「sequencing」の検索結果

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。

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。

Resolve subclonal copy number, whole-genome doubling, and copy-number tumor evolution from bulk sequencing with Battenberg, TITAN, and MEDICC2. Covers clonal versus subclonal copy-number states, haplotype phasing for subclonal resolution, cancer cell fraction, whole-genome-doubling detection and timing relative to mutations, mirrored subclonal allelic imbalance, and copy-number phylogenies. Use when a tumor is heterogeneous and bulk data shows non-integer copy number, when calling subclonal CNAs, detecting or timing whole-genome doubling, reconstructing copy-number evolution, or deciding between Battenberg and TITAN.

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。

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。

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。

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。

Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audit (library prep, read length, depth, replicates), STAR 2-pass cohort-style alignment, junction saturation curves and discovery plateau detection, novel-vs-known junction ratio diagnostics, junction-overhang distribution, splice-site strength scoring (MaxEntScan intrinsic + SpliceAI context-aware), strandedness verification, GENCODE basic vs comprehensive choice, and rRNA contamination screening. Splicing analysis is more demanding than DGE on read length, depth, library prep, alignment strategy, and annotation choice — failures silently bias PSI estimates and inflate novel-junction false positives. Use when evaluating data suitability for splicing analysis, troubleshooting low event detection, or designing sequencing experiments where AS is a primary endpoint.

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。

Comprehensive skill for GSAP (GreenSock Animation Platform) and ScrollTrigger plugin. Use this skill when creating web animations, scroll-driven experiences, timelines, tweens, scroll-triggered animations, pinning, scrubbing, parallax effects, or animating DOM elements, SVG, Canvas, WebGL, or Three.js. Triggers on tasks involving GSAP, ScrollTrigger, smooth animations, scroll effects, or animation sequencing.

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。

Designing meeting schedulers and booking experiences that qualify leads, set up calls well, and convert at higher rates than a generic Calendly link. Availability logic, qualification gating, prep automation, follow-up sequencing. Honest about any-time-friction (no qualification, just a booking link), interrogation-gate (so much qualification it scares users off), and qualified-fast-path (just enough qualification to set up the call well) patterns. Triggers on scheduler design, meeting booking, demo scheduling, sales call scheduling, calendar tool, booking page, qualification flow. Also triggers when sales team complains about cold demos, when booking conversion is poor, or when scheduler is being scoped for the first time.

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。

Query European Nucleotide Archive for 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。

Tools for deep-sequencing data analysis and visualization

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。

Translate product specs (PRDs, user stories) into a ship-ready repo plan: ticket decomposition, branch strategy, and PR sequencing. Use when breaking a PRD into tickets or designing the branch/PR sequence.

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。

Plan, sequence, and pressure-test internal announcements before they send. Use when announcing a reorg, policy, or product change, drafting an all-hands or exec update, or deciding who hears what and in which order.

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 retargeting strategy: audience windows, sequencing, frequency caps. "plan our remarketing campaigns"

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 elite legal writing techniques drawn from Justice Kagan, Boies & Olson, and other top advocates to any legal document — briefs, submissions, letters, opinions, memos, or persuasive correspondence. This skill covers both prose craft (clarity, examples, parallel construction, voice, quoting) and architectural strategy (argument sequencing, framing, openings, endings). Use this skill whenever the user asks you to draft, edit, or improve legal writing and wants it to be genuinely persuasive — not just correct. Also trigger when the user mentions 'make it more persuasive', 'sharpen this', 'strengthen the argument', 'rewrite this section', 'punch it up', 'legal writing', 'draft a brief', 'draft a submission', 'write like a top advocate', or asks you to improve the rhetoric, flow, or force of any legal document. This skill complements the larissa-legal-voice skill (which handles tone and personal voice) by adding the persuasive technique layer on top.

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 document set for a document-based lesson — selecting and sequencing sources for analytical tension around a central question. Use when assembling sources for a new lesson or when an existing set produces flat responses.

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。

Map the epistemic structure of a subject to determine knowledge types and inform curriculum sequencing. Use when designing courses, restructuring programmes, or analysing knowledge architecture.

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 a learning progression showing prerequisite-to-mastery steps for a target skill or understanding. Use when sequencing content, designing diagnostics, or mapping prerequisite gaps.

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。

The analysis and visualization of alternative splicing (AS) events from RNA sequencing data remains challenging. SpliceWiz is a user-friendly and performance-optimized R package for AS analysis, by processing alignment BAM files to quantify read counts across splice junctions, IRFinder-based intron retention quantitation, and supports novel splicing event identification. We introduce a novel visualization for AS using normalized coverage, thereby allowing visualization of differential AS across

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。

Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer the cell of origin of each single cell independently.

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。

The scDblFinder package gathers various methods for the detection and handling of doublets/multiplets in single-cell sequencing data (i.e. multiple cells captured within the same droplet or reaction volume). It includes methods formerly fou

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。

Uses DESeq2 to estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.

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。