「mapping」の検索結果

Master of text-based visual communication using ASCII art, Unicode box-drawing, and structured diagram notation. Creates clear, maintainable diagrams for systems, processes, hierarchies, relationships, and psychological structures. Proactively generates diagrams to enhance understanding. Activate on visualization needs, system architecture, process flows, psychological mapping, or when complex concepts would benefit from visual representation. NOT for photo editing, vector graphics, or GUI-based design tools.

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Strategic analyst that maps competitive landscapes, identifies white space opportunities, and provides positioning recommendations. Use when users need competitive analysis, market positioning strategy, differentiation tactics, or "how do I stand out?" guidance across any domain (portfolios, products, services). NOT for market size estimation or financial forecasting.

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Reads, inspects, and writes Flow Cytometry Standard (FCS) files from conventional, spectral, and mass cytometry (CyTOF), and parses FlowJo/Cytobank/Diva workspaces. Covers FCS 2.0/3.0/3.1/3.2 internals ($PnE linear-vs-log, $DATATYPE, $SPILLOVER vs SPILL vs $COMP, $TIMESTEP), channel/parameter metadata, the silent linearize/truncate defaults, and R (flowCore, flowWorkspace, CytoML) plus Python (FlowKit, readfcs) readers. Use when loading flow or mass cytometry data, mapping detector channels to antibodies, extracting the event matrix, choosing a reader, or bridging FCS to the scanpy/AnnData ecosystem before preprocessing.

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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.

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Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair tracking, antibody-lot metadata recording, replicate concordance via deepTools multiBamSummary + plotCorrelation, IP enrichment QC via plotFingerprint and per-transcript IP/input ratio distributions, library-complexity saturation curves via PreSeq, and the explicit do-NOT-deduplicate convention for standard non-UMI MeRIP. Use when preparing paired IP and input BAM files for exomePeak2 / MeTPeak / MACS3 peak calling, evaluating MeRIP replicate concordance and IP enrichment, deciding whether to deduplicate (standard MeRIP typically NOT), choosing genome-vs-transcriptome alignment for downstream peak vs m6Anet workflows, recording antibody clone and lot metadata for cross-batch reconciliation, detecting failed IPs via saturation curves and IP/input distribution shape, or generating IP-over-Input bigWig tracks for visualisation.

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Build clustered heatmaps for expression matrices and other features-by-samples data with rigorous distance/linkage/scaling choices, robust color mapping, optimal leaf ordering, and ComplexHeatmap/pheatmap/seaborn rendering. Covers the ward.D vs ward.D2 trap, the row-vs-column scaling decision, multi-track annotations, oncoPrint, and raster rendering for large matrices. Use when visualizing expression patterns across samples or identifying co-regulated clusters.

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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.

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Detect horizontal gene transfer (HGT / LGT) using compositional methods (GC%, codon usage, tetranucleotide z-scores via SIGI-HMM, AlienHunter, IslandViewer 4, IslandPath-DIMOB), phylogenetic-incongruence methods (AvP, HGTphyloDetect, ALE / GeneRax / AleRax reconciliation, RANGER-DTL), and BLAST-distribution methods (HGTector v2, DarkHorse, Alien Index). Use when screening prokaryote genomes for genomic islands and HGT events, distinguishing HGT from incomplete lineage sorting / differential gene loss / hybridization, mapping donor lineages via phylogenetic placement, separating eukaryotic HGT from contamination, ruling out gBGC as a false signal, or quantifying DTL rates with ALE/GeneRax on bacterial trees.

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Maps GWAS-implicated loci to candidate effector (causal) genes by integrating variant-to-gene (V2G) features via Open Targets L2G (Mountjoy 2021), MAGMA gene-based association (de Leeuw 2015), FUMA SNP2GENE, cS2G combined SNP-to-gene scores (Gazal 2022), Polygenic Priority Scores (PoPS, Weeks 2023), FLAMES, INQUISIT, DEPICT, and enhancer-gene predictors (ABC, ENCODE-rE2G). Use when narrowing a GWAS lead locus to a candidate causal gene, picking between proximity, eQTL-based, and similarity-based prioritizers, integrating multi-evidence streams (fine-mapping, colocalization, ABC enhancer-gene, distance, chromatin), reconciling discordant L2G vs PoPS calls, prioritizing tissue-specific eQTL evidence, or triangulating across at least three independent lines of evidence for a publication-grade effector-gene nomination.

