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Turns Hi-C/Micro-C FASTQ into a deduplicated, filtered .pairs file with pairtools and decides whether the library worked. Covers the bwa mem -SP5M / bwa-mem2 / chromap --preset hic alignment idiom (mates mapped as independent single-end reads), pairtools parse vs parse2 and the walks-policy choice (5unique pairwise vs all for Pore-C/Micro-C concatemers), pair-type classification (keep UU and rescued UC), dedup (PCR vs optical/by-tile), select by pair_type/MAPQ/distance, restriction-fragment handling (restrict, Arima dual-enzyme, Micro-C/DNase fragment-free), and allele-specific phasing (pairtools phase to two coolers). The library-QC decision uses % long-range cis as the one-number quality metric, trans as the noise floor, orientation balance as fragment-map-free dangling-end/self-circle QC, and % duplicates as a complexity proxy. Use when processing Hi-C/Micro-C/Omni-C reads into pairs, judging library quality, handling multi-enzyme or restriction-agnostic protocols, or generating allele-specific contacts.

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 genomes de novo from noisy long reads (Oxford Nanopore R9/R10/Dorado, PacBio CLR) with Flye (repeat graph), Canu (correct-trim-assemble OLC), NextDenovo, Shasta, Raven, wtdbg2, or miniasm, and reconciles bacterial assemblies into a consensus with Trycycler/Autocycler. Covers matching the input flag to the basecaller era (--nano-hq vs --nano-raw), why a raw long-read assembly is contiguous but low-QV and not finished until polished, haplotig false-duplication and purge_dups, coverage and read-N50 as non-substitutable inputs, and mid-read adapter de-chimerization. Use when assembling a bacterial or eukaryotic genome from ONT or PacBio noisy reads, choosing a long-read assembler, or diagnosing an over-collapsed or duplicated assembly. For PacBio HiFi use hifi-assembly instead.

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。

Phases small variants, SVs, and methylation from Oxford Nanopore and PacBio long reads (read-backed/physical phasing) with WhatsHap, LongPhase, or HiPhase, and haplotags the BAM (HP/PS tags) for allele-resolved downstream analysis. Covers why phase blocks break at het-sparse gaps (read length x heterozygosity), why phasing the VCF is useless until the BAM is haplotagged, the GT-pipe/PS and read HP/PS tag spec, reporting block N50 with switch error, the diploid-assumption/CNV/haploid-region traps, trio phasing as the gold standard, and the boundary to statistical panel phasing. Use when phasing long-read variants, haplotagging reads for allele-specific methylation/expression or phased SVs, choosing WhatsHap vs LongPhase vs HiPhase, trio phasing, or assessing phasing quality.

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 TAD boundaries from balanced Hi-C contact matrices via the diamond-window insulation score (cooltools insulation) and HiCExplorer hicFindTADs, returning a continuous log2 insulation track, valley-prominence boundary_strength, and Li/Otsu-thresholded is_boundary flags across a list of window sizes. Covers the multi-scale window sweep (sub-TAD to compartment-domain), why the boundary is reproducible but the domain partition is not, cross-condition comparison via differential SCORE not differential partition, and the insulation-vs-compartment orthogonality. Use when calling TADs or domain boundaries, computing insulation scores, choosing a window size, ranking boundary strength, comparing boundaries across conditions, or annotating CTCF-backed boundaries; route domain rendering to hic-visualization and boundary-feature overlap to genome-intervals.

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Imports gene expression count matrices from featureCounts, HTSeq, STAR ReadsPerGene, Salmon/kallisto via tximport or tximeta, RSEM, 10X Genomics MTX/H5, AnnData H5AD, and RDS. Handles silent-miscounting traps (featureCounts -p v2.0.2 API break, STAR strandedness column choice, salmon NumReads-sum without tximport, RSEM non-integer expected_count, GENCODE _PAR_Y suffix, zero-length-transcript TPM divide-by-zero), and encodes the tximport countsFromAbundance decision tree with the "lengthScaledTPM is not TPM" warning. Use when assembling a gene-by-sample count matrix from aligner or quantifier output, importing salmon/kallisto for DESeq2 vs limma-voom, choosing strandedness column for STAR, debugging zero-count panics, or building tx2gene mapping.

