「sequencing」の検索結果

Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR), CBE and ABE base editors (target conversion + bystander), and prime editor (pegRNA-templated) modes. Covers single-amplicon (CRISPResso), multi-sample batch (CRISPRessoBatch), pooled-amplicon (CRISPRessoPooled), WGS off-target (CRISPRessoWGS), and sample-comparison (CRISPRessoCompare) workflows; quantification-window math that controls what is called edited; substitution-vs-indel diagnostic to distinguish BE from Cas9 contamination; MMEJ deletion pattern interpretation; allele-frequency tables; and failure modes from amplicon misalignment or contamination. Use when quantifying editing from amplicon sequencing, choosing CRISPResso mode by design, distinguishing intended edits from bystanders and indel byproducts, debugging low-alignment runs, or generating publication-grade editing reports.

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。

Process Hi-C read pairs using pairtools. Parse alignments, filter duplicates, classify pairs, and generate contact statistics from Hi-C sequencing data. Use when processing raw Hi-C read pairs.

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。

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.

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。

Detect somatic and germline copy number variants from targeted, exome, and whole-genome sequencing with CNVkit, a read-depth caller that combines on-target and off-target (antitarget) coverage. Covers panel-of-normals construction, flat-reference tumor-only calling, hybrid/amplicon/WGS modes, CBS vs HMM segmentation selection, purity-aware integer calling, and reconciliation against GATK and allele-specific callers. Use when calling CNVs from hybrid-capture panels or exomes, deciding whether CNVkit (depth-only) is the right tool versus an allele-specific caller, building a panel of normals, diagnosing flat-reference false positives, or interpreting log2 ratios into copy-number states.

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 learning-based variant calling from long reads using Clair3 for SNPs and small indels. Use when calling germline variants from ONT or PacBio alignments, particularly when high accuracy is needed for clinical or research applications.

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。

Designs experiments to minimize and account for batch effects using balanced layouts and blocking strategies. Use when planning multi-batch experiments, assigning samples to sequencing lanes, or designing studies where technical variation could confound biological signals.

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。

Batch effect correction for CRISPR screens covering ComBat empirical-Bayes, RUV, SVA, control-sgRNA normalization, and the model-based alternative of including batch as a covariate in MAGeCK MLE or Chronos. Covers screen-specific batch sources (passage cohort, library lot, infection day, sequencing run, Cas9 lot, FBS lot), PCA + variance-decomposition diagnostic to decide if correction is needed, when correction harms biology by over-correcting condition into batch, limma removeBatchEffect for visualization-only correction, and relationship to multi-condition design matrices. Use when combining screens for joint analysis, when passage cohort confounds biology, when DepMap-style panels need Chronos with batch covariates, when picking ComBat vs RUV, or when correction harms biology and should be replaced with explicit covariate modeling.

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。

Amplicon sequence variant (ASV) inference from 16S rRNA or ITS amplicon sequencing using DADA2. Covers quality filtering, error learning, denoising, and chimera removal. Use when processing demultiplexed amplicon FASTQ files to generate an ASV table for downstream analysis.

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。

Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Supports single-end and paired-end reads, Illumina TruSeq, Nextera, and custom adapter sequences. Use when FastQC shows adapter contamination or before alignment of short reads.

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。

Workflow for sequencing read QC, trimming, contamination screening, and pre-alignment cleanup.

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。

Workflow for small-variant and structural-variant discovery, filtering, annotation, and interpretation from sequencing data.

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。

Workflow for copy-number estimation, segmentation, annotation, and visualization in sequencing-based assays.

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。

Apply before writing logic: choosing core types and data structures, sequencing scaffold-vs-feature work, asking what concurrent actors share. Get the data structures right so downstream code becomes obvious.

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。

Apply when sequencing an addition, refactor, or rewrite. Remove dead weight, redundant validators, and stub references first, then build on the simpler base.

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。

A great product that nobody knows about is a failed product. Go-to-market strategy is how you get your product into customers' hands. Not marketing in the abstract - specific motions, channels, and sequences for your specific situation. This skill covers GTM motion selection (product-led, sales-led, community), channel strategy, launch sequencing, early customer acquisition, and the critical transitions between GTM phases. Use when "go to market, GTM, launch strategy, how to get customers, sales vs product-led, channel strategy, market entry, customer acquisition, distribution strategy, product launch, getting first customers, sales motion, bottoms up, top down sales, go-to-market, gtm, launch, product-led-growth, sales, channels, customer-acquisition, distribution, marketing" mentioned.

