「sca」の検索結果

Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER, MEME-ChIP (STREME, CentriMo, TOMTOM, FIMO), monaLisa, and AME. Handles background selection (GC-matched, dinucleotide-shuffled, Markov order-2, peak-flanks), motif databases (JASPAR 2024 CORE PWMs, JASPAR 2026 deep-learning collection, HOCOMOCO v12, HOMER built-in), centrally-enriched motif testing, and differential motif analysis. Use when identifying TF binding motifs in peaks, testing for known TF enrichment, scanning for motif instances, comparing motif content between conditions, or interpreting motifs from deep learning models.

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Performs molecular similarity searching using Tanimoto, Tversky, Dice, and cosine coefficients on bit/count fingerprints with explicit choice rules for symmetric vs asymmetric measures, scaffold-hopping vs lead-optimization regimes, activity-cliff diagnosis, and large-library nearest-neighbor methods (BulkTanimoto, Annoy MHFP6, USRCAT). Use when ranking compounds by structural resemblance to a query, clustering libraries, finding analogs, or diagnosing activity cliffs.

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Normalizes ChIP-seq data using exogenous spike-in (ChIP-Rx with Drosophila chromatin per Orlando 2014 / Egan 2016; E. coli carryover for CUT&RUN/CUT&Tag). Distinguishes RRPM from Rx-Input scaling, integrates with DiffBind / DESeq2 / edgeR / csaw via sizeFactors and DiffBind library-size vectors, and applies the Patel et al 2024 *Nat Biotechnol* review's failure-mode framework to validate that normalization is correctly applied at the read level (not peak counts). Use when global signal shifts are expected (HDACi, BETi, EZH2i, dosage, target knockdown), when ChIPseqSpikeInFree detects post-hoc shifts, or when validating internal-control regions before publication.

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Segments the genome into chromatin states from combinatorial histone modification and chromatin factor ChIP-seq data. Uses ChromHMM (multivariate HMM on binarized signal, v1.27), Segway (Dynamic Bayesian Network on continuous signal), EpiSegMix (flexible-distribution HMM with duration modeling, 2024), EpiLogos (multi-biosample visualization), IDEAS (cell-type-aware joint), and full-stack ChromHMM (Vu Ernst 2022) for cross-cell-type segmentations. Handles state-count selection (15 vs 18 vs 25 states), binarization choice, OverlapEnrichment / NeighborhoodEnrichment downstream analysis, and cross-biosample integration. Use when learning chromatin states from a histone mark panel, characterizing learned states by genomic feature enrichment, or comparing chromatin landscapes across cell types.

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Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticity dialect, vector binding, atom map indices, and reactive/PAINS/REOS/Brenk/Aldridge filter catalogs. Use when filtering compounds by pharmacophore features, functional groups, scaffold matches, or screening for assay-interference / structural alerts.

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Analyzes CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data. Handles SEACR vs MACS2 peak calling (with the btaf375 2025 benchmark guidance), pA-MNase vs pA-Tn5 vs pAG-Tn5 chimera differences, E. coli spike-in carryover normalization, IgG-only control logic (no input), characteristic fragment-size signatures (25-75 bp for CUT&Tag), and lower depth requirements (5M reads typical vs 25M for ChIP). Use when calling peaks from CUT&RUN/CUT&Tag, scaling by E. coli spike-in carryover, choosing SEACR norm mode, or comparing CUT&RUN/Tag results to traditional ChIP.

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Builds QSAR / QSPR models using chemprop D-MPNN, MolFormer, Uni-Mol, ChemBERTa, random forest baselines, and Gaussian processes with explicit handling of OECD 5 principles, applicability domain (kNN, leverage, conformal prediction, Mahalanobis), scaffold-balanced splits, ensemble uncertainty, calibration (Platt, isotonic), feature importance (SHAP, atomic attribution), and prospective validation. Use when building target-specific predictive models from in-house bioassay data, ADMET endpoints, or selectivity profiles.

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Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al 2022/2023 J Chem Inf Model 63:147-158), Pharmer / Pharmit (search), and PharmacoForge (diffusion-based generation, Flynn et al 2025 Front Bioinform), covering ligand-based pharmacophore (from active set alignment) and receptor-based pharmacophore (from binding pocket geometry). Explicit handling of feature types, geometric tolerances, partial matching, and pharmacophore-based virtual screening. Use when identifying scaffold-hopping candidates, building shape-and-feature search queries, or transferring SAR across chemotypes.

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Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or MAnorm2. Distinguishes three distinct normalization problems (composition bias, trended bias, global shifts) and matches each to its appropriate fix including spike-in scaling. Use when comparing ChIP-seq binding between experimental conditions, choosing normalization for global vs local changes, integrating spike-in data, or reconciling DiffBind/DESeq2 disagreement.

