「filtering」の検索結果

Identifies differential m6A methylation between conditions from MeRIP-seq paired IP/input data using exomePeak2 (GC-bias-aware differential via its bam_ip/bam_input control + bam_treated_ip/bam_treated_input treatment arms), QNB beta-binomial, MeTDiff HMM, and RADAR, plus the paired-symmetric edgeR/DESeq2-on-peak-counts route when batch/lot covariates need fixed-effect handling that exomePeak2's API does not accept. Covers paired vs unpaired vs interaction designs, batch confounding and per-lot meta-analysis, the stoichiometry-vs-expression-vs-IP-efficiency confound, and effect-size filtering against under-powered N=2 designs. Use when comparing m6A across two or more conditions, choosing between exomePeak2/QNB/RADAR/MeTDiff for a design, handling batch confounding when exomePeak2's API is too rigid, distinguishing real hyper/hypo-methylation from expression shifts, applying effect-size thresholds, or planning orthogonal stoichiometry validation (GLORI/SAC-seq/m6Anet mod_ratio).

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Detects and removes doublets/aggregates from flow, spectral, and mass cytometry before clustering or quantification. Covers FSC-A vs FSC-H singlet discrimination (the Area-Height non-proportionality, not a 1D area gate), FSC-W/SSC width gating, CyTOF Gaussian discrimination parameters (Center/Offset/Width/Residual/Event_length) and DNA intercalator gating, and the residual heterotypic conjugates that survive scatter gating and masquerade as double-positive populations. Use when filtering aggregates before phenotyping, choosing a doublet method for flow vs CyTOF, or diagnosing a suspicious double-positive cluster.

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Work with FASTQ quality scores using Biopython - access Phred scores, filter and trim by quality, compute per-position profiles, and convert between Sanger/Phred+33, Solexa, and Illumina/Phred+64 encodings. Use when analyzing read quality, filtering or trimming low-quality bases, generating quality reports, or deciding which FASTQ quality encoding a file uses before parsing.

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Performs differential expression on bulk RNA-seq count data with DESeq2's negative-binomial GLM, Wald and LRT testing, apeglm/ashr/normal LFC shrinkage, independent filtering, Cook's outlier handling, VST/rlog transforms, and design formulas including paired, batch, and interaction terms. Use when running bulk DE, choosing DESeq2 over edgeR or limma-voom, building a paired or interaction design, applying LFC shrinkage for ranking or GSEA, choosing Wald vs LRT, troubleshooting padj=NA, picking VST vs rlog, importing salmon/kallisto via tximport, or analyzing prokaryotic RNA-seq.

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Analyzes base-editing screens for variant function. Covers library design (Hanna 2021 ClinVar-scale CBE screen benchmarked on BRCA1/2, Cuella-Martin 2021 DDR saturation), CBE vs ABE chemistry choice (BE3/BE4 vs ABE7.10/ABE8.20/ABE8e), editing-window math (positions 4-8 from PAM-distal end; 4-7 for ABE7.10), bystander-edit quantification and the variant-call ambiguity it creates, sgRNA-efficiency filtering before hit calling, indel byproduct interpretation, the substitution-vs-indel diagnostic, variant annotation against ClinVar / COSMIC, and the Broad be-validation-pipeline. Use when designing a BE variant screen, choosing CBE vs ABE for a specific edit, interpreting bystander-confounded hits, distinguishing functional signal from indel artifact, integrating CRISPResso2 output with screen scoring, or deciding BE vs PE for SNV installation.

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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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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.

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Calculates tumor mutational burden from WES/WGS/panel data with Friends of Cancer Research harmonization equations, per-assay calibration (FDA 10/Mb = 7.8 TSO500 = 8.4 OncomineTML), synonymous/indel/germline filtering, hypermutator tiering, blood TMB, and integration with HLA-LOH and neoantigen quality (Luksza 2017 fitness). Use when assessing ICI eligibility under tumor-specific cutoffs (McGrail 2021), comparing tissue vs bTMB, or auditing TMB-H reporting against ESMO 2024 and FDA pembrolizumab pan-tumor 2020.

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Queries gnomAD v4 (807k samples), v3, v2.1.1, and constraint metrics with grpmax FAF95, bottleneck-group exclusion, LOEUF interpretation, SV/CNV/mtDNA catalogs, and Whiffin max-credible-AF framework. Use when filtering rare variants, applying ACMG BS1/BA1, ranking genes by LoF intolerance, or selecting between v2 (GRCh37 + chrX/Y constraint) and v4 (GRCh38 + 807k samples).

