Data & AI skills

Standardizes molecular structures using ChEMBL chembl_structure_pipeline and RDKit rdMolStandardize covering sanitization, salt/solvent stripping, neutralization, tautomer canonicalization, stereochemistry standardization, mixture handling, and isotope normalization. Explicitly compares ChEMBL pipeline, canSARchem, and PubChem standardization choices. Use when preparing libraries for QSAR training, joining datasets across sources, deduplicating compound collections, or building canonical compound registries.

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Calculates molecular fingerprints (ECFP/Morgan, FCFP, MACCS, RDKit, AtomPair, TopologicalTorsion, Avalon, MAP4, MHFP6) and physicochemical descriptors (Lipinski, QED, TPSA, Crippen LogP, 3D shape) with explicit choice tables, bit vs count semantics, and partial-charge model selection. Use when featurizing molecules for similarity, QSAR, virtual screening, or ML, or selecting the correct fingerprint for a chemotype-aware task.

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Performs ML-based protein-ligand pose prediction and scoring using DiffDock-L (diffusion-based), Boltz-1 / Boltz-2 (foundation model with affinity), Chai-1, AlphaFold3 ligand, EquiBind, TANKBind, NeuralPLexer, and hybrid workflows (DiffDock pose + GNINA rescore + PoseBusters QC). Explicit handling of when ML beats classical docking, when classical beats ML, the PB-invalid pose problem, and rescoring as the standard production hybrid. Use when modern docking is needed: foundation-model ligand-pose prediction, AI rescoring of classical poses, or scaffold-hopping in cross-docking scenarios.

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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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Generate alignment statistics using samtools flagstat, stats, depth, coverage, and mosdepth. Use when assessing alignment quality, calculating coverage, or generating QC reports.

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Process and analyze single-cell ATAC-seq data with Signac, ArchR, SnapATAC2, or Cell Ranger ATAC. Use when handling 10X scATAC or 10X Multiome (paired RNA+ATAC) data, performing per-cell QC, choosing between ArchR/Signac/SnapATAC2 ecosystems, building per-cluster consensus peaksets, integrating with paired scRNA-seq, doublet detection (AMULET vs ArchR vs scDblFinder), or running pseudobulk differential accessibility per cluster.

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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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Detects aberrant splicing in single rare-disease patients vs a control panel using FRASER 2.0 (Bioconductor; Beta-binomial autoencoder on Intron Jaccard Index, default delta cutoff 0.1, q hyperparameter), OUTRIDER (gene-level outlier expression via autoencoder denoising), LeafcutterMD (Dirichlet-multinomial outlier mode of LeafCutter for annotation-free junctions), and DROP (Snakemake pipeline integrating FRASER2 + OUTRIDER + monoallelic expression for clinical diagnostics). The statistical model is fundamentally different from differential splicing — single-sample-vs-cohort outlier detection rather than two-group comparison. Standard tool in EU rare-disease (Solve-RD) and NIH UDN programs. Use when applying RNA-seq to undiagnosed Mendelian disease, validating predicted splice variants in clinical samples, or detecting cryptic splicing in disease tissue.

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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.

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Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when comparing alignment quality, measuring sequence divergence, and analyzing evolutionary patterns.

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Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.

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Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling, analyzing per-position read data, or calculating allele frequencies.

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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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集群数据管理 Skill —— 涵盖数据使用规范、压缩优化、数据共享（ACL）、文件扫描与清理、文件完整性校验、genozip 基因组压缩等全流程。Use when the user asks about: managing data on the HPC cluster, compressing genomic files (fq/bam/vcf), sharing data between users/groups, scanning for large files or cleaning up disk space, checking file integrity (md5/gzip/bam), using genozip, checking disk quota, or any data lifecycle management task on the NCPGR HPC cluster.

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Use when a carrier asks which KPIs to track, how to build a fleet dashboard, what targets to set, cadence for reviewing metrics (daily / weekly / monthly / quarterly), and how to operationalize data into actions. Covers safety, operations, financial, driver, and customer KPIs.

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Use this skill when the user asks about trucking rate negotiation — cost-plus pricing, market rate benchmarking via DAT/Truckstop, fuel surcharge math, how to negotiate with brokers/shippers, when to walk away, contract pricing vs spot rates. Reference DAT Rate Analytics + freight market reports.

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Use this skill when an inspector requests ELD records during a roadside inspection. Covers the three required transfer methods, what data must be transmitted, and common failure modes.

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Use this skill when the user asks where to find specific information at fmcsa.dot.gov — the SAFER (Safety and Fitness Electronic Records System), Carrier Snapshot, Compliance Safety Accountability (CSA) data, PSP (Pre-Employment Screening Program), Clearinghouse, Unified Carrier Registration (UCR), MCS-150 update, complaints, DataQs, and the FMCSA Portal login. Reference fmcsa.dot.gov.

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Use this skill to understand what CSA data the public sees about your carrier and how that affects business. Covers SAFER, accessibility, and what's hidden vs visible.

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Use this skill when the user asks about Electronic Logging Device (ELD) compliance under 49 CFR 395.20-38 — ELD mandate, AOBRD vs ELD transition, ELD exemptions, ELD malfunctions, 8-day paper backup, ELD certification on FMCSA registered list, data file integrity, edits + annotations, driver portability, and how to handle ELD failures at roadside. Cite 49 CFR 395.20-395.38.

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Use this skill when the user asks about DataQ — FMCSA's data review system at dataqs.fmcsa.dot.gov — for disputing inspection violations, crash records, or other entries that appear in a carrier's CSA / SMS score. Covers Request for Data Review (RDR) process, success rates, common dispute grounds, what evidence to attach, timeline expectations, and how successful disputes reduce BSI (BASIC Severity Indicator) scores. Cite 49 CFR 392.7 and the FMCSA DataQs User Guide.

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Use this skill to explain to customers/sales prospects why FMCSA CSA scores are not available in real-time. Covers the SAFER refresh cycle and what 'real-time' actually means for CSA data.

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Use this skill when the user asks how to investigate a CMV accident — what to do at the scene, the first 24 hours, evidence preservation, who to call, preventability determination, ELD data preservation, dash cam review, witness interviews, working with insurance + attorney, and how to build a learning culture from incidents. Reference 49 CFR 392.7 + insurance industry best practices.

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S3, multipart uploads, CDN integration, and presigned URLs for file storage. Activate on: file upload, S3, presigned URL, multipart upload, CDN, blob storage, image upload, media storage. NOT for: data warehouse storage (use lakehouse-architect), database design (use dimensional-modeler).

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