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LSF 作业内存不足时的调整技能。当作业因内存不够被挂起(SSUSP)或终止(EXIT/MEMLIMIT)时，通过调整 bsub -n 的节点（核数/slot）数量来扩大可用内存——可用运行内存 ≈ 5GB × 申请节点数。当用户说内存不足、作业被杀、OOM、需要更大内存，或排查 EXIT/SSUSP 作业时，配合 lsf-ncpgr skill 一起使用。

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Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audit (library prep, read length, depth, replicates), STAR 2-pass cohort-style alignment, junction saturation curves and discovery plateau detection, novel-vs-known junction ratio diagnostics, junction-overhang distribution, splice-site strength scoring (MaxEntScan intrinsic + SpliceAI context-aware), strandedness verification, GENCODE basic vs comprehensive choice, and rRNA contamination screening. Splicing analysis is more demanding than DGE on read length, depth, library prep, alignment strategy, and annotation choice — failures silently bias PSI estimates and inflate novel-junction false positives. Use when evaluating data suitability for splicing analysis, troubleshooting low event detection, or designing sequencing experiments where AS is a primary endpoint.

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Infer cis-regulatory connections (peak-to-peak co-accessibility) from scATAC-seq using Cicero, ArchR getCoAccessibility, or SCENIC+. Use when linking enhancer accessibility to promoter accessibility, identifying enhancer-gene pairs from chromatin alone (without paired RNA), running gene-regulatory inference combining ATAC + RNA, or comparing predicted regulatory contacts against Hi-C/Micro-C ground truth.

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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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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 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 you receive an IFTA audit notification and need to defend your records. Covers preparation, common arguments, and dispute escalation.

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Use when a carrier asks about electric trucks — Tesla Semi, Freightliner eCascadia, Volvo VNR Electric, Peterbilt 579EV, range, charging, total cost of ownership, regulatory pushes (CARB ACT, ACF), incentives, infrastructure, depot vs en-route charging, and which routes/applications are EV-ready today.

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Use when a manager, dispatcher, or safety director needs to have a coaching conversation with a driver — about a safety event (harsh brake, hard turn, distraction), an HOS violation, a customer complaint, a missed delivery, repeated minor incidents, or to deliver positive recognition. Covers conversation structure, language, documentation, and escalation.

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Use this skill when the user asks how to manage a trucking carrier's public reputation — handling a major accident in the news, social media + Glassdoor + Indeed reviews, customer disputes that escalate, employee disputes, regulator perception, and how to communicate during a crisis. Reference industry PR + crisis communication practices.

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Analyze a Coval adversarial / red-team testing report and turn it into an agent-hardening plan. Use when a user provides a Coval report URL, report export, run IDs, screenshots, or a per-scenario scorecard from an adversarial sweep and wants evidence-backed next steps such as prompt/guardrail changes, refusal hardening, verification fixes, escalation routing, or expanded attack coverage.

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Delegating work down to subagents: briefs, report statuses, independent review. Use when writing an implementer or verifier brief, dispatching a subagent to build, fix, or verify work you own, or a subagent reports DONE, blocked, or concerns. NOT for campaign-scale doctrine (use campaign-pattern).

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Find and identify the CBasePlayerController_SetPawn and CBasePlayerController_GetPawn functions in CS2 binary using IDA Pro MCP. Use this skill when reverse engineering CS2 server.dll / libserver.so to locate the pawn-assignment routine by scanning for its distinctive multi-register-push prologue directly (no pre-resolved anchor needed), confirming uniqueness and byte-level match against a known reference signature. Trigger: CBasePlayerController_SetPawn, CBasePlayerController_GetPawn

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Find and identify the CBaseEntity_GetChangeAccessorPathInfo_1 virtual function in CS2 binary using IDA Pro MCP. Use this skill when reverse engineering CS2 server.dll or libserver.so to locate the second GetChangeAccessorPathInfo override by scanning CBaseEntity vtable slots near the known CBaseEntity_GetChangeAccessorPathInfo_2 slot for an implementation identical to CBaseEntity_GetChangeAccessorPathInfo_2. Trigger: CBaseEntity_GetChangeAccessorPathInfo_1

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When the user wants to audit, review, or diagnose SEO issues on their site. Also use when the user mentions "SEO audit," "technical SEO," "why am I not ranking," "SEO issues," "on-page SEO," "meta tags review," or "SEO health check." For building pages at scale to target keywords, see programmatic-seo. For adding structured data, see schema-markup.

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