「calling」の検索結果

Call copy number variants with the GATK best-practices workflows — the somatic CNV pipeline (CollectReadCounts, DenoiseReadCounts with tangent normalization, ModelSegments, CallCopyRatioSegments) and the germline GATK-gCNV pipeline (DetermineGermlineContigPloidy, GermlineCNVCaller cohort/case mode, PostprocessGermlineCNVCalls). Covers panel-of-normals construction, AnnotateIntervals/FilterIntervals, allelic-count integration, and QS-based filtering. Use when integrating CNV calling into a GATK variant pipeline, calling rare germline CNVs from an exome cohort, deciding between the somatic and germline GATK workflows, or diagnosing why tangent normalization removed a real event or why gCNV output has low precision.

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。

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。

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。

Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling, analyzing per-position read data, or calculating allele frequencies.

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。

Automate Callingly tasks via Rube MCP (Composio). Always search tools first for current schemas.

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 m6A peaks from MeRIP-seq / m6A-seq paired IP-vs-input data using exomePeak2 (transcript-aware, GC-bias-corrected Poisson GLM; Liu 2022 *NAR Genom Bioinform* 4:lqac046), MeTPeak (HMM over sliding windows; Cui 2016 *Bioinformatics* 32:i378), MACS3 / MACS2 with --nomodel --broad --keep-dup all (genome-wide broad alternative), and DRACH motif enrichment confirmation via HOMER or ggseqlogo as a sanity check (NOT a filter). Covers BED12 vs narrowPeak output formats, exonic vs intronic peak handling, multi-tool reconciliation (intersection vs union; cross-caller IDR-equivalent), the m6A-vs-m6Am ambiguity at 5'UTR peaks that antibody-based methods cannot resolve, and orthogonal-validation routes (miCLIP / GLORI / m6A-SAC-seq / m6Anet). Use when calling peaks from paired IP/input genome BAMs, choosing exomePeak2 (transcript-aware default) vs MACS3 (broad genomic) vs MeTPeak (HMM-smoothed low-coverage), confirming DRACH enrichment as a sanity check on the peak set as a whole, reconciling differing peak sets across tools, validating MeRIP peaks against orthogonal single-base methods, interpreting peaks at the 5' end where m6Am contamination is possible, or recommending a multi-tool consensus 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。

Cross-method decision tree for calling hits in pooled CRISPR screens. Catalogs statistical models (MAGeCK RRA, MAGeCK MLE, BAGEL2, drugZ, JACKS, Chronos, CERES), experimental designs each is built for, failure modes outside design domain, reconciliation when methods disagree, multiple-testing and effect-size thresholds, the order of operations (count -> QC -> CN-correct -> hit-call -> validate), the second-best-sgRNA conservative rule, and consensus-hit strategy. Use when choosing among MAGeCK / BAGEL2 / drugZ / JACKS / Chronos for a given design, reconciling disagreement across two or three methods on the same screen, deciding whether to require consensus, gating downstream validation by hit-confidence tier, or interpreting unstable hit lists across reruns.

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 copy number variants with the GATK best-practices workflows — the somatic CNV pipeline (CollectReadCounts, DenoiseReadCounts with tangent normalization, ModelSegments, CallCopyRatioSegments) and the germline GATK-gCNV pipeline (DetermineGermlineContigPloidy, GermlineCNVCaller cohort/case mode, PostprocessGermlineCNVCalls). Covers panel-of-normals construction, AnnotateIntervals/FilterIntervals, allelic-count integration, and QS-based filtering. Use when integrating CNV calling into a GATK variant pipeline, calling rare germline CNVs from an exome cohort, deciding between the somatic and germline GATK workflows, or diagnosing why tangent normalization removed a real event or why gCNV output has low precision.

