4.5万 件 ・ 関連度順
概要と使いどころ
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.
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Select, document, download, and checksum-verify the most appropriate NCBI reference genome on an HPC cluster. Use whenever an analysis needs a reference genome, genome FASTA, genome annotation, assembly accession, or genome index and no exact approved assembly is already available; when a user asks to fetch a species genome from NCBI; or when a pipeline must resolve and cache a reproducible reference assembly on a remote cluster.
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ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds. Use when assessing whether an ATAC-seq library passes ENCODE acceptance criteria, diagnosing transposition artefacts, comparing Omni-ATAC vs standard prep quality, or selecting which replicates to drop before peak calling.
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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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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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Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR. Use when comparing ATAC-seq accessibility between treatment groups, choosing between consensus-peak vs sliding-window approaches, picking the correct normalization (full library vs reads-in-peaks), correcting batch with SVA/RUVseq, or interpreting log2FC and FDR thresholds in a chromatin context.
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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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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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Test whether two or more traits share a causal variant at a locus using Bayesian colocalization (coloc.abf, coloc.susie, HyPrColoc, moloc, eCAVIAR, SMR/HEIDI, PWCoCo, SharePro). Use when integrating GWAS with eQTL/sQTL/pQTL/mQTL, distinguishing shared causal variants from LD-driven coincidence, handling allelic heterogeneity, choosing between single-causal vs multi-causal methods, picking PP.H4 thresholds, running sensitivity over p12, or harmonising summary statistics for colocalization.
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Use this skill when the user asks about passenger-carrying CMVs — buses, motorcoaches, charter operations, school buses, limousines, shuttle services. Covers different HOS rules (10-hour driving / 15-hour on-duty / no 34-restart), Class C CDL with P endorsement, S endorsement for school bus, FMCSA Hours-of-Service for passenger vehicles, $5M insurance minimum, BMC-32 filing, accessibility requirements, and how passenger ops differ from property. Cite 49 CFR 395.5 + 387.33.
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Use this skill when the user asks about getting/maintaining motor carrier operating authority — USDOT number, MC number, BOC-3 process agent, insurance filing (MCS-90, BMC-91/91X), Unified Carrier Registration (UCR), International Registration Plan (IRP), International Fuel Tax Agreement (IFTA), state-level permits (NY HUT, KY weight distance, OR weight-mile, NM weight distance), new entrant safety audit, intra vs interstate, for-hire vs private. Cite 49 CFR 365, 387, 390.
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Use this skill when the user asks how to design or improve a Preventive Maintenance (PM) program for a fleet — mileage vs time intervals, A/B/C/D inspection levels, ATA standards, common PM tasks, scheduling software, cost tracking, and how PM affects roadside inspections + CSA scores. Reference ATA Equipment Maintenance Council standards.
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Use when a carrier or driver asks about winter trucking, snow chain requirements, hot-weather precautions, summer tire failures, fuel additive use (anti-gel), idle management in extreme temperatures, weight restrictions in spring thaw, or how seasonal demand patterns affect freight rates and capacity.
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Use this skill when the user asks about towing + recovery operations — separate FMCSA authority class, light-duty vs medium-duty vs heavy-duty wrecker rules, AAA + AAA-Plus contracts, Roadside-Assistance (RA) operations, "non-consensual tow" rules + state-by-state, and how towing operations differ from general freight. Reference state Public Utility Commission + 49 CFR 395 application.
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Use this skill to understand FMCSA tire tread depth requirements. Covers steer tires (4/32 minimum) and other axles (2/32 minimum), and how to measure correctly.
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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.
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Use when a carrier asks about trailer types — dry van, reefer, flatbed, step-deck, conestoga, tanker, dump, lowboy, intermodal chassis, auto-hauler. Covers length / weight rules, common specs, reefer unit options (Carrier vs Thermo King), liftgate options, kingpin setting, and trailer-to-tractor matching.
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Use this skill to evaluate which defensive driving program is best for your fleet. Compares Smith System, CarriersEdge, Compass-native training, and other options.
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Use this skill when the user asks about team driving — two-driver OTR operations, how teams maximize miles, HOS rules with sleeper berth swap, pay structures, equipment requirements (sleeper berth specs), team retention, and common challenges. Reference 49 CFR 395.1(g).
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Use this skill for training drivers on effective pre-trip inspection technique. Covers the comprehensive walk-around, time investment, and common areas drivers miss.
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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 for vehicle brake system inspection requirements. Covers daily DVIR, weekly maintenance, brake adjustment check, and the 'percent of out-of-adjustment' rule.
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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 about refrigerated (reefer) trucking — cold chain compliance, FDA temperature recording requirements, Sanitary Transportation Rule (STR / 21 CFR 1.900-1.934), commodity-specific temperature ranges, refrigeration unit operation, temperature recorder calibration, and how a load is challenged if temperature deviates. Cite 21 CFR Part 1 Subpart Q.
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。