「pth」の検索結果

Assembles a genome de novo from Illumina short reads with SPAdes (isolate/careful/sc/meta/plasmid/rna modes), MEGAHIT (low-memory, huge datasets), Unicycler (bacterial finishing/hybrid), MaSuRCA (large hybrid), ABySS (Bloom-filter), and Platanus (heterozygous diploids), using multi-k de Bruijn graphs. Covers the repeat-resolution limit, why N50 plateaus at the genome not the depth, GenomeScope2 k-mer profiling first, the heterozygosity/haplotig trap, error-correction erasing rare alleles, GC dropout, and NG50/auN/BUSCO reporting. Use when assembling a bacterial isolate, fungal, small-eukaryotic, single-cell, or metagenome genome from Illumina reads, or when deciding whether short reads can even produce the assembly being asked for.

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。

Detects focal chromatin loops (point interactions / corner-dots) in balanced Hi-C and Micro-C contact maps and aggregates/validates a loop set. Covers de-novo calling with cooltools dots (HiCCUPS-style 4-background local enrichment with lambda-chunked FDR), chromosight (template-correlation), and Mustache (scale-space blob detection); aggregate peak analysis (APA) via cooltools pileup for confirmation; the depth/resolution prerequisite (de-novo needs ~5-10kb resolution = hundreds of millions to billions of valid pairs); consensus across callers and convergent-CTCF support as validation; and differential loops via union anchors plus chromosight quantify. Use when calling chromatin loops or dots from a cooler, deciding whether a map is deep enough to call de-novo vs running APA on known CTCF/cohesin anchors, building an aggregate peak pileup, comparing loops across conditions, or validating loop calls. For HiChIP/PLAC-seq/PCHi-C protein-anchored data use FitHiChIP/MAPS, not dots.

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。

Compares Hi-C contact maps between conditions across the right scale -- differential bin-pair contacts (multiHiCcompare, diffHic), differential A/B compartments (dcHiC), differential TAD boundaries (delta insulation), and differential loops (diffloop, DiffHiChIP) -- with distance-stratified between-sample normalization, replicate-aware NB-GLM FDR, HiCRep SCC reproducibility gating, and CNV correction for cancer/aneuploid samples. Use when comparing Hi-C between treatment and control, finding differential contacts/compartments/boundaries/loops, normalizing two maps of unequal depth, choosing a replicate-aware test, gating replicates with SCC, or correcting copy-number artifacts before a tumor-vs-normal comparison.

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。

Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS, Sequenza, and other callers. Covers genome-wide and per-chromosome log2 scatter plots, B-allele-frequency/minor-allele-fraction tracks, ideograms, cohort heatmaps, circos views, and caller-native plots. Use when creating publication CNV figures, choosing which plot answers a given question, diagnosing a wrong diploid baseline visually, displaying loss of heterozygosity, or deciding what depth-only plots cannot reveal.

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。

Resolve the architecture of focal oncogene amplifications — extrachromosomal DNA (ecDNA), breakage-fusion-bridge (BFB) cycles, homogeneously staining regions (HSR), and linear amplification — from whole-genome sequencing with AmpliconArchitect, the AmpliconSuite pipeline, and AmpliconClassifier. Covers copy-number seed selection, breakpoint-graph reconstruction, balanced-flow optimization, ecDNA classification, and the limits of depth-only amplification calls. Use when a focal amplification needs structural characterization, when distinguishing ecDNA from chromosomal amplification, suspecting ecDNA-driven oncogene amplification or therapy resistance, or selecting copy-number seeds for amplicon reconstruction.

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。

Infer integer allele-specific copy number, tumor purity, and ploidy from tumor sequencing by jointly modeling read depth (logR) and B-allele frequency (BAF) with ASCAT, Sequenza, FACETS, PURPLE, and PureCN (tumor-only). Covers the purity-ploidy identifiability problem, the diploid-baseline (dipLogR) anchor, major/minor copy number, loss of heterozygosity, sunrise/contour fit diagnostics, and reconciliation of conflicting fits. Use when tumor analysis needs absolute copy number rather than relative log2, when estimating purity and ploidy, calling LOH or copy-neutral LOH, resolving whole-genome doubling, running tumor-only allele-specific calling, or choosing among ASCAT, Sequenza, FACETS, and PureCN.

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。

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.

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。

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.

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。

Expert in building 3D experiences for the web - Three.js, React Three Fiber, Spline, WebGL, and interactive 3D scenes. Covers product configurators, 3D portfolios, immersive websites, and bringing depth to web experiences.

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。

Extract typical annual GPP, annual evapotranspiration, mid-season LAI, mid-season root biomass, mid-season shoot biomass, median canopy height, maximum primary-root depth, Vcmax at 25oC, and Jmax at 25oC from EcoSIM h0 NetCDF output files. Use when asked to derive these EcoSIM output targets from a selected .ecosim.h0.*.nc file for model-output processing, trait checks, or benchmark summaries.