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。

Profiles a genome from raw reads BEFORE assembly with a k-mer spectrum (KMC or Jellyfish histogram), then models it with GenomeScope2 to estimate genome size, heterozygosity, repeat content, and ploidy, and Smudgeplot to infer ploidy from heterozygous k-mer pairs (diploid AB vs triploid AAB vs tetraploid AABB). Covers choosing k via Merqury best_k.sh, the k-mer-coverage vs sequencing-coverage confusion, reading het/repeat/contamination/organelle peaks, why noisy ONT must not be used for counting, and how the estimate becomes the NG50 denominator, the Flye -g value, the hifiasm --hom-cov/purge setting, and the 1.5-2x-too-big haplotig sanity check. Use when starting any de novo assembly, deciding whether short reads can work, estimating genome size for an unknown organism, diagnosing ploidy, or sanity-checking an assembly's size against expectation.

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。

Download large datasets from NCBI efficiently using EPost, history server, batching, rate limiting, and retry logic. Use when bulk-fetching tens of thousands of sequences, pulling all results of a large ESearch, designing reproducible pipelines, comparing E-utilities to NCBI Datasets v2 CLI, or implementing checksum-validated downloads. Encodes WebEnv TTL (~8h), EPost 200-ID limit, retmax caps, parallelization design, and integrity verification.

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Reads, validates, and prepares CDISC SDTM and ADaM clinical trial data for analysis. Covers SDTM domain joins (DM, AE, EX, VS, LB, DS), ADaM architecture (ADSL, BDS, OCCDS, ADTTE) with traceability, treatment-emergent AE conventions, baseline derivation, SUPPQUAL/NSV handling, Define-XML 2.1, and Pinnacle 21 / CORE validation. Use when working with clinical trial datasets in CDISC SDTM/ADaM format, preparing analysis-ready data, or validating for regulatory submission.

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 tasks involve creating, editing, analyzing, or formatting spreadsheets (`.xlsx`, `.csv`, `.tsv`) with formula-aware workflows, cached recalculation, and visual review.

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Use this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx files) or Word templates (.dotx files). Triggers include: any mention of 'Word doc', 'word document', '.docx', '.dotx', or requests to produce professional documents with formatting like tables of contents, headings, page numbers, or letterheads. Also use when extracting or reorganizing content from .docx or .dotx files, inserting or replacing images in documents, performing find-and-replace in Word files, working with tracked changes or comments, or converting content into a polished Word document. If the user asks for a 'report', 'memo', 'letter', 'template', or similar deliverable as a Word or .docx file, use this skill. Do NOT use for PDFs, spreadsheets, Google Docs, or general coding tasks unrelated to document 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。

Via modeling: pads, antipads, ground return vias, GRV placement, and signal integrity for high-speed layer transitions. TRIGGER: user asks to model a via, design a via transition, place ground return vias, analyze via performance, or check signal integrity through layer transitions. Invoke BEFORE writing code — only viaSingleEnded exists (no viaDifferential), and the location format is non-obvious. SKIP: general signal integrity without vias (use matlab-analyze-em), transmission line design (use matlab-design-pcb-transmission-line), PDN analysis (use matlab-analyze-pcb-pdn), material/stackup setup only (use matlab-manage-pcb-material).

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。

Exchange data between Excel and MATLAB using Spreadsheet Link VBA macros and worksheet functions. Use when writing Excel VBA macros that call MLPutMatrix, MLGetMatrix, MLPutVar, MLGetVar, MLPutRanges, MLEvalString, MLGetFigure, or MatlabRequest.

