「appi」の検索結果

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 c_curve / lc_extrap, 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 — see Tips), choosing genome-vs-transcriptome alignment for downstream peak vs m6Anet workflows, recording antibody clone and lot metadata for downstream cross-batch reconciliation, detecting failed IPs via saturation curves and IP/input distribution shape, or generating IP-over-Input bigWig tracks for downstream visualisation.

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。

Transfers gene annotations between genome assemblies via coordinate liftover (UCSC liftOver, CrossMap for same-species version updates) or feature/sequence projection (Liftoff for same/close species, miniprot for protein-level cross-species, TOGA/GeMoMa/CAT for distant clades). Covers the coordinate-vs-projection decision by divergence, why a successful lift is not biological confirmation, reference bias, the silent-dropping of unmapped features, build/PAR/MHC/inversion hazards, and transfer-vs-de-novo validation. Use when annotating a new assembly of a species with an existing reference, harmonizing coordinates across builds, or mapping annotations across related species.

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Pull pre-computed ortholog calls from public databases (OrthoDB, Ensembl Compara, OMA browser, eggNOG, PANTHER, KEGG Orthology, HomoloGene) via their REST APIs. Use when orthologs are already curated upstream, when the question is "what is the X ortholog of Y" rather than "how to infer orthology de novo", when batch-mapping gene IDs across species, or when comparing the resources for consensus calls. Encodes confidence-level semantics, 1:1 vs 1:many vs many:many, HomoloGene deprecation, and when to defect to de novo computation.

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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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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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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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Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, population frequencies, and clinical-variant content. Covers bedtools/pybedtools interval intersection, AnnotSV comprehensive annotation and ranking, ClinGen haploinsufficiency/triplosensitivity scoring, gnomAD-SV/DGV frequency filtering, COSMIC Cancer Gene Census, and ClinVar overlap. Use when interpreting which genes a CNV affects, distinguishing the driver gene of a focal event from passengers, filtering against population CNVs, separating whole-gene from partial-gene overlap, or preparing CNVs for clinical classification.

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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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Calls microsatellite instability from WES/WGS/targeted-panel with MSIsensor, MSIsensor-pro, MSIsensor-ct (panel-aware), MSIngs, MANTIS, MSIPanel, MSIDetect, and ngsMSI for FDA pembrolizumab MSI-H pan-tumor / Lynch syndrome / dMMR ICI biomarker. Use when stratifying ICI eligibility (Le 2015), pairing MSI with TMB-H (Sha 2020 / Salem 2018), screening Lynch syndrome (universal IHC + MSI), or distinguishing MSI-H tumors from POLE-exo hypermutator with overlapping signatures.

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Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and Reaction templates, with explicit handling of atom mapping, template extraction (RDKit reaction mining), product validation, RECAP/BRICS fragmentation, R-group decomposition, matched molecular pair analysis (MMPA), and Free-Wilson analysis. Use when generating combinatorial libraries from building blocks, enumerating analog series, deriving structure-activity rules, or extracting transformations from reaction data.

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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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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.

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。

Provides expert knowledge of JPA entity design, relationship mapping, Flyway migrations, and PostgreSQL-specific optimizations.

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Use when generating REST controllers, response wrappers, DTOs, error handlers, or any HTTP-facing code. Defines response envelope, HTTP status mapping, pagination, and versioning.

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Sets up Convex auth, identity mapping, and access control. Use for login, auth providers, users tables, protected functions, or roles in a Convex app.

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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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Convert Claude markdown subagent files to Codex CLI TOML format. Parses YAML frontmatter and body, applies model/permission/tool mappings, and outputs to agents/codex/<name>.toml.

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Convert AmeriFlux ERA5 half-hourly meteorological CSV files into EcoSIM hourly climate forcing NetCDF files, compare generated forcing against overlapping measured tower meteorology when a FULLSET file is available, and report large biases or errors. Use when preparing or validating EcoSIM climate inputs for AmeriFlux sites, checking ERA5 against in situ records, diagnosing forcing discrepancies, or writing climate-quality reports. For non-AmeriFlux paper sites that need a fresh Copernicus CDS ERA5 point download by longitude/latitude, use era5-cds-point-download first.

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Estimate calcium-normalized Gapon selectivity coefficients from paired exchange and solution chemistry, or initialize depth-explicit EcoSIM Gapon inputs from the closest bundled ecosystem template when paired chemistry is unavailable. Use when deriving or checking EcoSIM GKC4, GKCH, GKCA, GKCM, GKCN, or GKCK values; matching a target ecosystem, climate, vegetation, and management regime to a starting profile; remapping template values to target soil layers; or documenting that template-based values require calibration or tuning.

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Pro-camera HUD mockup template — full-viewport black canvas wrapping a real video with monospace overlays (corner brackets, top status bar, side AF/exposure columns, bottom timecode + aperture/shutter/ISO row, vertical 8-filter wheel, animated reticle). For cinematographer portfolios, camera-app demos, LUT pack previews, filter-look auditions. NOT a TikTok/Reels mockup, NOT a storyboard, NOT a shot list, NOT a script document. The chrome wraps real footage — never a div placeholder.

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When the user wants help with paid advertising campaigns on Google Ads, Meta (Facebook/Instagram), LinkedIn, Twitter/X, or other ad platforms. Also use when the user mentions 'PPC,' 'paid media,' 'ROAS,' 'CPA,' 'ad campaign,' 'retargeting,' 'audience targeting,' 'Google Ads,' 'Facebook ads,' 'LinkedIn ads,' 'ad budget,' 'cost per click,' 'ad spend,' or 'should I run ads.' Use this for campaign strategy, audience targeting, bidding, and optimization. For bulk ad creative generation and iteration, see ad-creative. For landing page optimization, see page-cro.

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When the user wants to plan, design, or implement an A/B test or experiment. Also use when the user mentions "A/B test," "split test," "experiment," "test this change," "variant copy," "multivariate test," "hypothesis," "should I test this," "which version is better," "test two versions," "statistical significance," or "how long should I run this test." Use this whenever someone is comparing two approaches and wants to measure which performs better. For tracking implementation, see analytics-tracking. For page-level conversion optimization, see page-cro.

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When the user wants to optimize content for AI search engines, get cited by LLMs, or appear in AI-generated answers. Also use when the user mentions 'AI SEO,' 'AEO,' 'GEO,' 'LLMO,' 'answer engine optimization,' 'generative engine optimization,' 'LLM optimization,' 'AI Overviews,' 'optimize for ChatGPT,' 'optimize for Perplexity,' 'AI citations,' 'AI visibility,' 'zero-click search,' 'how do I show up in AI answers,' 'LLM mentions,' or 'optimize for Claude/Gemini.' Use this whenever someone wants their content to be cited or surfaced by AI assistants and AI search engines. For traditional technical and on-page SEO audits, see seo-audit. For structured data implementation, see schema-markup.

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