「ar」の検索結果

Detects differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcutter (Dirichlet-multinomial GLM on intron clusters), MAJIQ V3 deltapsi/HET (Bayesian posterior on LSVs), SUPPA2 (empirical-null on TPM-derived PSI), or Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage). Reports FDR-corrected significance and delta PSI effect sizes. Tools differ in statistical model, annotation dependence, calibration regime, and replicate-count requirements. Use when comparing splicing patterns between treatment groups, tissues, or disease states.

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Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.

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 consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, indexing references, or creating sequence dictionaries.

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Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter (annotation-free intron clusters), VAST-TOOLS (cross-species with microexon support), Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage), or IRFinder-S (intron retention coverage-aware). Distinguishes the five canonical event classes (SE, A5SS, A3SS, MXE, RI), special classes (microexons, exitrons, AFE/ALE), intron retention subtypes (canonical RI vs detained introns), and applies effective-length normalization. Use when measuring splice-site usage or isoform inclusion ratios from short-read RNA-seq.

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Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt rule, ORF disruption, protein domain loss/gain, signal peptide changes, IDR alterations, coding-potential shifts). Tools include IsoformSwitchAnalyzeR v2 (auto-selects satuRn for >5 reps else DEXSeq), the manual DRIMSeq -> DEXSeq/satuRn -> stageR DTU pipeline, and fishpond/swish for inferential-uncertainty-aware DTE. Distinguishes DTU from DGE and DTE; integrates external annotators (CPC2, Pfam, SignalP, IUPred2A or DeepTMHMM). Use when investigating how splicing differences alter protein function or trigger NMD-mediated degradation.

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Creates sashimi-style plots showing RNA-seq read coverage and splice junction counts using ggsashimi (general-purpose, condition-grouped overlays), rmats2sashimiplot (rMATS-output-aware), MAJIQ-VOILA (LSV posteriors interactive HTML), leafviz (leafcutter clusters Shiny), Jutils (tool-agnostic heatmaps and sashimi for rMATS/leafcutter/SUPPA2/MAJIQ output), or pyGenomeTracks (multi-track publication figures). Tool choice depends on the upstream differential-splicing tool's output format and the publication vs interactive use case. Use when visualizing specific splicing events, validating differential splicing calls, or producing publication-quality figures.

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Detect transcription factor binding footprints in ATAC-seq using TOBIAS, HINT-ATAC, Wellington, or scprinter. Use when identifying bound TF sites within accessible regions, correcting Tn5 insertion bias before footprinting, choosing between cleavage-based and aggregate-based footprinters, or comparing differential TF activity between conditions.

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Build a differential-ready consensus peakset from per-replicate ATAC-seq peaks using iterative overlap removal, fixed-width re-centering, and majority-rule overlap. Use when generating a stable peak coordinate system for downstream differential accessibility, ML feature engineering, cross-sample comparison, or fixed-width peak counts; covers Corces 2018 iterative overlap (501 bp), DiffBind summit re-centering, and ENCODE consistency rules.

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Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when verifying alignment data quality before variant calling or quantification.

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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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Installs 425 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and 56 more categories. Use when setting up bioinformatics capabilities or when a bioinformatics task requires specialized skills not yet installed.

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生成图文并茂的分析报告/实验报告/质检报告（固定模版）。当用户要求"生成报告/总结报告/实验报告/质检报告/QC报告"，或分析流程收尾需要交付报告时使用。报告必须基于真实分析输出，包含固定章节结构、关键指标表格和真实结果图。

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NCPGR高性能计算集群软件使用注意事项与优化指南。聚焦各软件的坑点、加速技巧、资源节省建议与软件选型推荐。当用户询问集群上如何高效使用软件、编写LSF作业、或需要软件选型建议时使用。

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Use when users need bioinformatics analysis on the NCPGR cluster, especially when converting analysis requests into local software choices, resource plans, and LSF job scripts.

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Use this skill when the user asks about oversize / overweight load permits — state-by-state permitting process, escort vehicle (pilot car) requirements, route surveys, federal axle weight limits (Federal Bridge Formula), holiday restrictions, multi-state permits, and how to determine if a load needs a permit. Reference state DOT permitting offices.

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Use this skill to develop the capability to investigate crashes internally. Covers what to look for, when to escalate to outside experts, and documentation standards.

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Use this skill when the user asks about CMV roadside inspection levels (Level I through Level VIII), what each level inspects, average inspection times, CVSA decal eligibility, what triggers a level upgrade, and how to coach drivers through a roadside inspection. Reference CVSA North American Standard Inspection Program.

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Use this skill when the user asks about CMV maintenance program requirements under 49 CFR 396.3 — what records must be kept, retention periods (12-18 months on vehicle file + 1 year after disposal), what counts as systematic inspection/repair/maintenance, preventive maintenance scheduling, brake adjustment records, and what auditors look for in vehicle files. Cite 49 CFR 396.3 + 396.21.

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Use this skill when the user asks the cost of pulling a Motor Vehicle Record (MVR) in a specific state, or wants to compare MVR fees across multiple states, or is budgeting annual compliance costs for a multi-state fleet. Reference the canonical fee table below; flag that fees change (re-verify with state DMV before annual budget planning).

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Use this skill when documenting supervisor reasonable-suspicion training for Part 382 compliance. Covers what to log, what to retain, and what training providers to use.

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Use this skill to understand trailer-specific inspection requirements when a trailer is not coupled to a tractor. Covers annual inspection, DVIR rules, and parking inspections.

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Use when a safety director, operations manager, or fleet owner asks for templates, topics, or structure for recurring safety meetings — weekly driver meetings, monthly safety committee meetings, quarterly all-hands safety reviews, or post-incident safety stand-downs.

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Use this skill when the user asks about weigh-station bypass services — Drivewyze, PrePass, BestPass, NORPASS, OOIDA toll savings — how they work, eligibility criteria, costs, and how they tie into CSA scores. Reference each provider's coverage area + pricing.

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Use this skill when the user asks about trucking insurance — types of coverage (commercial auto, cargo, occupational accident, workers comp, bobtail/non-trucking, MCS-90 endorsement), federal minimums (49 CFR 387), what each covers, owner-operator vs company-driver implications, and how to read a Certificate of Insurance (COI). Cite 49 CFR 387.

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。