT REPORTING EVERY ANALYSIS RUN" — a numbered Gate Function (IDENTIFY the claim, LIST every test actually run including the ones that did not "work", CHECK assumptions were reported, CHECK effect size with 95% CI is present, CHECK pre-registration deviations are disclosed, ONLY THEN write the sentence), plus an Excuse-vs-Reality table and Red-Flags-STOP list for selective reporting, cherr...Votes: 0GitHub stars: 158
- Alterlab RfdiffusionGenerate de-novo protein backbones with RFdiffusion (Watson 2023) — a diffusion model for unconditional monomer generation, motif scaffolding, binder design against a target, and symmetric oligomers. Use when generating a new protein backbone from scratch, scaffolding a functional motif into a fold, designing a binder backbone to a target surface, or building symmetric assemblies; RFdiffusion produces the STRUCTURE, then alterlab-proteinmpnn designs its sequence and alterlab-alphafold validat...Votes: 0GitHub stars: 158
- Alterlab Rnaseq QuantQuantifies bulk RNA-seq transcript abundance with salmon (v1.11.4 selective alignment) and kallisto (v0.52.0, kb-python workflow), builds a decoy-aware gentrome index, runs quant with --validateMappings --gcBias -l A, then imports estimates via tximport/tximeta with a tx2gene map and hands differential expression to alterlab-pydeseq2. Warns that salmon's index format changed to SSHash (rebuild pre-v1.11.2 indices) and that 'salmon alevin' was REMOVED (single-cell now uses piscem + alevin-fry)...Votes: 0GitHub stars: 158
- Alterlab ScgptApply the scGPT single-cell foundation model (Cui 2024) to annotate and embed cells — zero-shot and fine-tuned cell-type annotation, gene/cell embeddings, batch integration, and gene-regulatory / perturbation inference from AnnData. Use when annotating cell types with a pretrained foundation model, generating scGPT embeddings, integrating batches with a transformer, or running zero-shot single-cell inference on an h5ad. For probabilistic latent models (scVI/scANVI) prefer alterlab-scvi-tools;...Votes: 0GitHub stars: 158
- Alterlab Sem PsychometricsFits and evaluates measurement models — confirmatory factor analysis, full structural equation models, exploratory factor analysis, item response theory, and multi-group measurement invariance — using the verified Python stack: semopy (model syntax =~ / ~ / ~~, Model.fit, inspect(std_est=True), calc_stats for CFI/TLI/RMSEA), factor_analyzer (EFA, KMO, Bartlett, ConfirmatoryFactorAnalyzer), and pingouin/girth, computing McDonald's omega from standardized loadings and judging fit against Hu & B...Votes: 0GitHub stars: 158
- Alterlab Skill FinderThe AlterLab front door and multi-agent launcher — routes a task to the right AlterLab skill(s) when the user invokes the suite without naming one, and for a multi-stage goal (or on the keyword 'alterflow', aliases 'alterresearch' / 'ultralab') it CLARIFIES the goal with a few questions, SELECTS the skills the task needs, and runs a dynamic multi-agent workflow composing them (via alterlab-workflow-orchestration, alterlab-research-pipeline, or alterlab-ssci-orchestrator). Triggers on 'use Alt...Votes: 0GitHub stars: 158
- Alterlab SnaApplies social-network-analysis method discipline to relational data — degree/betweenness/closeness/eigenvector centrality and PageRank, community detection (Louvain and greedy-modularity native in networkx, Leiden via igraph), and inferential network models (ERGM) — choosing the measure that matches the substantive question and the right dependence assumptions, then routing computation to the existing networkx (and igraph/R) tooling. Use when the request mentions social network analysis, cen...Votes: 0GitHub stars: 158
- Alterlab Squidpy SpatialAnalyzes spatial transcriptomics with squidpy (1.8.x) on AnnData and SpatialData objects, routing platforms correctly: Visium spots use spatial_neighbors(coord_type='grid') and pair with deconvolution, while Xenium/MERFISH single-cell data use coord_type='generic'/Delaunay neighbors and spatialdata-io readers (xenium, visium_hd, merscope). Runs sq.gr.spatial_neighbors, nhood_enrichment, co_occurrence, spatial_autocorr (Moran's I for spatially variable genes), ripley, and ligrec. Use when the ...Votes: 0GitHub stars: 158
- Alterlab Ssci Design GateRoutes a social-science study to its research design — true experiment, quasi-experiment (difference-in-differences, instrumental variables, regression discontinuity, interrupted time series, fixed effects), observational/correlational, qualitative, or mixed — by walking the random-selection and random-assignment decisions, then PINS the identifying assumption the causal claim will rest on (parallel trends, exclusion restriction, continuity at the cutoff, selection-on-observables, or qualitat...Votes: 0GitHub stars: 158
- Alterlab Ssci Inference GateAudits final inferential claims against the design, sample, and uncertainty before they are written or published — refuses causal language unless the design's identifying assumption is defended (else downgrades to associational), corrects p-value and confidence-interval misreadings (a p-value is not the probability the null is true, non-significance is not proof of no effect, a 95% CI is not a 95% probability the parameter is inside it), demands effect sizes with intervals rather than signifi...Votes: 0GitHub stars: 158
- Alterlab Ssci Measurement GateGates measurement quality before a scale or instrument is trusted — checks that each construct is defined and operationalized, that reliability is evidenced with McDonald omega (not Cronbach alpha alone, which assumes tau-equivalence and is only a lower bound), that reliability is not confused with validity (content, criterion, convergent/discriminant construct validity), and that measurement invariance is tested before comparing groups. Use when asking whether a scale or survey instrument is...Votes: 0GitHub stars: 158
- Alterlab Ssci OrchestratorCoordinates a social-science study through the stage-gated methods pipeline — question then design-gate then measurement-gate then sampling-gate then the right analysis module then inference-gate then reporting — holding a single YAML Design Passport that each gate reads and appends, and enforcing gate order with PASS / WARN / BLOCK semantics (design-gate and inference-gate are fail-closed). It is thin: it routes and holds the artifact, it does not run analysis itself. Use when a researcher d...Votes: 0GitHub stars: 158
- Alterlab Ssci Reflexivity GateGates trustworthiness before qualitative or interpretivist claims are written — the qualitative analog of the measurement gate. Checks that researcher positionality and role are stated, that the four Lincoln & Guba trustworthiness criteria are addressed (credibility via triangulation / member-checking / prolonged engagement, transferability via thick description, dependability via an audit trail, confirmability via reflexive bracketing), and that reflexivity is evidenced rather than asserted....Votes: 0GitHub stars: 158
- Alterlab Ssci Sampling GateGates who is sampled, how, and how many before data collection — checks that the sampling FRAME matches the target population (coverage error), that the METHOD is named (probability vs non-probability: simple random, stratified, cluster, systematic, quota, convenience, snowball), that sample SIZE follows the inference paradigm (an a-priori power analysis for hypothesis tests, a precision/margin-of-error target for estimation, or saturation/information power for qualitative studies — never a r...Votes: 0GitHub stars: 158
- Alterlab Survey AnalysisAnalyzes complex-sample survey data with design-based inference — declares a survey design (weights, strata, PSUs/clusters, FPC) before estimating means, totals, proportions, ratios, and quantiles, computes design-adjusted standard errors via Taylor linearization or replicate weights (BRR, Jackknife, Bootstrap), calibrates with post-stratification / raking / GREG, and fits design-adjusted GLMs (linear, logistic, Poisson). Uses samplics (stable Python), the emerging svy successor, or the field...Votes: 0GitHub stars: 158