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。

Offsite Ads analysis — when to opt out, ROI tracking, fee impact on margins, attribution

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Etsy Ads strategy — budget allocation, bid management, promoted listings, offsite ads opt-out analysis

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Use when managing Apple Ads with asc, including OAuth profiles, ad-account discovery, Platform API v1 campaigns and targeting, reports, assets, recommendations, guarded mutations, raw requests, and Campaign Management API v5 migration.

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Use when a YouTube channel is the focus: pasted @handles or channel URLs, requests to browse a creator's uploads, see what a channel has posted recently, search within a channel, or resolve a handle to a channel ID. Also use when the user names a creator and wants to explore their content or monitor their uploads. Not for creating channels or account management.

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 YouTube is relevant: pasted video links or IDs, @handles, quick video lookups, summaries, channel latest uploads, topic search, or any request involving YouTube content — even if YouTube is not mentioned explicitly. Covers transcripts, search, and channel latest. Not for uploads or account management.

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。

When the user wants to create Reddit post copy, comments, or optimize for Reddit. Also use when the user mentions "Reddit post," "subreddit," "r/," "Reddit marketing," "post to Reddit," "Reddit thread," "Reddit comment," "Reddit copy," "Reddit content," or "Reddit engagement." For Reddit ads, use reddit-ads.

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。

When the user wants to optimize YouTube videos for search, create video descriptions, or improve channel visibility. Also use when the user mentions "YouTube SEO," "YouTube description," "YouTube tags," "YouTube thumbnail," "YouTube title," "YouTube channel," or "video SEO." For YouTube ads, use youtube-ads.

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。

When the user wants to submit a product or app to directories, curated lists, launch platforms, or app stores—and needs ready-to-paste copy per platform. Reads root contextus.md when present. Also use when the user mentions "directory submission," "get listed," "app store listing," "submit to directories," "curated list," "best tools list," "Taaft," "Product Hunt," "directory ads," "newsletter feature," "directory campaign," "tailor description per platform," "Shopify App Store," "Chrome Web Store," "navigation site," or "product directory." For Product Hunt launch day tactics (hunter, first comment, timing), use product-hunt-launch. For full 0→1 channel planning, use cold-start-strategy.

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。

When the user wants to create LinkedIn post copy or optimize for LinkedIn. Also use when the user mentions "LinkedIn post," "LinkedIn article," "professional post," "post to LinkedIn," "LinkedIn content," "LinkedIn copy," "B2B LinkedIn," "LinkedIn engagement," "LinkedIn feed," "share box," "document post," "poll," "Newsletter," "reshare," or "LinkedIn marketing." For LinkedIn ads, use linkedin-ads.

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。

When the user wants to create TikTok video captions, scripts, or optimize for TikTok. Also use when the user mentions "TikTok post," "TikTok caption," "TikTok video," "post to TikTok," "TikTok script," "TikTok content," "TikTok copy," "TikTok hashtags," or "TikTok marketing." For TikTok ads, use tiktok-ads.

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。

Migrates a traditional Power Pages site from Bootstrap 3 to Bootstrap 5. Downloads the site, runs the pac pages bootstrap-migrate engine, reviews the change report, applies AI-assisted fixes for the residual hierarchy/CSS changes the engine only flags, uploads the migrated site (which auto-enables the Bootstrap 5 runtime flag), verifies the flag, and validates. Use when the user wants to upgrade an older Bootstrap-3 portal to Bootstrap 5. NOT for code sites (React/Vue/Angular/Astro) — those are never Bootstrap-3.

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 building a Unity 6.3 level or open world: terrain from code or heightmaps, procedural islands, erosion, splat and foliage rules, trees and grass, ProBuilder graybox, level gym, modular kit and prefab placement, set dressing, landmarks and player guidance, the island's edge, spline roads, WFC, fog, additive scene streaming, or a world that hitches, pops in, leaks memory or runs slow on mobile. Keywords: Terrain, TerrainData, ProBuilder, blockout, graybox, modular kit, NavMesh, LoadSceneAsync, open world.

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。