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Claude Skills by stanfish06
github.com/stanfish061,773 skills143 installs3,463 views
- Ngs Bcl To FastqValidate Illumina BCL run folders and sample sheets, plan demultiplexing, review index/UMI/lane choices, run BCL-to-FASTQ conversion, and interpret demux metrics while surfacing license/download boundaries.Votes: 0GitHub stars: 8
- Ngs Bulk Rnaseq Counts QcRun or plan bulk RNA-seq FASTQ-to-count processing with sample-sheet, strandedness, genome annotation, alignment or pseudoalignment, MultiQC, and count-matrix QC checks.Votes: 0GitHub stars: 8
- Ngs Bulk Rnaseq Differential ExpressionRun or plan bulk RNA-seq differential-expression analysis from count matrices with replicate, design formula, contrast, batch, normalization, QC plot, and result-table checks.Votes: 0GitHub stars: 8
- Ngs Bulk RnaseqDispatch bulk RNA-seq requests to FASTQ-to-count QC or count-matrix differential-expression skills using nf-core/rnaseq, STAR, Salmon, featureCounts, MultiQC, and R/Bioconductor workflows.Votes: 0GitHub stars: 8
- Ngs Chip Cutrun Peaks QcRun or plan ChIP-seq, CUT&RUN, or CUT&Tag QC, control handling, spike-in, peak calling, broad-vs-narrow target selection, replicate, bigWig, and differential binding workflows.Votes: 0GitHub stars: 8
- Ngs Cli ToolkitThe core command-line NGS workhorses for going from raw reads to variants — bwa-mem2/minimap2/bowtie2 (alignment), samtools (BAM sort/index/stats/view), bcftools (VCF call/filter/normalize/query), GATK4 (BQSR, HaplotypeCaller, best practices), and plink2 (genotype QC, PCA, GWAS). Use for read alignment, BAM/CRAM manipulation, variant calling and VCF wrangling on the command line. For Python-native BAM/VCF access use pysam; for full managed pipelines use the nf-core wrappers.Votes: 0GitHub stars: 8
- Ngs Dna Germline VariantsRun or plan deep germline WGS, WES, targeted-panel, cohort, or trio variant-calling workflows with reference-build, known-sites, QC, joint-calling, and annotation checks.Votes: 0GitHub stars: 8
- Ngs Dna Somatic VariantsRun or plan tumor-normal, tumor-only, WGS, WES, or cancer-panel somatic variant workflows with pairing, contamination, panel-of-normals, purity, QC, and annotation checks.Votes: 0GitHub stars: 8
- Ngs Dna Umi Panel VariantsRun or plan targeted DNA panel variant workflows that use UMIs, duplex consensus reads, molecular barcodes, low-frequency calling, target coverage, and panel-specific QC.Votes: 0GitHub stars: 8
- Ngs Dna Variant CallingDispatch WGS, WES, or targeted DNA variant requests to germline, somatic, or UMI-panel skills, then plan public nf-core/sarek, GATK4, DeepVariant, samtools, or bcftools workflows.Votes: 0GitHub stars: 8
- Ngs Epigenomics PeaksDispatch ATAC-seq, ChIP-seq, CUT&RUN, or CUT&Tag requests to assay-specific QC, alignment, signal-track, peak-calling, consensus, and differential peak workflows.Votes: 0GitHub stars: 8
- Ngs Fastq QcValidate FASTQ inputs, run local FastQC/MultiQC QC, interpret QC signals, and optionally execute fastp or Cutadapt trimming branches without overwriting raw reads.Votes: 0GitHub stars: 8
- Ngs Runtime EnvCheck whether public NGS tools and packages already exist before downloading, installing, or running a sequencing pipeline.Votes: 0GitHub stars: 8
- Ngs Scrna SeqRoute single-cell or single-nucleus RNA-seq FASTQs to public count-generation workflows and defer post-count matrix QC, annotation, clustering, and UMAP analysis to the embedded scrna-seq-qc skill.Votes: 0GitHub stars: 8
- Ngs Shotgun MetagenomicsKick off public shotgun metagenomics QC, host-depletion, taxonomic profiling, and functional profiling workflows using nf-core/taxprofiler, Kraken2, Bracken, MetaPhlAn, and HUMAnN.Votes: 0GitHub stars: 8
- Node Link And Diagram LayoutChoose and apply automatic layout strategies for node-link diagrams and connected-node visuals. Use when the user asks how to auto-arrange nodes, reduce line crossings, route edges, avoid overlaps, stabilize layout, or choose graph-layout algorithms for network diagrams, dependency graphs, database schema diagrams, ERDs, state machines, decision trees, flow diagrams, box-and-line editors, or other line-connected nodes.Votes: 0GitHub stars: 8
- Nonlinear Dynamics Chaos ScientistExpert-thinking profile for Nonlinear Dynamics & Chaos Scientist (theoretical / computational / experimental dynamical systems): Reasons from flows, maps, bifurcations, and invariant sets; continues with MatCont/AUTO/COCO, validates chaos with IAAFT surrogates and embedding convergence, and treats spurious Lyapunov exponents, stiff integrator artifacts, and colored-noise confounds as first-class failure modes.Votes: 0GitHub stars: 8