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。

Build and analyze pangenomes for prokaryotes (Panaroo, PPanGGOLiN, PEPPAN, GET_HOMOLOGUES, anvi'o pangenomics) and eukaryotes (Minigraph-Cactus, PGGB, vg pangenome graphs). Implement Tettelin core/accessory/cloud genome decomposition (Tettelin 2005), Heap's law open/closed pangenome modeling, gene presence/absence GWAS (Scoary, pyseer), pangenome graph variant calling (vg, PanGenie), and structural-variation graph indexing. Use when assembling species- or genus-level pan-gene catalogs, separating core from accessory/shell/cloud genes, testing gene-content associations with phenotypes, building pangenome graphs from haplotype-resolved assemblies, calling SVs from pangenome graphs, or selecting between bacterial-pangenome and eukaryotic-pangenome workflows.

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。

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。

Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling, analyzing per-position read data, or calculating allele frequencies.

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 with OpenAI's stateless APIs - Chat Completions (GPT-5, GPT-4o), Embeddings, Images (DALL-E 3), Audio (Whisper + TTS), and Moderation. Includes Node.js SDK and fetch-based approaches for Cloudflare Workers. Use when: implementing chat completions with GPT-5/GPT-4o, streaming responses with SSE, using function calling/tools, creating structured outputs with JSON schemas, generating embeddings for RAG (text-embedding-3-small/large), generating images with DALL-E 3, editing images with GPT-Image-1, transcribing audio with Whisper, synthesizing speech with TTS (11 voices), moderating content (11 safety categories), or troubleshooting rate limits (429), invalid API keys (401), function calling failures, streaming parse errors, embeddings dimension mismatches, or token limit exceeded.

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。

Extracts structured data from LLM responses using JSON schemas, Zod validation, and function calling for reliable parsing. Use when users request "structured output", "JSON extraction", "parse LLM response", "function calling", or "typed 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。

Designs robust function/tool calling schemas for LLMs with JSON schemas, validation strategies, typed interfaces, and example calls. Use when implementing "function calling", "tool use", "LLM tools", or "agent actions".

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。

OpenClawから指定した電話番号へ音声通話を開始し、通話中のメッセージ送信、状態確認、終了までをCLIやエージェント用ツールで操作するスキル。

• 電話番号へメッセージを伝えたいとき
• 通話中に追加メッセージを送りたいとき
• 通話状態の確認と終了

AIエージェントと外部ツールをつなぐMCPサーバーを、コマンドで一覧表示・設定・認証し、ツールの呼び出しや入出力の仕様確認まで行うスキル。

• MCPツールと引数の仕様確認
• MCPの接続設定と認証
• JSON引数でツールを呼びたいとき

参考素材の見た目やカットのリズムを再利用できる設定に整理し、手元の映像の編集計画、画像・動画・3D素材の生成計画、編集可能なタイムラインをオフラインで作るスキル。

• 映像の好みを聞き取り設定にまとめたいとき
• スタイルパックの検証と出所確認
• 参考映像のリズムで編集を計画

AIエージェントが使うツールの種類や入出力、エラーからの復帰手順を設計・見直します。文脈の情報量も整理し、作業完了率や再試行回数で改善を評価します。

• エージェントのツールや入力形式の設計
• ツールの結果と次の行動を明確にしたいとき
• 安全な再試行と停止条件を定めたいとき

Twilioの電話番号を取得・保存し、SMS・MMSの送信や受信確認、音声通知、AIによる発信を扱います。同じ番号を次のセッションでも使えるスキル。

• エージェント用番号の取得と再利用
• 作業完了をSMSで通知
• 前回以降に届いたSMSの確認

Interact with the Paperclip control plane API for task coordination and governance. Use when checking assignments, updating issue status, posting comments, delegating work, managing routines, or calling Paperclip API endpoints.

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。

Scaffold a custom AI agent harness via `metaharness new {name} --template {id} --host {id}`. Defaults to DRY-RUN (no writes) unless --confirm is passed. Refuses to write to the calling repo root or anywhere inside it. Honors ADR-150 architectural constraint + ruflo's "destructive-action confirmation" pattern.

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。