「downstream」の検索結果

End-to-end CLIP-seq pipeline from FASTQ to ENCODE-compliant binding sites, single-nucleotide crosslink maps, annotation, motifs, and (optionally) differential binding. Use when running the full Yeo lab eCLIP / iCLIP / iCLIP2 / iCLIP3 / irCLIP / PAR-CLIP analysis with SMInput control, protocol-specific UMI extraction, ENCODE STAR parameters, CLIPper or Skipper peak calling with stringent log2 FC and -log10 p thresholds, IDR rescue and self-consistency QC, and downstream motif registration with mCross or PEKA.

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。

Segments the genome into chromatin states from combinatorial histone modification and chromatin factor ChIP-seq data. Uses ChromHMM (multivariate HMM on binarized signal, v1.27), Segway (Dynamic Bayesian Network on continuous signal), EpiSegMix (flexible-distribution HMM with duration modeling, 2024), EpiLogos (multi-biosample visualization), IDEAS (cell-type-aware joint), and full-stack ChromHMM (Vu Ernst 2022) for cross-cell-type segmentations. Handles state-count selection (15 vs 18 vs 25 states), binarization choice, OverlapEnrichment / NeighborhoodEnrichment downstream analysis, and cross-biosample integration. Use when learning chromatin states from a histone mark panel, characterizing learned states by genomic feature enrichment, or comparing chromatin landscapes across cell types.

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。

Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate removal using fgbio. Applies cfDNA-specific quality thresholds and fragment length filtering. Use when processing plasma cfDNA sequencing data before 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。

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.

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。

Reconstruct ancestral states at internal phylogenetic nodes for sequences (PAML codeml, IQ-TREE --ancestral, GRASP, FastML), discrete traits (corHMM hidden-rate Markov, ape::ace, phytools::make.simmap stochastic mapping, BayesTraits), and continuous traits (phytools::fastAnc, geiger Brownian/OU, RPANDA). Use when designing constructs for ancestral protein resurrection, tracing trait evolution along a tree, performing stochastic character mapping, testing models of trait evolution (BM vs OU vs EB), inferring ancestral genome content via Dollo or DTL reconciliation, or quantifying ancestral-state uncertainty for downstream comparative analyses.

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。

Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying variants with allelic effects on TF binding, fine-mapping causal regulatory variants, validating deep-learning variant predictions, or characterizing cis-acting regulatory effects.

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。

Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when removing unreliable columns or contaminating residues before phylogenetic inference, HMM building, or selection 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。

Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL. Use when mapping cis-regulatory genetic variants from heterozygous SNPs, separating cis from trans regulation, building chromatin QTL (caQTL) maps, validating GWAS variant function with allelic imbalance, or detecting reference allele mapping bias before 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。

BED file format fundamentals, creation, validation, and basic operations. Covers BED3 through BED12 formats, coordinate systems, sorting, and format conversion using bedtools and pybedtools. Use when working with genomic coordinates or preparing interval files for downstream tools.

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。

Call accessible chromatin regions from ATAC-seq BAM files using MACS3, MACS2, Genrich, or HMMRATAC. Use when identifying open chromatin from aligned ATAC-seq, choosing between point-source vs HMM peak callers, applying ENCODE-style pseudoreplicate IDR, removing blacklist regions, or fixing 501bp consensus peaks for downstream differential 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。

ChIP-seq peak calling and downstream interpretation with MACS3, signal track export, annotation, motif analysis, and differential binding review.

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 read alignment, sorting, indexing, mapping statistics, and downstream-ready alignment artifacts.

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。

Python-first workflow for bulk RNA-seq expression intake, normalization, sample QC, and downstream-ready matrices.

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。

Kaggle-first end-to-end competition workflow for scored submissions. Use when Codex must run Kaggle or competitive ML workflows through scored submission, including code competitions, validation, metrics, policy-safe public notebook/discussion intel, tabular/text/image modeling, tuning, ensembling/stacking, proactive multi-notebook architectures, producer notebooks that train models and export private Kaggle artifact datasets, downstream consumer notebooks, Kaggle GPU offload, kagglehub access, hidden-test debugging, and public score retrieval.

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。

Kaggle-first end-to-end competition workflow for scored submissions. Use when Codex must run Kaggle or competitive ML workflows through scored submission, including code competitions, validation, metrics, policy-safe public notebook/discussion intel, tabular/text/image modeling, tuning, ensembling/stacking, proactive multi-notebook architectures, producer notebooks that train models and export private Kaggle artifact datasets, downstream consumer notebooks, Kaggle GPU offload, kagglehub access, hidden-test debugging, and public score retrieval.

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。

Define measurable success metrics (KPIs) tied to product type during PRD v0.3 Commercial Model. Triggers on requests to define success metrics, set KPI targets, determine what to measure, establish go/no-go thresholds, or when user asks "how do we measure success?", "what metrics matter?", "what's our target?", "how do we know if this works?", "define KPIs", "success criteria". Consumes Product Type Classification (BR-) from v0.2. Outputs KPI- entries with thresholds, evidence sources, and downstream gate linkages.

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。

Extract brand identity from a website URL — voice, colors, typography, imagery, values, and target audience — into a structured brand-profile.json. The profile feeds downstream skills (seo-content-writer, email-composer, frontend-design, pro-deck-builder, cross-platform-audit) for brand-consistent output. Use when the user says brand DNA, brand profile, extract brand, analyze brand, brand voice, brand identity, brand colors, or brand style guide.

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 has a long-form video (interview / lecture / podcast / conversation) and a transcript SRT, and wants to extract 3–6 stand-alone topical short clips from it. This skill ONLY cuts and crops — it produces raw clips + per-clip SRTs as a hand-off package for downstream post-production (`/wjs-overlaying-video`). Triggers — "切成几段", "分主题", "拆成短视频", "切片", "topic segments", "split into clips".

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 has one or more video clips and wants to add post-production on top — AI-generated cover as first frame, HTML/CSS captions synced to SRT, kinetic illustration overlays at hook moments, chapter chips, end-card CTA, or any other timed motion graphics. Most often used as the downstream of `/wjs-segmenting-video` — pick up where that skill stopped (raw cropped clip + per-clip SRT) and produce the upload-ready MP4. Backed by HyperFrames so everything compiles to ONE final encode — no cascade of re-encodes. Triggers — "加封面", "加字幕", "加动画", "加 CTA", "做后期", "post-production", "title card", "kinetic captions", "end card".

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。

Front-door router for the product-shots ecosystem. Clarifies underspecified visual creation requests through a 4-stage state machine, injects platform visual DNA (Amazon + 7 social platforms) and industry visual DNA (7 industries), enforces a unified Negative Constraints prompt patch, then routes to one of five downstream business skills (product-shots-main-image / product-shots-detail-page / product-shots-multi-angle / product-shots-ad-creative / product-shots-social-post). Use when the user says "I need a product image", "design something for my listing", "I need content for Instagram", "make an ad for me", "make a cover image", "create a post", "做一个商品图", "帮我做个详情页", "帮我做个广告图", "做一个社媒图", "做一张图", "帮我设计", "做个封面" — i.e. any underspecified visual creation request that needs clarification before generation. This is the intent-routing hub of the product-shots ecosystem.

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。

Extracting and structuring design context from Figma via MCP Server for downstream implementation agents. Use for Figma-to-code bridging or Code Connect 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。

Condense any input — an idea, brief, PRD, transcript, or mixed notes — into a short spec: one kernel file plus supporting files that downstream skills build from. Also updates and validates existing specs. Use when the user says "create a spec", "distill this into a spec", "validate this spec", or "update the spec"

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。