- Notion Knowledge CaptureCapture conversations and decisions into structured Notion pages; use when turning chats/notes into wiki entries, how-tos, decisions, or FAQs with proper linking.Votes: 0GitHub stars: 8
- Notion Meeting IntelligencePrepare meeting materials with Notion context and Codex research; use when gathering context, drafting agendas/pre-reads, and tailoring materials to attendees.Votes: 0GitHub stars: 8
- Notion Research DocumentationResearch across Notion and synthesize into structured documentation; use when gathering info from multiple Notion sources to produce briefs, comparisons, or reports with citations.Votes: 0GitHub stars: 8
- Notion Spec To ImplementationTurn Notion specs into implementation plans, tasks, and progress tracking; use when implementing PRDs/feature specs and creating Notion plans + tasks from them.Votes: 0GitHub stars: 8
- Nuclear ChemistExpert-thinking profile for Nuclear Chemist (clinical / research): Reasons from decay- corrected activity ledgers, decay modes and cross sections, and ALARA dose control through Bateman/ORIGEN modeling, extraction-chromatography separations (TRU/Sr/TEVA resins), and HPGe/alpha/LSC spectroscopy while treating daughter ingrowth, generator breakthrough, spectral pile-up and sum peaks...Votes: 0GitHub stars: 8
- Nuclear EngineerExpert-thinking profile for Nuclear Engineer (reactor physics / thermal hydraulics / safety & licensing): Reasons from k_eff, DNBR/CHF margins, xenon transients, and defense-in-depth; couples SCALE/MCNP, PARCS, TRACE/RELAP, and MELCOR to 10 CFR and PRA; treats nodalization, nuclear-data, and CHF-correlation uncertainties as first- class failure modes.Votes: 0GitHub stars: 8
- Nuclear Medicine ScientistExpert-thinking profile for Nuclear Medicine Scientist (clinical / research): Reasons from radioactive decay, biodistribution kinetics, and detector physics through HPLC/TLC radiochemical-purity QC, dose-calibrator cross-calibration, OSEM/PSF reconstruction, and MIRD/OLINDA dosimetry while treating partial-volume effects, attenuation mismatch, 68Ge breakthrough and other radionuclidic impurity...Votes: 0GitHub stars: 8
- Nuclear PhysicistExpert-thinking profile for Nuclear Physicist (experimental / theoretical / nuclear data & applications): Reasons from shell and collective structure, reaction mechanisms, and ENDF/EXFOR data; matches FRIB–CEBAF–RHIC science to R-matrix, Hauser- Feshbach, chiral ab initio, and GEANT4 tools; treats dead time, normalization, and evaluation covariances as first-class failure modes.Votes: 0GitHub stars: 8
- NumbaA Just-In-Time (JIT) compiler for Python that translates a subset of Python and NumPy code into fast machine code. Developed by Anaconda, Inc. Highly effective for accelerating loops, custom mathematical functions, and complex numerical algorithms. Use for @njit, @vectorize, prange, cuda.jit, numba.typed, JIT compilation, parallel loops, GPU acceleration with CUDA, Monte Carlo simulations, numerical algorithms, and high-performance Python computing.Votes: 0GitHub stars: 8
- Number TheoristExpert-thinking profile for Number Theorist (theoretical / computational pure and arithmetic number theory): Reasons from primes, congruences, L-functions, and the Langlands web; chooses algebraic, analytic, and sieve methods; validates with SageMath/PARI/LMFDB while treating PARI stack overflows, conditional-proof leaks, and CRT moduli errors as first-class failure modes.Votes: 0GitHub stars: 8
- Numerical AnalystExpert-thinking profile for Numerical Analyst (theoretical / computational scientific computing): Reasons from well-posedness, discretization, conditioning, and stability; verifies codes with MMS and convergence studies; treats cancellation, stiffness, and solver tolerance floors as first-class failure modes.Votes: 0GitHub stars: 8
- Nutrigx AdvisorPersonalised nutrition report from consumer genetic data (23andMe, AncestryDNA, VCF) — interrogates nutritionally-relevantVotes: 0GitHub stars: 8
- Nutrition ScientistExpert-thinking profile for Nutrition Scientist (nutritional epidemiology / controlled feeding trials / dietary assessment & biomarker validation / survey analysis (NHANES, DLW)): Reasons from intake measurement error, energy balance, and causal triangulation through doubly-labeled-water validation, NCI usual-intake models, DRI (EAR/RDA/UL) frameworks, crossover feeding trials, and Mendelian randomization while treating dietary underreporting, reverse causation (sick-quitter), unadjusted...Votes: 0GitHub stars: 8
