「binding」の検索結果

Detect single-nucleotide crosslink (CL) sites in CLIP-seq data using truncation patterns (iCLIP/eCLIP CITS), crosslink-induced mutations (HITS-CLIP CIMS deletions, PAR-CLIP T-to-C), or HMM/kernel-density methods (PureCLIP, PARalyzer, CTK). Use when single-nucleotide resolution is required for motif registration (mCross), allele-specific binding (BEAPR), variant-effect prediction, or comparing crosslink chemistry across CLIP variants.

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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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Profiles RNA-binding protein targets without antibody or UV crosslinking using STAMP (APOBEC1-RBP fusion, C-to-U editing), scSTAMP (single-cell), TRIBE/HyperTRIBE (ADAR-RBP, A-to-I editing), DART-seq (APOBEC1-YTH for m6A), or Bullseye/SAILOR edit-site detection pipelines. Use when antibody is unavailable or specificity is doubtful, when single-cell RBP profiling is needed (scSTAMP), or when in vivo RBP profiling without UV is preferred.

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Call protein-RNA binding sites from CLIP-seq BAM with CLIPper, PureCLIP, Skipper, Piranha, omniCLIP, CTK, CLAM, or Paraclu. Use when choosing between coverage-based, HMM-based, beta-binomial window-based, and crosslink-site-based peak callers; applying ENCODE eCLIP thresholds (log2 IP/SMInput >= 3, -log10 p >= 3); deciding when SMInput is mandatory; or reconciling peak-set discordance between callers for the same RBP.

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Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER, MEME-ChIP (STREME, CentriMo, TOMTOM, FIMO), monaLisa, and AME. Handles background selection (GC-matched, dinucleotide-shuffled, Markov order-2, peak-flanks), motif databases (JASPAR 2024 CORE PWMs, JASPAR 2026 deep-learning collection, HOCOMOCO v12, HOMER built-in), centrally-enriched motif testing, and differential motif analysis. Use when identifying TF binding motifs in peaks, testing for known TF enrichment, scanning for motif instances, comparing motif content between conditions, or interpreting motifs from deep learning models.

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Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021 Nat Genet 53:354; soft motif syntax from ChIP-nexus), chromBPNet (Pampari A et al 2024 bioRxiv; bias-factorized base-resolution profiles), EnFormer (Avsec 2021 Nat Methods 18:1196; 196 kb input, ~100 kb effective receptive field), DeepSEA (Zhou 2015; multi-task CNN), and JASPAR 2026 deep-learning collection (1259 BPNet ChIP models). Performs in silico mutagenesis for variant-effect prediction, DeepLIFT/Grad attribution, and TF-MoDISco motif discovery from attribution scores. Use when predicting variant effects on TF binding, discovering soft motif syntax / cooperativity, integrating ChIP-seq with sequence-only predictions, or applying precomputed JASPAR Deep Learning models to new variants.

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Detect transcription factor binding footprints in ATAC-seq using TOBIAS, HINT-ATAC, Wellington, or scprinter. Use when identifying bound TF sites within accessible regions, correcting Tn5 insertion bias before footprinting, choosing between cleavage-based and aggregate-based footprinters, or comparing differential TF activity between conditions.

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How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv, Foundry API, protein binding assays, protein screening experiments, BLI/SPR assays, thermostability assays, or wants to submit protein sequences for experimental characterization. Also trigger when code imports `adaptyv`, `adaptyv_sdk`, or `FoundryClient`, or references `foundry-api-public.adaptyvbio.com`.

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Plan, execute, and document validation, verification, and transfer of analytical procedures under the governing framework - ICH Q2(R2) and Q14, USP <1220>/<1225>/<1226>, ICH M10 bioanalytical, CLSI EP, or ISO/IEC 17025. Use for HPLC, LC-MS/MS, GC, CE, ICP-MS, dissolution, qNMR, qPCR, NIR, and ligand binding or cell-based assays whenever the question is whether a procedure is fit for its intended purpose. Triggers include "method validation", "analytical method validation", "AMV", "validation protocol", "acceptance criteria", "linearity", "reportable range", "accuracy and precision", "repeatability", "intermediate precision", "recovery", "LOD", "LOQ", "detection limit", "quantitation limit", "specificity", "robustness", "method transfer", "method comparison", "Deming", "Passing-Bablok", "Bland-Altman", "equivalence testing", "OOS investigation", "ICH Q2", "Q2(R2)", "Q14", "USP 1225", "ICH M10", "incurred sample reanalysis", "ISR", "CLSI EP", and any request to show that an assay works.

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Contract document for the binding test verdict file at .claude/state/last_test_result. Format spec for callers (integrate, simplify, chore, the verify-tick worker) that inline the four mechanical operations. Not Skill-tool-invocable.

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Workflow Phase 9 — Integration and Verification. Runs the full test suite, stamps the binding verdict at .claude/state/last_test_result, optionally runs a cross-engine smoke check, and writes harness_state so the harness auto-continues or yields. No subagent delegation.

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Use when building APIs on Hono (Cloudflare Workers, Bun, Deno, Node), debugging route ordering, wiring middleware, validating with @hono/zod-validator, returning streaming responses, configuring CORS with credentials, handling errors via app.onError, or composing typed RPC clients. Triggers: c.env binding types, c.header + c.redirect interaction, missing await next() bugs, Set-Cookie not attaching to redirect, route-precedence surprises, JWT middleware setup, hono/client typed RPC end-to-end. NOT for Express/Fastify/Koa idioms, tRPC/GraphQL paradigms, or Next.js Route Handlers.