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Comprehensive backend development guide for Langfuse's Next.js 14/tRPC/Express/TypeScript monorepo. Use when creating tRPC routers, public API endpoints, BullMQ queue processors, services, or working with tRPC procedures, Next.js API routes, Prisma database access, ClickHouse analytics queries, Redis queues, OpenTelemetry instrumentation, Zod v4 validation, env.mjs configuration, tenant isolation patterns, or async patterns. Covers layered architecture (tRPC procedures → services, queue processors → services), dual database system (PostgreSQL + ClickHouse), projectId filtering for multi-tenant isolation, traceException error handling, observability patterns, and testing strategies (Jest for web, vitest for worker).

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Predicts ADMET properties using ADMETlab 3.0 (119 platform features, including 77 prediction models with modeled-endpoint uncertainty), ADMET-AI, DeepChem MolNet, and chemprop D-MPNN with explicit handling of OECD QSAR principles, applicability domain assessment, calibration, hERG/CYP/AMES endpoints, and PAINS / Lipinski / Ro5 / Veber / BBB druglikeness filters. Use when filtering compounds for drug-likeness, prioritizing leads by predicted safety, or building an in-house ADMET QSAR model.

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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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Discover and list a site's URLs, with search filtering. Use for "map the site" or "find the URL for" requests — when the user knows the site but not the exact page, or wants site structure.

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Vitest fast unit testing framework powered by Vite with Jest-compatible API. Use when writing tests, mocking, configuring coverage, or working with test filtering and fixtures.

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Command-line fuzzy finder for interactive filtering.

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Expert-level signal processing covering Fourier analysis, sampling theory, digital filters, FFT, spectral estimation, and adaptive filtering.

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Design and review intuitive, scalable, maintainable HTTP APIs. Use this skill whenever the user wants to design a new REST API, review an existing API or spec, write OpenAPI 3.x definitions, or work with HTTP semantics (GET/POST/PUT/PATCH/DELETE), status codes, idempotency (Idempotency-Key), error envelopes (RFC 7807 problem+json), pagination, filtering, versioning, or API auth (API keys, OAuth2 client credentials, rate limits). Also trigger for "API design", "RESTful", "endpoints", "OpenAPI", "Swagger", "ReDoc", "contract testing", or GraphQL and gRPC design questions.

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Use when running verbose CLI commands — wraps them with rtk (Rust Token Killer, third-party Apache-2.0; upstream reports 60-90% token savings). Covers installation, configuration, and usage patterns.

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Use when packaging a codebase to a single AI-friendly file for LLM analysis — local or remote, XML/Markdown/JSON, token counting, gitignore filtering, peer-side `repomix` CLI.

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Use when creating or modifying Laravel middleware — request/response filtering, groups, priority, terminable middleware, or route-level assignment.

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Harness-first workflow for evaluating and improving terminal UIs through real interaction. Use this whenever the user wants to review a TUI experience, compare before/after behavior, identify UX friction, validate navigation or filtering flows, inspect visual stability, or turn observed interaction problems into concrete follow-up tests and improvement recommendations. Prefer this skill any time a TUI should be exercised through a reproducible PTY/session harness instead of only reading code.

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Banco de dados de embeddings de código aberto para aplicações de IA. Armazene embeddings e metadados, realize buscas vetoriais e full-text, filtre por metadados. API simples com 4 funções. Escala de notebooks para clusters de produção. Use para busca semântica, aplicações RAG ou recuperação de documentos. Melhor para desenvolvimento local e projetos de código aberto.

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Framework de segurança em runtime da NVIDIA para aplicações LLM. Com detecção de jailbreak, validação de entrada/saída, verificação de fatos, detecção de alucinações, filtragem de PII, detecção de toxicidade. Usa DSL Colang 2.0 para rails programáveis. Pronto para produção, executa em GPU T4.

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Curação de dados acelerada por GPU para treinamento de LLM. Suporta texto/imagem/vídeo/áudio. Recursos incluem deduplicação fuzzy (16× mais rápida), filtragem de qualidade (30+ heurísticas), deduplicação semântica, redação de PII, detecção NSFW. Escala em GPUs com RAPIDS. Use para preparar datasets de treinamento de alta qualidade, limpar dados web ou deduplicar grandes corpora.

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。