- Nvmolkit UsageWrite code that calls the installed nvMolKit Python API for GPU-accelerated, batched RDKit-style operations - Morgan fingerprints, Tanimoto/cosine similarity, ETKDG conformer embedding, MMFF/UFF optimization, TFD, conformer RMSD, Butina clustering, and substructure search. Use when the user is importing `nvmolkit.*`, debugging an `nvmolkit` call, choosing between nvMolKit and RDKit for a batched cheminformatics workflow, or wiring nvMolKit results into a torch/numpy pipeline. Out of scope: bu...Votes: 0GitHub stars: 8
- Observability And InstrumentationInstruments code so production behavior is visible and diagnosable. Use when adding logging, metrics, tracing, or alerting. Use when shipping any feature that runs in production and you need evidence it works. Use when production issues are reported but you can't tell what happened from the available data.Votes: 0GitHub stars: 8
- Observational AstronomerExpert-thinking profile for Observational Astronomer (multi-wavelength observational / calibration & photometry / time-domain & transients / Bayesian inference / multi- messenger): Reasons from radiative transfer, the distance ladder, and statistical- versus-systematic error budgets through HST/JWST/ALMA pipelines, Gaia DR3 astrometry, archives (SIMBAD, MAST, HEASARC), and emcee/dynesty inference while treating the look- elsewhere effect, PSF and flat-field artifacts, photo-z catastrophic...Votes: 0GitHub stars: 8
- Obsidian CliInteract with Obsidian vaults using the Obsidian CLI to read, create, search, and manage notes, tasks, properties, and more. Also supports plugin and theme development with commands to reload plugins, run JavaScript, capture errors, take screenshots, and inspect the DOM. Use when the user asks to interact with their Obsidian vault, manage notes, search vault content, perform vault operations from the command line, or develop and debug Obsidian plugins and themes.Votes: 0GitHub stars: 8
- Occupational Health ScientistExpert-thinking profile for Occupational Health Scientist (industrial hygiene / exposure assessment / occupational epidemiology / sampling and OELs (PEL, TLV, REL) / hierarchy of controls): Reasons from exposure route and receptor, dose-response, and the hierarchy of controls through SEG-based personal sampling, NIOSH/OSHA analytical methods, AIHA Bayesian exceedance statistics, and SMR cohort analysis, while treating healthy worker effect, below-LOD censoring, fraction-size and OEL mismatch,...Votes: 0GitHub stars: 8
- OceanographerExpert-thinking profile for Oceanographer (seagoing / interdisciplinary / water-mass & tracer analysis / air-sea flux & biogeochemistry / TEOS-10): Reasons from basin-scale budgets, three-dimensional circulation, and forcing-transport-transformation coupling through θ–S and OMP water-mass analysis, transient-tracer ventilation ages (CFC/SF₆/¹⁴C), GO-SHIP/Argo/SOCAT networks, and TEOS-10 thermodynamics while treating mesoscale aliasing of single sections, mixed...Votes: 0GitHub stars: 8
- Officecli Academic PaperUse this skill to build academic-style .docx output: journal / conference / thesis chapters carrying formal citation style (APA, Chicago, IEEE, MLA), numbered equations, figure & table cross-references, footnotes/endnotes, bibliography, or multi-column journal layout. Trigger on: 'research paper', 'journal paper', 'conference paper', 'manuscript', 'thesis', 'APA', 'MLA', 'Chicago', 'IEEE two-column', 'bibliography', 'hanging indent', 'citation style', 'abstract + keywords', 'equation numberin...Votes: 0GitHub stars: 8
- Officecli Data DashboardUse this skill to build a multi-element Excel dashboard — Dashboard sheet on open, multiple formula-driven KPI cards, multiple charts, sparklines, and conditional formatting — from CSV or tabular input. Trigger on: 'dashboard', 'KPI dashboard', 'analytics dashboard', 'executive dashboard', 'metrics dashboard', 'CSV to dashboard', 'data visualization'. Output is a single .xlsx. Scene-layer on officecli-xlsx: inherits every xlsx hard rule. DO NOT invoke for: a single budget tracker / one-sheet ...Votes: 0GitHub stars: 8
- Officecli DocxUse this skill any time a .docx file is involved -- as input, output, or both. This includes: creating Word documents, reports, letters, memos, or proposals; reading, parsing, or extracting text from any .docx file; editing, modifying, or updating existing documents; working with templates, tracked changes, comments, headers/footers, or tables of contents. Trigger whenever the user mentions 'Word doc', 'document', 'report', 'letter', 'memo', or references a .docx filename.Votes: 0GitHub stars: 8
