1,311 件 ・ 関連度順
概要と使いどころ
Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific reference sequences or reconstructing haplotypes.
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。
End-to-end pooled and single-cell CRISPR screen analysis from FASTQ to hit genes. Orchestrates library design QC, guide counting, six-stage screen QC (plasmid Gini, replicate Pearson, CEGv2 PR-AUC, copy-number artifact), method-appropriate hit calling across MAGeCK RRA/MLE, BAGEL2, drugZ, JACKS, and Chronos, cancer-cell-line copy-number correction (CRISPRcleanR / Chronos), batch correction for multi-batch screens, and the specialized branches for combinatorial paralog screens, single-cell Perturb-seq, base-editor variant-function screens, prime-editor screens, and in vivo bottleneck-aware screens. Use when analyzing any pooled CRISPR screen end-to-end, choosing the correct hit-calling method by experimental design, integrating copy-number correction into the pipeline, or branching the workflow for single-cell, combinatorial, base-editor, prime-editor, or in vivo variants.
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。
End-to-end ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3 (or HOMER), and peak annotation with ChIPseeker. Use when processing ChIP-seq data from alignment through peak annotation.
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。
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。
Align preprocessed CLIP-seq reads (eCLIP, iCLIP, iCLIP2, PAR-CLIP) to genome with STAR or bowtie2 using crosslink-preserving parameters, choosing between unique-mapper-only and multi-mapper-aware alignment for repeat-binding RBPs, deciding STAR vs HISAT2 memory trade-offs, and applying ENCODE-compatible filters. Use when turning preprocessed CLIP FASTQ into a deduplicated, MAPQ-filtered BAM ready for peak calling or crosslink-site detection.
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。
Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extraction, adapter trimming, length filtering, and post-alignment PCR-duplicate collapse. Use when raw CLIP FASTQ must be turned into deduplicated, crosslink-preserving BAM input for peak calling; choosing between two-pass and single-pass adapter trimming; deciding minimum read length; or mapping UMI patterns to specific eCLIP/iCLIP/iCLIP2/iCLIP3 library preps.
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 orthologous genes and gene families across species using OrthoFinder3 (HOG-based phylogenetic orthology), SonicParanoid2, Broccoli, ProteinOrtho, OMA / FastOMA hierarchical orthologous groups, eggNOG-mapper, JustOrthologs, and TOGA whole-genome-alignment orthology. Use when building single-copy ortholog sets for phylogenomics, classifying co-orthologs and in/out-paralogs after gene duplication, propagating functional annotation via orthology with awareness of the ortholog conjecture, distinguishing speciation from duplication via gene-tree species-tree reconciliation, computing Quest-for-Orthologs benchmark performance, or running synteny-aware ortholog detection in WGD-affected lineages.
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 circadian and ultradian rhythms in time-series omics data using CosinorPy cosinor models, MetaCycle (JTK_CYCLE, ARSER), and RAIN non-parametric tests. Fits cosine models to estimate phase and amplitude, tests rhythmicity significance at pre-specified periods. Use when testing for 24-hour or other known-period oscillations in circadian, feeding-fasting, or light-dark cycle experiments. Not for unknown-period discovery (see temporal-genomics/periodicity-detection).
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。
Align DNA short reads to reference genomes using bwa-mem2, the faster successor to BWA-MEM. Use when aligning DNA short reads to a reference genome.
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。
Generates standardized quality control reports by aggregating metrics from FastQC, alignment, and other tools using MultiQC. Use when summarizing QC metrics across samples, creating shareable quality reports, or building automated QC pipelines.
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。
Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller. Covers model selection, GPU acceleration, modified base detection, and quality filtering. Use when processing raw Nanopore data before alignment. Note: Guppy is deprecated; use Dorado for all new 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。
Integrate multiple scRNA-seq samples/batches using Harmony, scVI, Seurat anchors, and fastMNN. Remove technical variation while preserving biological differences. Use when integrating multiple scRNA-seq batches or datasets.
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。
Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.
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。
AlphaFold2 / AlphaFold-Multimer structure prediction for validation and confidence scoring. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer. For faster single-chain prediction, use esm2-sequence-scoring. For QC thresholds, use protein-design-qc.
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。
End-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built-in AF2 validation, (2) Running production-quality binder campaigns, (3) Using different design protocols (fast, default, slow), (4) Need joint backbone and sequence optimization, (5) Want high experimental success rate. For backbone-only generation, use rfdiffusion. For QC thresholds, use protein-qc. For tool selection guidance, use binder-design.
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。
Validate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer. For faster single-chain prediction, use esm. For QC thresholds, use protein-qc.
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。
Guide for creating high-quality MCP (Model Context Protocol) servers that enable LLMs to interact with external services through well-designed tools. Use when building MCP servers to integrate external APIs or services, whether in Python (FastMCP) or Node/TypeScript (MCP SDK).
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。
Optimize MATLAB code for better performance through vectorization, memory management, and profiling. Use when user requests optimization, mentions slow code, performance issues, speed improvements, or asks to make code faster or more efficient.
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。
Add fast, local, typed decisions to any project with Laya, an open-source non-generative decision model (pip install laya). It classifies, routes, scores and answers yes/no questions about a piece of text, returning calibrated probabilities in roughly 20-35 ms on a laptop GPU, with no LLM call and no data leaving the machine. Use this skill whenever the user wants to classify or route text, triage tickets or emails, detect spam, phishing, toxicity or intent, put a guardrail in front of an agent or LLM, score something against a rubric, or replace an LLM-based classifier to cut latency or cost. Also use it when they mention Laya, Jev, a "System 1 model", "typed decisions" or a "decision model", even if they never name Laya.
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。
Classify product approach into one of six types (Clone, Unbundle, Undercut, Slice, Wrapper, Innovation) based on competitive landscape. Triggers on PRD v0.2 work after competitive analysis, or when user asks "what type of product should we build?", "should we clone or innovate?", "is this a fast-follow opportunity?", "how should we position against competitors?", "clone vs undercut", "unbundle vs slice", or requests help choosing product strategy. Outputs BR- entries for product type classification and inherited GTM constraints.
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。
Systematically QA test any application — web apps, native macOS apps, Electron apps, CLI tools, interactive REPLs, or anything on screen. Three modes: browser (chromux/CDP, fast, DOM-level), computer (MCP computer-use, screenshot + pixel clicks, any app), and cli (tmux, send-keys + capture-pane for interactive terminals). Auto-selects mode or accepts --browser / --computer / --cli override. Use when asked to "qa", "QA", "test this site", "test this app", "find bugs", "test and fix", "fix what's broken", "dogfood", "exploratory test", "bug hunt", "QA this app", "사이트 테스트", "앱 테스트", "브라우저 QA", "화면 보고 테스트해줘", "네이티브 앱 테스트", "screen test". Three tiers: Quick (critical/high only), Standard (+ medium), Exhaustive (+ cosmetic). Produces before/after health scores, fix evidence, and a ship-readiness summary.
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。
Survey a whole React codebase as a senior React engineer, using React Doctor's scan as evidence, then produce a prioritized audit and self-contained implementation plans for other agents (or cheaper models) to execute. Read-only on source code — it plans improvements, it does not apply them. Use when the user asks to "improve the React code", "audit this codebase", "make this app faster / more robust", or wants a roadmap of fixes rather than a review of a single diff. For a regression check or a fix-it-now pass, use the `react-doctor` skill 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。
Define reproducible development environments with Dev Containers. Use when a user asks to standardize dev environments, set up VS Code remote containers, create reproducible dev setups, or onboard developers faster.
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。