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。

Apply the strategic thinking of Thai Lee, CEO of SHI International. Use this skill when the user is navigating bootstrapping vs. venture capital, long-term career sequencing, building an egalitarian corporate culture, or scaling a customer-centric B2B sales organization. Trigger this skill for topics involving decade-by-decade life planning, empowering employees with extreme ownership, or turning personal disadvantages into fuel for preparation. Apply her frameworks whenever these themes arise, even if the user doesn't explicitly name her.

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。

Applies the operational and scientific frameworks of Stacey Gabriel (genomicist and sequencing platform leader at the Broad Institute). Use this skill whenever the user is designing large-scale biomedical research, operationalizing lab workflows, standardizing data governance, or transitioning from bespoke academic experiments to industrial-scale science. It is highly relevant for queries involving genomics, precision medicine, multiomics, cellular perturbation pipelines, or building massive datasets to fuel AI. Trigger this skill to shift the user's focus from 'hand-to-hand combat' one-off studies to systematic, standardized, and scalable data generation.

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。

Suede-affiliated onboarding and activation strategy for first-run sequencing, empty states, setup checklists, activation milestones, time to value, and retention-linked measurement. Use when users sign up but fail to reach first value or the product needs a new first-session flow. NOT FOR: registration optimization (use suede-signup), lifecycle email sequences (use suede-emails), or monetization prompts (use suede-paywalls).

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。

Suede-affiliated directory distribution strategy for selecting listings, sequencing submissions, tailoring positioning, and verifying backlinks. Use when a product needs startup, SaaS, AI, MCP, marketplace, or review-directory submissions and a measurable tracker. NOT FOR: broader launch orchestration (use suede-launch-packaging), scalable destination-page production (use suede-programmatic-seo), or citation and search auditing (use suede-seo-audit).

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。

Build and debug SceneKit scenes where one 3D object (a product, badge, coin, wheel) performs on a transparent stage inside a SwiftUI app - studio lighting, real shadows, baked keyframe choreography, hand-rolled physics, gestures and haptics, multi-scene sequencing. Use when working with SCNView or SceneView in SwiftUI, UIViewRepresentable 3D scenes, product or hero-object animation, roll or spin entrances, a first-frame hitch when a scene appears, shadows missing or wrong, metal rendering black, choreographed 3D motion that must stay interruptible, a continuous vapor stream (vent air, steam, mist) drawn as a shader-driven sheet, a liquid-metal or jelly blob (noise-deformed surface with mirror reflections and tap ripples), chrome or gold that looks cartoon-flat instead of real, HDRI image-based lighting, free trackball rotation of an actor, deterministic screenshot testing of shader-driven scenes, cutting an actor in two with a finger swipe (runtime mesh slicing with sealed cross-sections and a falling piece), a die-struck relief object (badge, coin, medallion) built from a heightfield with multiple finishes on one mesh, an actor crumbling into debris that falls and rests on the floor, reproducing a real object's motion from photos or video, or keyframed motion that stutters at its own keyframes. Not for RealityKit, ARKit, visionOS, or full game worlds.

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 the user wants intellectual understanding — learning how or why something works, not getting a task done or soliciting Claude's judgment. Trigger for: - Explicit learning requests: teach, explain, ELI5, walk me through, quiz me, flashcards, "I'm rusty on"; definitions ("what is X") - Terse concept names implying "help me understand this": "Galois theory," "transformers, from scratch" - Confusion signals: "won't stick," "keep mixing these up," "not getting it" - Learning-path questions: prerequisites, sequencing, what to study before X - Conceptual questions about mechanisms, causes, or dynamics Don't trigger for: - Tasks: coding, writing, calculation, translation, factual lookup, news updates - Personal troubleshooting; resource/textbook recommendations - Claude's evaluative verdict: opinion prompts ("do you think X", "settle this", "honest take", "is X dead / still taken seriously") and interpretive takes ("was X really as harsh as people say")

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。

Theory of Constraints primitives for focusing steps, drum-buffer-rope, throughput accounting, critical chain, and policy constraints. Use when sequencing by bottleneck.

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。

Design a scope and sequence showing vertical and horizontal curriculum coherence across a programme or year. Use when building new programmes, restructuring subjects, or ensuring progression.

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。