- Officecli Financial ModelUse this skill when the user wants to build a financial model — 3-statement model, DCF valuation, LBO, SaaS unit economics, sensitivity / scenario analysis, debt schedule, or fundraising projections — in Excel. Trigger on: 'financial model', '3-statement model', 'P&L + BS + CF', 'DCF', 'WACC', 'NPV', 'terminal value', 'LBO', 'debt schedule', 'cash sweep', 'MOIC', 'IRR / XIRR', 'sensitivity table', 'scenario analysis', 'ARR model', 'unit economics', 'CAC / LTV', 'cap table forecast'. Output is...Votes: 0GitHub stars: 8
- Officecli Pitch DeckUse this skill when the user is building a fundraising / investor pitch deck — seed, Series A / B / C, convertible note, SAFE round, strategic raise. Trigger on: 'pitch deck', 'investor deck', 'Series A deck', 'Series B deck', 'Series C deck', 'fundraising deck', 'seed pitch', 'VC deck', 'raising capital', 'term sheet presentation'. Output is a single .pptx. This skill is a scene layer on top of officecli-pptx — inherits every pptx v2 rule (visual floor, grid, palettes, connector canon, Deliv...Votes: 0GitHub stars: 8
- Officecli PptxUse this skill any time a .pptx file is involved -- as input, output, or both. This includes: creating slide decks, pitch decks, or presentations; reading, parsing, or extracting text from any .pptx file; editing, modifying, or updating existing presentations; combining or splitting slide files; working with templates, layouts, speaker notes, or comments. Trigger whenever the user mentions 'deck', 'slides', 'presentation', 'pitch', or references a .pptx filename.Votes: 0GitHub stars: 8
- Officecli Word FormUse this skill to create fillable Word forms (.docx) with real Content Controls (SDT) + legacy FormField checkboxes + MERGEFIELD mail-merge placeholders + document protection. Trigger on: 'fillable form', 'form fields', 'content controls', 'SDT', 'word form', 'fill in', 'only editable fields', 'protect document', 'onboarding form', 'HR intake', 'survey template', 'contract / SOW template', 'mail-merge template', 'compliance checklist', 'medical intake questionnaire'. Output is a single .docx ...Votes: 0GitHub stars: 8
- Officecli XlsxUse this skill any time a .xlsx file is involved -- as input, output, or both. This includes: creating spreadsheets, financial models, dashboards, or trackers; reading, parsing, or extracting data from any .xlsx file; editing, modifying, or updating existing workbooks; working with formulas, charts, pivot tables, or templates; importing CSV/TSV data into Excel format. Trigger whenever the user mentions 'spreadsheet', 'workbook', 'Excel', 'financial model', 'tracker', 'dashboard', or reference...Votes: 0GitHub stars: 8
- OfficecliCreate, analyze, proofread, and modify Office documents (.docx, .xlsx, .pptx) using the officecli CLI tool. Use when the user wants to create, inspect, check formatting, find issues, add charts, or modify Office documents.Votes: 0GitHub stars: 8
- Omero IntegrationMicroscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.Votes: 0GitHub stars: 8
- Omniverse Cad To SimreadyCoordinate the end-to-end CAD/source-asset to SimReady workflow. Use for broad requests such as CAD to SimReady, source asset to simulation-ready USD, or prop packaging that require conversion, material/physics assignment, SimReady conformance, validation, and optional package creation; deploy or verify Content Agents services first when property assignment is enabled; route single-stage work through nested references.Votes: 0GitHub stars: 8
- Omniverse Usd Performance TuningTop-level workflow skill for USD performance diagnosis and optimization. Use for slow loading, high memory, low FPS, or 'optimize my scene' requests; delegates auth/runtime setup to Phase 0 owners.Votes: 0GitHub stars: 8
- Oncall IrmRoute alerts, run on-call rotations, and drive incidents in Grafana IRM / OnCall — integrations (Alertmanager / Grafana Alerting / generic webhook / PagerDuty), Jinja2 routing + grouping templates, escalation chains (wait → notify schedule → notify team → webhook → auto-resolve), schedules (web + iCal + Terraform `grafana_oncall_schedule`), Slack chatops with Acknowledge/Resolve/Silence, and the P1-P4 incident lifecycle. Use when wiring Alertmanager to OnCall, deciding which team gets paged, ...Votes: 0GitHub stars: 8
- OncologistExpert-thinking profile for Oncologist (clinical / multidisciplinary oncology): Stages with AJCC TNM and molecular prognostic groups, selects biomarker-matched therapy from NCCN guidelines, assesses response with RECIST 1.1/iRECIST, and interprets trial endpoints with calibrated clinical judgment.Votes: 0GitHub stars: 8