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Use when wrangler deploys silently fail or produce wrong artifacts, secrets upload as empty strings, custom domain DNS is not resolving, route assignment broke after rename, observability/tail logs are needed, D1/KV/R2 bindings are missing, OAuth scope errors block a command, cookies on a redirect are not attaching, or the worker exceeds CPU time. Triggers: "Tenant or user not found", "Authentication error" on wrangler d1 push, secret length is 0 after upload, route returns origin not worker, "compatibility_date too old", 1101 errors, custom_domain assignment lost on script rename. NOT for AWS Lambda / Vercel Edge / Deno Deploy (different runtimes), Cloudflare Zero Trust, or R2-specific tuning.

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Accounts for estrogen-induced elevation of total serum cortisol via increased corticosteroid-binding globulin (CBG) when evaluating adrenal reserve or hydrocortisone replacement adequacy. Triggered when assessing glucocorticoid adequacy in patients receiving estrogen therapy (e.g., oral estrogen replacement) or interpreting cortisol levels in estrogen-exposed individuals.

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Run local AI services on Windows — port binding, firewall, WSL2 networking, and common pitfalls.

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Expert-level medicinal chemistry knowledge. Use when working with drug design, structure-activity relationships, ADMET properties, pharmacophores, lead optimization, target identification, drug metabolism, or pharmaceutical development. Also use when the user mentions 'SAR', 'drug design', 'pharmacophore', 'ADMET', 'lead compound', 'hit to lead', 'drug metabolism', 'bioavailability', 'selectivity', 'binding affinity', 'scaffold hopping', or 'bioisostere'.

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Claude Code workflow tips from Boris Cherny (creator of Claude Code) and the Claude Code team. Use when: setting up Claude Code, optimizing workflows, running parallel sessions, configuring CLAUDE.md, using skills/commands, subagents, hooks, MCP integrations, or learning best practices. Covers: git worktrees, plan mode, verification, permissions, Slack MCP, BigQuery, prompting tips, plugins, custom agents, sandboxing, keybindings, status lines, output styles, customization, /simplify for code quality, /batch for parallel code migrations, /loop for scheduled tasks, code review agents, /btw for mid-task questions, /effort max reasoning, remote control sessions, voice mode, setup scripts, session naming, /color, PostCompact hook, auto mode, /schedule cloud jobs, iMessage plugin, auto-memory, and auto-dream, mobile app, session teleporting, Cowork Dispatch, Chrome extension, Desktop app, /branch forking, --bare SDK startup, --add-dir multi-repo, --agent custom agents, /voice input.

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Codex workflow tips from Boris Cherny (creator of Codex) and the Codex team. Use when: setting up Codex, optimizing workflows, running parallel sessions, configuring AGENTS.md, using skills/commands, subagents, hooks, MCP integrations, or learning best practices. Covers: git worktrees, plan mode, verification, permissions, Slack MCP, BigQuery, prompting tips, plugins, custom agents, sandboxing, keybindings, status lines, output styles, customization, /simplify for code quality, /batch for parallel code migrations, /loop for scheduled tasks, code review agents, /btw for mid-task questions, /effort max reasoning, remote control sessions, voice mode, setup scripts, session naming, /color, PostCompact hook, auto mode, /schedule cloud jobs, iMessage plugin, auto-memory, and auto-dream, mobile app, session teleporting, Cowork Dispatch, Chrome extension, Desktop app, /branch forking, --bare SDK startup, --add-dir multi-repo, --agent custom agents, /voice input.

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Bootstrap or harden a project's operating model for mixed human and AI delivery teams. Use when starting a repository, adopting an agent harness, defining authority and risk tiers, coordinating parallel agents safely, binding evidence and review to an exact candidate, or correcting fragmented rules that prevent coherent, consistent, complete delivery.

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Diagnose and fix CJK (Korean, Japanese, Chinese) text-wrapping issues in web UIs. Systematically traces mid-syllable breaks, orphaned glyphs, and awkward line splits through a layered fix strategy covering global CSS cascade, component-library overrides, headline balancing, and translation-level phrase binding. Produces an evidence-based diagnosis and verification report before any code change is applied.

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This skill should be used when designing terminal user interfaces, creating TUI layouts, choosing TUI color schemes, implementing keyboard navigation, building terminal dashboards, or working with any TUI framework. Activates on mentions of TUI design, terminal UI, Ratatui layout, Ink components, Textual widgets, Bubbletea views, terminal color palette, keybinding design, panel layout, split panes, terminal dashboard, box-drawing characters, sparklines, progress bars, modal dialogs, focus management, or terminal accessibility.

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Use this skill whenever the user wants to create, edit, explain, validate, or troubleshoot a proctmux.yaml/procmux.yaml file, add or change proctmux processes, configure lifecycle behavior such as stop signals/on_kill/autostart, customize unified-mode layout/keybindings/style, or enable Makefile/package.json process discovery. Use it even when the user says this casually, such as "add my dev server to proctmux", "fix this proctmux config", "write a config for these services", or "what YAML option controls focus".

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Auditing Kubernetes cluster RBAC configurations to identify overly permissive roles, wildcard permissions, dangerous ClusterRoleBindings, service account abuse, and privilege escalation paths using kubectl, rbac-tool, KubiScan, and Kubeaudit.

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