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Predict RBP binding from RNA sequence using deep learning models (RBPNet sequence-to-signal, RNAProt RNN, GraphProt2 GCN with structure, DeepCLIP, DeepRiPe multi-modal CNN) for variant-effect prediction, in silico binding-site discovery, model interpretation, and transfer learning from CLIP and RBNS datasets. Use when computational prediction of RBP binding from sequence is needed, evaluating variant effects on binding without further wet-lab experiments, comparing model performance, or training a custom model on ENCODE eCLIP data.

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End-to-end CLIP-seq pipeline from FASTQ to ENCODE-compliant binding sites, single-nucleotide crosslink maps, annotation, motifs, and (optionally) differential binding. Use when running the full Yeo lab eCLIP / iCLIP / iCLIP2 / iCLIP3 / irCLIP / PAR-CLIP analysis with SMInput control, protocol-specific UMI extraction, ENCODE STAR parameters, CLIPper or Skipper peak calling with stringent log2 FC and -log10 p thresholds, IDR rescue and self-consistency QC, and downstream motif registration with mCross or PEKA.

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Align preprocessed CLIP-seq reads (eCLIP, iCLIP, iCLIP2, PAR-CLIP) to genome with STAR or bowtie2 using crosslink-preserving parameters, choosing between unique-mapper-only and multi-mapper-aware alignment for repeat-binding RBPs, deciding STAR vs HISAT2 memory trade-offs, and applying ENCODE-compatible filters. Use when turning preprocessed CLIP FASTQ into a deduplicated, MAPQ-filtered BAM ready for peak calling or crosslink-site detection.

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Discover RBP binding motifs from CLIP-seq peaks or single-nucleotide crosslink sites using HOMER, MEME/STREME, kpLogo, mCross (CL-position-registered motifs), PEKA (positional k-mer enrichment), RBPamp (affinity), and RNA Bind-n-Seq (RBNS) cross-validation. Use when characterizing RBP sequence specificity, registering motifs to crosslink positions, validating in vivo CLIP motifs against in vitro RBNS Kd, reconciling motif disagreements across tools, or correcting for the uracil crosslinking bias that contaminates raw CLIP motif logos.

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Run Bayesian phylogenetic analysis with MrBayes, BEAST2, RevBayes, and PhyloBayes including MCMC convergence diagnostics and model comparison. Use when needing posterior probability support, Bayesian model averaging, site-heterogeneous models for deep phylogenies, or formal model comparison via stepping-stone sampling.

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Calculates species richness, diversity, and turnover using the Hill number framework with iNEXT coverage-based rarefaction/extrapolation, asymptotic diversity estimation, and beta diversity partitioning (betapart turnover vs nestedness). Compares assemblages using coverage-standardized rather than size-standardized rarefaction. Use when quantifying biodiversity from species abundance or incidence data, comparing diversity across sites, or constructing rarefaction curves. Not for clinical 16S microbiome alpha/beta diversity (see microbiome/diversity-analysis).

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Analyze DNA/RNA/protein sequences. Use when the user provides a sequence and asks for analysis, translation, GC content, ORFs, motifs, restriction sites, or primer design. Triggers on "sequence", "translate", "GC content", "ORF", "primer", "restriction", "complement", "reverse complement".

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Protein 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 composite scoring. This skill provides research-backed thresholds from binder design competitions and published benchmarks.

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Workflow for ribosome profiling, P-site aware preprocessing, periodicity checks, ORF detection, and translation efficiency analysis.

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Quality control metrics and filtering thresholds for protein design. 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 composite scoring. This skill provides research-backed thresholds from binder design competitions and published benchmarks.

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Automates browser interactions for web testing, form filling, screenshots, and data extraction. Use when the user needs to navigate websites, interact with web pages, fill forms, take screenshots, test web applications, or extract information from web pages.

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Use when event content or site changes are finished and need to reach devopsdays.org - covers branching, rebasing on upstream main, local preview, committing, pushing to a fork or to upstream, opening the pull request, and interpreting a failing check.

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Use when a devopsdays event has sold or confirmed a sponsorship and the sponsor needs to appear on the event's site - covers both sponsors already in the shared directory and brand-new ones needing a logo and data file.

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Use when a devopsdays event has confirmed a speaker and their talk, workshop, ignite, or keynote needs to appear on the event site - covers the speaker bio page, the talk page, the headshot, and multi-speaker talks.

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Use when a devopsdays event that is already listed on the site has to be cancelled or postponed, and its pages need to stop advertising dates, registration, and sponsorship.

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QA test a live website with Firecrawl browser and scrape evidence. Use when the user wants exploratory QA, form testing, navigation/link checks, responsive checks, performance observations, bug reports, or a pre-launch quality review.

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Run outcome-focused Firecrawl workflows that produce deliverables such as research reports, literature reviews over published papers, SEO audits, QA reports, lead lists, knowledge bases, website design systems, and other structured web-data artifacts. Use when the user wants Firecrawl to complete a business, marketing, product, or creative workflow rather than merely scrape a page or integrate API calls into code.

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Produce an intensive, cited analytical report: executive summary, multi-angle findings, contrarian views, open questions, and full sources. Use only when the user needs rigorous synthesis of a complex topic (scientific, technical, policy, or market-analytical) that cannot be answered with a short search, and wants a formal written report, not a recommendation list. Do not use for product picks, top-N lists, quick lookups, or routine "find out about X" tasks. If the request does not clearly need this kind of report, do not use this skill. Do not use for a literature review over published papers. This skill collects evidence from the open web. A request for the literature on a biomedical, clinical, life-science, or other scientific topic — papers, studies, trials, preprints — belongs to firecrawl-research-papers, which queries Firecrawl's paper index (PubMed, bioRxiv, medRxiv, arXiv) instead of searching websites.

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Ingest public or authenticated knowledge bases and docs portals with Firecrawl browser. Use for JS-heavy docs, login-gated portals, paginated help centers, support knowledge bases, or structured JSON/markdown extraction from documentation sites.

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Safe refactoring workflow using trace-mcp — assess risk, find candidates, check impact, and rename symbols across all files without missing import sites or cross-file references.

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Create evidence-aware, interactive visual explainers as self-contained offline HTML. Use when a user asks to explain a concept, repository module, engineering tradeoff, or incident with a diagram, walkthrough, ELI5 treatment, data/request trace, failure view, or teach-back. Do not use for a plain short answer, ordinary prose rewrite, generic website implementation, or unsupported claims presented as facts.

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Use when an instructor asks for a setup guide, adoption guide, planning guide, implementation checklist, prerequisite check, MATLAB Course Designer course structure plan, Common Cartridge workflow, Simulink starter and solution model planning, LMS import plan, or starter prompt for creating a MATLAB and Simulink enabled course with the matlab-generate-course skill.

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Establish the shared environment, source/runtime correspondence, target confirmation and validation evidence for MetaX vLLM upgrades. Use as the common prerequisite of the patch, attention, registry and model upgrade skills, or for an explicitly requested MetaX environment preflight; it does not perform domain-specific adaptations.

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Launches 5 parallel AI agents to produce a comprehensive property analysis with composite Property Score (0-100), investment grade, and actionable recommendations

日本語の概要は準備中です。原文の説明を表示しています。