「agm」の検索結果

Select colormaps and qualitative palettes for scientific figures using perceptual-uniformity, color-vision-deficiency safety, and luminance-monotonicity criteria. Covers Crameri scientific colormaps, viridis/cividis/magma, Okabe-Ito categorical, ColorBrewer, and the rainbow/jet critique. Use when choosing palettes for heatmaps, scatter, networks, or any encoding where color carries quantitative or categorical meaning.

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Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contracted families. Use when correlating gene-family changes with phenotype evolution, ranking lineages by adaptive gene-family-rate shifts, post-WGD dosage-balance analysis, or building Birth-death models from OrthoFinder presence/absence matrices.

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Normalize read-depth copy-ratio profiles and segment them into copy-number regions using circular binary segmentation (CBS, DNAcopy), hidden Markov models, HaarSeg, and fused-lasso methods. Covers GC-content, mappability, and replication-timing (wave-artifact) bias correction, panel-of-normals/PCA denoising, diploid-baseline centering, and algorithm selection by sequencing depth and event size. Use when choosing a segmentation algorithm, correcting depth bias, diagnosing oversegmentation or a mis-centered baseline, tuning CBS or HMM parameters, or understanding why a downstream CNV caller produced fragmented or shifted segments.

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Comprehensive quality control for CLIP-seq libraries (eCLIP, iCLIP, iCLIP2, PAR-CLIP) covering library complexity (preseq), FRiP, IDR replicate reproducibility, read-distribution metagene, SMInput vs IgG control rationale, rRNA / snoRNA contamination, fragment-length distribution, and ENCODE-compliance thresholds. Use when assessing whether a CLIP library passed, deciding lenient vs stringent peak thresholds, comparing replicates with IDR rescue and self-consistency ratios, or distinguishing failed IP from over-amplified library.

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Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and reaction templates, with explicit handling of atom mapping, RDChiral template extraction, product validation, RECAP/BRICS fragmentation, R-group decomposition, matched molecular pair analysis (MMPA), and Free-Wilson analysis. Use when generating combinatorial libraries from building blocks, enumerating analog series, deriving structure-activity rules, or extracting transformations from reaction data.

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Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input control matching, fragment-size modeling vs --nomodel, effective genome size, ENCODE-style IDR vs naive overlap, hyper-ChIPable artifacts, and aligner-specific shifts. Use when calling peaks from ChIP-seq alignments, choosing between narrow vs broad mode for a histone mark, deciding model vs nomodel for low-depth data, applying ENCODE pseudoreplicate IDR, or reconciling MACS vs HOMER vs SPP results.

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Assesses ChIP-seq quality across antibody specificity, fragmentation, enrichment, replicate concordance, and library complexity. Computes FRiP, NSC/RSC (phantompeakqualtools), library complexity (NRF/PBC1/PBC2), deepTools plotFingerprint (JS distance, AUC, synthetic JS), ChIPQC, IDR with ENCODE Nself/Nt rules, and detects hyper-ChIPable artifacts. Use when validating an antibody, diagnosing failed peak calls, deciding whether to proceed with downstream analysis, grading against ENCODE thresholds, or auditing replicate concordance.

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Analyzes CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data. Handles SEACR vs MACS2 peak calling (with the btaf375 2025 benchmark guidance), pA-MNase vs pA-Tn5 vs pAG-Tn5 chimera differences, E. coli spike-in carryover normalization, IgG-only control logic (no input), characteristic fragment-size signatures (25-75 bp for CUT&Tag), and lower depth requirements (5M reads typical vs 25M for ChIP). Use when calling peaks from CUT&RUN/CUT&Tag, scaling by E. coli spike-in carryover, choosing SEACR norm mode, or comparing CUT&RUN/Tag results to traditional ChIP.

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Designs novel molecules using REINVENT 4 (de novo, scaffold decoration, linker design, R-group, molecular optimization), MolMIM, Diffusion-based generators (DiGress, DiffSMol), and JT-VAE with explicit handling of multi-parameter optimization (MPO), goal-directed scoring functions, transfer/reinforcement/curriculum learning, synthetic accessibility scoring, and chemical space exploration vs exploitation. Use when designing new chemical matter against a target, decorating a scaffold, linking fragments, or optimizing a hit for multiple ADMET / activity properties simultaneously.

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Reads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, and BinaryCIF) using RDKit and Open Babel with rigorous handling of aromaticity perception, stereochemistry, implicit/explicit hydrogens, kekulization, and salt/fragment separation. Use when loading chemical libraries, debugging parse failures, or preparing molecules for downstream standardization, descriptor calculation, or docking.

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ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds. Use when assessing whether an ATAC-seq library passes ENCODE acceptance criteria, diagnosing transposition artefacts, comparing Omni-ATAC vs standard prep quality, or selecting which replicates to drop before peak calling.

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Maps GWAS-implicated loci to candidate effector (causal) genes by integrating variant-to-gene (V2G) features via Open Targets L2G (Mountjoy 2021), MAGMA gene-based association (de Leeuw 2015), FUMA SNP2GENE, cS2G combined SNP-to-gene scores (Gazal 2022), Polygenic Priority Scores (PoPS, Weeks 2023), FLAMES, INQUISIT, DEPICT, and enhancer-gene predictors (ABC, ENCODE-rE2G). Use when narrowing a GWAS lead locus to a candidate causal gene, picking between proximity, eQTL-based, and similarity-based prioritizers, integrating multi-evidence streams (fine-mapping, colocalization, ABC enhancer-gene, distance, chromatin), reconciling discordant L2G vs PoPS calls, prioritizing tissue-specific eQTL evidence, or triangulating across at least three independent lines of evidence for a publication-grade effector-gene nomination.