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Bulk-query Ensembl BioMart (and other BioMart instances) for cross-database ID mapping, gene/transcript/exon coordinates, and ortholog tables. Use when batch-converting Ensembl IDs to other namespaces (HGNC, RefSeq, UniProt, Entrez), pulling gene coordinate tables for thousands of genes, building ortholog wide-tables across species, or replacing slow Ensembl REST loops with one-shot bulk export. Encodes BioMart's XML query format, R biomaRt vs Python pybiomart trade-off, mart-vs-dataset hierarchy, and the URL endpoint that's BioMart-specific (separate from rest.ensembl.org).

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Predict enhancer-gene regulatory connections from ATAC-seq using ABC, ENCODE-rE2G, HiChIP, or Cicero. Use when linking distal enhancers to target genes, choosing between contact-aware (ABC, ENCODE-rE2G), accessibility-only (Cicero), and orthogonal (HiChIP H3K27ac, EpiMap) approaches, validating predictions against CRISPRi-FlowFISH gold-standard, or building cell-type-specific regulatory maps for fine-mapping or therapeutic target discovery.

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Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.

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The primary tool for code-navigation questions in ANY language (frontend or backend) — walk the structural graph from an entry point (page, route, handler, command, `main`) down through imports to the IO boundary (network call, query, file read). Use this skill, in preference to the Explore agent or global grep, whenever the user asks "where does X come from?", "what API/data populates Y?", "what renders or wraps the Z panel?", "which file for feature F?", "how is this wired up?", or any code-navigation question mapping a UI element, route, or feature concept to source files. Also reverse queries ("what uses /api/foo?", "who consumes this service?"). Keyword search routinely picks up unrelated flows sharing a domain word and produces wrong answers; the walk follows the actual graph. The JS/TS `walk.mjs`/`discover.mjs` are an optional accelerator, not required — the walk is language-agnostic.

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Build comprehensive attack trees to visualize threat paths. Use when mapping attack scenarios, identifying defense gaps, or communicating security risks to stakeholders.

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Use when assessing AI/ML systems for prompt injection, jailbreak vulnerabilities, model inversion risk, data poisoning exposure, or agent tool abuse. Covers MITRE ATLAS technique mapping, injection signature detection, and adversarial robustness scoring.

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PR formatting reference — title, body template, label mapping, assignment, and draft policy. Invoked by pr/create and pr/update-desc commands to ensure consistent PR formatting.

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kpopper Hub: optional experimental application for exploring the project record. Use when the user explicitly requests kpopper Hub or its record page, its graph, layout or verification, or has a standing preference for this application. Do not render automatically after mapping or recording. Install the HTML runtime before use. Not for ordinary HTML documents or a text answer from the record. Requests come in any language.

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Raw discovery primitives — project discovery, version resolution, docs loading, architecture mapping, execution flow. Called by `universal-project-analysis`. Single-pass scan → `project-analyzer`.

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Use when creating a Laravel/PHP DTO with the SimpleDto base class and attribute mapping. For DTOs in other stacks, use the stack-native skill (TypeScript, Python, Rust, Go).

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When shaping cadence — evergreen / campaign / reactive split, beat-mapping across channel stages, content-debt management. Triggers on 'plan our content cadence', 'what should we publish'.

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Grounded brand decisions from a curated corpus — archetype, voice, naming, colour psychology, logo-style fit, messaging frameworks, archetype→type mapping. Use to ground brand strategy and identity.

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Use when mapping competitors, naming defensibility, and finding white-space — moat reasoning, where-to-play, where-not-to-play. Triggers on 'who are we competing with', 'what's our moat'.

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Use when mapping funnel-stage to content shape — conversion-pathway, content-as-system, leverage-point selection. Triggers on 'design our content funnel', 'why does mid-funnel leak'.

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Load this skill when configuring axe-core scans, reviewing automated accessibility test results, or writing tests that use @axe-core/playwright, @axe-core/react, or similar integrations. Provides a quick reference to axe 4.x rule IDs, their WCAG mapping, and default severity levels.

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。