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。

Estimate calcium-normalized Gapon selectivity coefficients from paired exchange and solution chemistry, or initialize depth-explicit EcoSIM Gapon inputs from the closest bundled ecosystem template when paired chemistry is unavailable. Use when deriving or checking EcoSIM GKC4, GKCH, GKCA, GKCM, GKCN, or GKCK values; matching a target ecosystem, climate, vegetation, and management regime to a starting profile; remapping template values to target soil layers; or documenting that template-based values require calibration or tuning.

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。

Extract dominant-component soil profile variables for EcoSIM grid or template inputs from gSSURGO, with FAO HWSD v2.0 fallback when gSSURGO data are unavailable or incomplete. Use when deriving soil depth, bulk density, field capacity, wilting point, hydraulic conductivity, texture, rock fraction, pH, CEC, or soil organic carbon; or when converting EcoSIM grid NetCDF files to editable Excel workbooks and back.

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。

Use this skill when you need to derive, from web-sourced evidence, typical values for a named plant's annual GPP, LAI, specific LAI or specific leaf area, Rubisco Vcmax at 25oC, Jmax at 25oC, root-to-shoot ratio, rooting depth, leaf protein nitrogen, and leaf chlorophyll nitrogen.

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。

Spatial depth design with isometric views, vanishing points, and layered elements that guide attention through 3D-like realism.

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。

Smooth color transitions and gradient-rich surfaces for modern, playful interfaces with visual depth.

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。

Frosted glass effect with translucent layers, subtle blur, and luminous borders for depth and modern elegance.

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。

Use when the user wants the project instructions file generated or updated from the detected stack and conventions — 'gerar o arquivo de instruções do projeto', 'criar convenções do projeto', 'setup governance', 'gerar AGENTS'. Writes the shared instructions file read by Claude Code, Codex, Hermes and OpenCode. Do NOT use to analyze the codebase in depth (feat-map) or to initialize the workspace (feat-init).

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Implement comprehensive security patterns to protect applications against OWASP Top 10 vulnerabilities including XSS, CSRF, SQL injection, authentication bypass, and data exposure. Use when handling user data, implementing authentication and authorization, validating input, encrypting sensitive data, preventing injection attacks, securing API endpoints, managing sessions and tokens, implementing rate limiting, configuring security headers, or building security-critical features that require defense-in-depth protection.

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。

Apple's approach to interface design and fluid, physical motion, translated for the web. Use when building or reviewing gesture-driven UI, spring animations, drag/swipe/sheet interactions, momentum and interruptible transitions, translucent materials and depth, typography (optical sizing, tracking, leading), reduced-motion, or the design foundations (feedback, spatial consistency, restraint) behind Apple-style interfaces.

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。

Deep reasoning mode for complex problems requiring maximum cognitive depth. Use when facing difficult architectural decisions, complex debugging, multi-step problem solving, or situations requiring careful analysis before implementation.

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。

Apple's approach to interface design and fluid, physical motion, translated for the web. Use when building or reviewing gesture-driven UI, spring animations, drag/swipe/sheet interactions, momentum and interruptible transitions, translucent materials and depth, typography (optical sizing, tracking, leading), reduced-motion, or the design foundations (feedback, spatial consistency, restraint) behind Apple-style interfaces.

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。

Conduct multi-round deep research on any GitHub Repo. Use when users request comprehensive analysis, timeline reconstruction, competitive analysis, or in-depth investigation of GitHub. Produces structured markdown reports with executive summaries, chronological timelines, metrics analysis, and Mermaid diagrams. Triggers on Github repository URL or open source projects.

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。

Detects focal chromatin loops (point interactions / corner-dots) in balanced Hi-C and Micro-C contact maps and aggregates/validates a loop set. Covers de-novo calling with cooltools dots (HiCCUPS-style 4-background local enrichment with lambda-chunked FDR), chromosight (template-correlation), and Mustache (scale-space blob detection); aggregate peak analysis (APA) via cooltools pileup for confirmation; the depth/resolution prerequisite (de-novo needs ~5-10kb resolution = hundreds of millions to billions of valid pairs); consensus across callers and convergent-CTCF support as validation; and differential loops via union anchors plus chromosight quantify. Use when calling chromatin loops or dots from a cooler, deciding whether a map is deep enough to call de-novo vs running APA on known CTCF/cohesin anchors, building an aggregate peak pileup, comparing loops across conditions, or validating loop calls. For HiChIP/PLAC-seq/PCHi-C protein-anchored data use FitHiChIP/MAPS, not dots.

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。

Assembles a genome de novo from Illumina short reads with SPAdes (isolate/careful/sc/meta/plasmid/rna modes), MEGAHIT (low-memory, huge datasets), Unicycler (bacterial finishing/hybrid), MaSuRCA (large hybrid), ABySS (Bloom-filter), and Platanus (heterozygous diploids), using multi-k de Bruijn graphs. Covers the repeat-resolution limit, why N50 plateaus at the genome not the depth, GenomeScope2 k-mer profiling first, the heterozygosity/haplotig trap, error-correction erasing rare alleles, GC dropout, and NG50/auN/BUSCO reporting. Use when assembling a bacterial isolate, fungal, small-eukaryotic, single-cell, or metagenome genome from Illumina reads, or when deciding whether short reads can even produce the assembly being asked for.

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。