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Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC, ATACseqQC, DANPOS3, or scprinter. Use when characterizing nucleosome organization at promoters and enhancers, calling +1/-1 nucleosomes flanking NFRs, generating V-plots for chromatin structure visualization, or comparing nucleosome positioning between conditions.

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Walk through a live web app AS a real user to find usability + behavioural bugs that static reviews miss. REQUIRES proof of interaction (typing, clicking, sending, observing) before any verdict — a sweep that didn't interact terminates with verdict 'Incomplete'. Walks threads, exercises every element, runs the multi-pane stress matrix, visual polish sweep, component perfection checklist, automated a11y (axe-core), pragmatic performance budget (LCP/CLS/INP), scenario battery (11 scenarios), and stress recipes including the real-flavour data battery. Hard gates: console errors/warnings = 0, network 5xx = 0, layout collapse = 0, axe Critical/Serious = 0, perf budget green. Audit-the-audit meta-check rejects rushed reports. Each finding has reproduction steps, evidence path, and suspected code location. Trigger with 'ux audit', 'walkthrough', 'qa sweep', 'audit the app', 'dogfood this', 'check all pages', 'find what's broken', 'stress the UI'.

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Analyse the vault's link graph and report on its shape: orphan rate, average degree, components, hubs, bridges and clusters, with what each number means for retrieval. Use this skill when the user asks about the health or structure of their graph, wants metrics, asks which pages are most connected or most isolated, or asks whether the vault is fragmented. Do NOT use for fixing what it finds, which is second-brain-lint, or for answering a content question.

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Fully automated review pipeline: CEO, Design, and Eng reviews with auto-decisions using 6 principles (completeness, boil lakes, pragmatic, DRY, explicit over clever, bias toward action). Only pauses for premise confirmation. Classifies decisions as Mechanical (silent) or Taste (surfaced at final gate).

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Manage capa CLI configuration — `capabilities.yaml` / `capabilities.json`, skills, MCP servers, tools, hooks, sub-agents, rules, plugins, AGENTS.md / CLAUDE.md, security options, tool exposure modes, `capa wrap` shadow workspaces, `--passthrough` native writes, registries (including Claude marketplaces), activity traces, and the local Web UI. Use whenever the user edits the capabilities file, runs any `capa` command (init, install, add, wrap, clean, sh, start/stop/restart/status, auth, upgrade, cache, registry), wires up an MCP server, adds a skill from GitHub / GitLab / a registry / a remote URL / a local path, configures secrets via `${VarName}` placeholders, installs lifecycle hooks, defines sub-agents, or troubleshoots a failed install. Use even when the user only names a fragment ("add a skill", "wire up brave search", "wrap cursor", "block this phrase in skills") without saying "capa" — if a `capabilities.yaml` or `capabilities.json` lives at the project root, this is almost certainly the right skill. If the project does NOT yet have a capabilities file, point at the `bootstrap` skill instead.

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Review local code changes for bugs, regressions, missing tests, and pragmatic improvements. Use when the user asks to review the current changes from `git status`, or to review a specific backlog task by id such as `task-65` or `TASK-65`. Also trigger when the user says things like "review", "review current changes", "check my changes", "look over the diff", or "review task-42".

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Transform ordinary snapshots—including daily moments, portraits, objects, pets, food, interiors, streets, architecture, landscapes, travel, and humanistic scenes—into the restrained Shijing Paper Zine visual style. Use when the user wants any real photo turned into a spacious paper-editorial composition with an irregular photographic fragment, simplified source-derived drawing, one structural print color, tactile torn-paper texture, minimal micro-copy, a consistent multi-image series, or a source-to-poster comparison.

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Use when the user asks for a slideshow, presentation, pitch deck, or interactive deck, or to convert an existing page into a deck. Authors a HyperFrames deck with fragments, branching and presenter mode; unclear -> /hyperframes.

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Take a markdown file of raw material and shape it into an article through a conversational session — drafting candidate openings, growing the piece paragraph by paragraph, arguing about format (lists, tables, callouts, quotes) at each step. Use when the user has a pile of notes, fragments, or a rough draft and wants help turning it into something publishable.

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Generate, derive, optimize, and diagnose structured AI image prompts for luminous cinematic Eastern xianxia environments under one inherited master canon with measurable divine scale, fixed five-layer space, 40–60% content-bearing breathing air, monumental Eastern architecture, railing-free edges, and coherent immortals and costume. Cover one-location scenic landmarks, immense inhabited celestial realms, cloud-borne palace cities, high-key Eastern sky-megastructure imagery, and the explicit `仙界大境原典` creative route. Use for Chinese fantasy scenery, places where immortals live, heavenly capitals, colossal celestial gates, architectural fragments above cloud seas, measurable divine scale, unusual framing, color and lighting direction, style-preserving variants, prompt rewrites, diagnosis, or direct image generation. Support 16:9, 21:9, 4:3, 3:2, 4:5, and 9:16; default to 16:9 for one prompt and never infer a nine-image series from a vertical ratio.

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Write safe, structured concurrent code with Kotlin Coroutines. Use for suspend functions, coroutine scopes, cancellation, and coroutine leaks; defer Java Virtual Threads, Android WorkManager/Fragment lifecycle, Compose state hoisting, and Detekt/tooling configuration.

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Implement screen routes and deep-link/App Link routing with Jetpack Compose Navigation on Android. Use when the primary task is Compose route configuration or external URL routing; defer typed-route APIs, XML/fragments, generic back-stack, and transition questions to their specific navigation skills.

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