892 skills · sorted by relevance
Prepare bulk RNA-seq sequencing files or quantification outputs for gene-level comparisons. Check sample information and data quality, configure processing workflows, and assemble validated count tables and metadata for downstream differential expression analysis with PyDESeq2.
Plan protein characterization experiments with Adaptyv's cloud laboratory, estimate costs, submit sequences, track progress, and retrieve measured results. Supports binding, thermal stability, expression, fluorescence, and enzyme activity workflows through the API and Python SDK.
Review supplied writing through twelve DHDNA dimensions, a framework for describing reasoning and expression. Receive observations supported by quotations, optional scores, and comparisons between samples, with clear limits separating textual patterns from psychological traits.
Find agent skills for a specific task, compare candidates using their capabilities, sources, and installation history, and install a selected skill into Cherry after the user has expressed an intent to install it.
Implement Zoom webhooks, HTTP notifications sent when events occur, such as meetings starting or recordings becoming available. Use reference guidance for event selection, subscriptions, signature verification, endpoint validation, delivery handling, and retries.
Scan API route definitions and generate test files for authentication, input validation, error responses, pagination, uploads, and rate limits. Supports Next.js App Router, Express, FastAPI, and Django REST, with Node and Python test outputs.
Integrate Stripe payments and subscriptions into web applications, including trials, prorated plan changes, usage billing, customer portals, and invoices. Follow implementation patterns and local testing steps, with webhook signature checks and duplicate event handling to support reliable billing updates.
Write, review, and refactor Python code using concrete readability rules. Keep functions focused, reduce nested logic, clarify names and expressions, and apply Python features such as comprehensions, dataclasses, and pathlib while respecting existing codebase conventions.
Add URL handlers to a TypeScript server built with Node's native HTTP module. The skill follows an existing switch/case router, connects named asynchronous handlers, and covers JSON responses, error handling, and optional shared request body parsing.
Add purposeful color to monochromatic interfaces so key actions, statuses, and categories are easier to recognize. Refine backgrounds, text, and charts around a consistent palette while checking contrast and avoiding reliance on color alone.
Predict patterns of gene expression and other genomic measurements from DNA sequences with Borzoi. Compare reference and altered sequences to estimate regulatory effects, generate predicted coverage tracks, and prioritize variants in regions that do not encode proteins.
Use scGPT to convert single-cell gene expression data into numerical representations of cells and genes. These representations support clustering, data integration, cell-type annotation, and analyses of gene perturbations or regulatory relationships.
Create original posters and static artwork by first defining a visual philosophy, then expressing it through color, shapes, spacing, and minimal text. Receive the artwork as PNG or PDF alongside a Markdown design statement.
Investigate server-side template injection, where user input is interpreted as template code. The skill covers engine identification, testing email and PDF rendering, and checking whether an injection can lead to command execution on the server.
Generate OpenAPI 3.0.3 specifications, a standard format for describing APIs, from route definitions in supported web frameworks. Extract paths, HTTP methods, parameters, and available model information into JSON or YAML for Swagger UI or Redoc.
Use this skill when working with symbolic mathematics in Python. This skill should be used for symbolic computation tasks including solving equations algebraically, performing calculus operations (derivatives, integrals, limits), manipulating algebraic expressions, working with matrices symbolically, physics calculations, number theory problems, geometry computations, and generating executable code from mathematical expressions. Apply this skill when the user needs exact symbolic results rather than numerical approximations, or when working with mathematical formulas that contain variables and parameters.
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Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.
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Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing protein design workflows with wet-lab validation.
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Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API. Use when the user asks about non-coding variant effects, pathogenicity, clinical significance, disease associations, functional effects, gene expression changes, splicing disruption, or regulatory effects in promoters and enhancers. Also use for resolving biological terms to tissue/cell-type ontologies (UBERON/CL) or analyzing variants in chr:pos:ref>alt format.
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Use when you want to retrieve quantitative RNA expression data and variant eQTL information from the GTEx (Genotype-Tissue Expression) Project across 54 non-diseased tissue sites.
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Gene Set Enrichment Analysis using clusterProfiler gseGO and gseKEGG. Use when analyzing ranked gene lists to find coordinated expression changes in gene sets without arbitrary significance cutoffs. Detects subtle but coordinated expression changes.
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Cell type assignment from marker expression in IMC data. Covers manual gating, clustering, and automated classification approaches. Use when assigning cell types to segmented IMC cells based on protein marker expression or when phenotyping cells in multiplexed imaging data.
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Remove batch effects from RNA-seq data using ComBat, ComBat-Seq, limma removeBatchEffect, and SVA for unknown batch variables. Use when correcting batch effects in expression data.
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Visualize differential expression results using DESeq2/edgeR built-in functions. Covers plotMA, plotDispEsts, plotCounts, plotBCV, sample distance heatmaps, and p-value histograms. Use when visualizing differential expression results.
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