Results for “profiling”

Generates complete programmed-cell-death (PCD) / regulated-cell-death (RCD) bulk-transcriptome oncology research designs from a user-provided disease and mechanism theme. Always use this skill whenever a user wants to design, plan, or structure a cancer bioinformatics study built around cell-death patterns, tumor microenvironment, prognostic modeling, immune landscape analysis, mutation profiling, and computational drug sensitivity. Covers five study patterns (mechanism-gene-set, subtype-discovery, prognostic-signature, immune-response stratification, translational drug-hypothesis) and always outputs four workload configs (Lite / Standard / Advanced / Publication+) with recommended primary plan, step-by-step workflow, figure plan, validation strategy, minimal executable version, publication upgrade path, and a strictly verified reference literature retrieval layer with real references only.

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Use when profiling CPU/memory hot paths, generating flame graphs, or capturing JFR/perf evidence.

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Use when mapping code paths, entrypoints, and likely hot files before profiling.

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Optimize Python code for reduced memory usage and improved memory efficiency. Use when asked to reduce memory footprint, fix memory leaks, optimize data structures for memory, handle large datasets efficiently, or diagnose memory issues. Covers object sizing, generator patterns, efficient data structures, and memory profiling strategies.

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Zep memory server integration for long-term conversation memory and user profiling

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Entity and fact extraction for user profiling and personalization

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Session-scoped hook lifecycle management with enable/disable/status controls, execution profiling, and color-coded performance alerts.

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Master systematic debugging techniques, profiling tools, and root cause analysis to efficiently track down bugs across any codebase or technology stack. Use when investigating bugs, performance issues, or unexpected behavior.

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Optimize end-to-end application performance with profiling, observability, and backend/frontend tuning. Use when coordinating performance optimization across the stack.

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Optimize multi-agent systems with coordinated profiling, workload distribution, and cost-aware orchestration. Use when improving agent performance, throughput, or reliability.

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Generates an x-ray.md pre-audit report covering overview, enhanced threat model (protocol-type profiling, git-weighted attack surfaces, temporal risk analysis, composability dependency mapping), invariants, integrations, docs quality, test analysis, and developer/git history. Triggers on 'x-ray', 'audit readiness', 'readiness report', 'pre-audit report', 'prep this protocol', 'protocol prep', 'summarize this protocol'.

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Estimates Fabric capacity cost before a migration by profiling Spark, SQL, Power BI, and Real-Time workloads, then recommending SKU size and comparing Reserved, Pay-As-You-Go, and Autoscale billing. Use only for capacity sizing and pricing questions, not for general migration or connectivity work.

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Reverse-engineer a company's sales and marketing tech stack from public signals. Detects CRMs, cold email tools, people databases, ad pixels, email delivery services, and outbound sending domains via DNS records, website source inspection, Apify technology profiling, blacklist checks, and public spam complaint searches. Works on single companies or batches. Outputs a structured markdown report per company.

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Assembles a genome de novo from Illumina short reads with SPAdes (isolate/careful/sc/meta/plasmid/rna modes), MEGAHIT (low-memory, huge datasets), Unicycler (bacterial finishing/hybrid), MaSuRCA (large hybrid), ABySS (Bloom-filter), and Platanus (heterozygous diploids), using multi-k de Bruijn graphs. Covers the repeat-resolution limit, why N50 plateaus at the genome not the depth, GenomeScope2 k-mer profiling first, the heterozygosity/haplotig trap, error-correction erasing rare alleles, GC dropout, and NG50/auN/BUSCO reporting. Use when assembling a bacterial isolate, fungal, small-eukaryotic, single-cell, or metagenome genome from Illumina reads, or when deciding whether short reads can even produce the assembly being asked for.

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Profiles a genome from raw reads BEFORE assembly with a k-mer spectrum (KMC or Jellyfish histogram), then models it with GenomeScope2 to estimate genome size, heterozygosity, repeat content, and ploidy, and Smudgeplot to infer ploidy from heterozygous k-mer pairs (diploid AB vs triploid AAB vs tetraploid AABB). Covers choosing k via Merqury best_k.sh, the k-mer-coverage vs sequencing-coverage confusion, reading het/repeat/contamination/organelle peaks, why noisy ONT must not be used for counting, and how the estimate becomes the NG50 denominator, the Flye -g value, the hifiasm --hom-cov/purge setting, and the 1.5-2x-too-big haplotig sanity check. Use when starting any de novo assembly, deciding whether short reads can work, estimating genome size for an unknown organism, diagnosing ploidy, or sanity-checking an assembly's size against expectation.

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Identify direct miRNA-target interactions from AGO HITS-CLIP, AGO-CLEAR-CLIP (chimeric reads), HEAP (Halo-Ago2 mouse), chimeric eCLIP / miR-eCLIP (deep miRNA-target profiling), or CLASH using chimeric-read processing pipelines, seed-pairing analysis, and 3' auxiliary pairing rules. Use when distinguishing direct miRNA targets from indirect, integrating CLIP-derived target maps with TargetScan / miRDB / DIANA predictions, applying canonical 7mer-8mer seed matching with 3' UTR context, or recovering miRNA-mRNA chimeras at scale.

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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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Use when an Apple-platform app feels slow, memory grows, battery drains, or ANY performance issue needs diagnosing. Covers memory leaks, profiling, Instruments workflows, retain cycles, optimization.

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Use when the user wants automated performance profiling, headless Instruments analysis, or CLI-based trace collection.

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Debug iOS apps and profile performance using LLDB, the interactive Memory Graph Debugger, and Instruments. Use for crashes, retain-cycle inspection, hangs, build failures, and generic CPU, memory, energy, or network profiling. Use ios-memgraph-analysis for .memgraph capture, leaks CLI ownership paths, or persistent heap growth; use ios-ettrace-performance for ETTrace capture and JSON.

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Integrate Core ML models in iOS apps for on-device machine learning inference. Covers model loading (.mlmodel, .mlpackage, .mlmodelc), predictions with auto-generated classes and MLFeatureProvider, compute unit configuration (CPU, GPU, Neural Engine), MLTensor, VNCoreMLRequest, MLComputePlan, multi-model pipelines, and deployment strategies. Use when loading Core ML models, making predictions, configuring compute units, or profiling model performance.

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Use when capturing or analyzing ETTrace profiles for a focused iOS launch or runtime flow, including exact-build dSYM UUID matching, Simulator or device capture, processed per-thread flamegraph JSON, sampled inclusive/exclusive time, unresolved symbols, and comparable verification. Use debugging-instruments or swiftui-performance for generic profiling instead.

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Speed up local parfor, parfeval, or spmd by switching to a thread-based parallel pool. Trigger when a user describes slow or disappointing local parallel performance, even if they don't mention threads. Symptoms: parfor on a laptop/workstation is slower than expected or "only slightly faster than for"; parfor scales poorly with the number of workers; ticBytes/tocBytes, the Parallel Pool dashboard, mpiprofile, or system tools show large per-worker data transfer; large broadcast variables or sliced inputs make iterations slow; opening a process pool dominates a short workload; user mentions serialisation or data transfer overhead. Also trigger on any question about whether code or a function works on a thread pool. For non-pool MATLAB performance work (vectorisation, preallocation, profiling), defer to matlab-optimize-performance.

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Use DuckDB from MATLAB via Database Toolbox (R2026a+) as a non-math operations engine on large tabular files (CSV/Parquet/JSON) and as a zero-config embedded database. Use when connecting to DuckDB, querying CSV, Parquet, and JSON files directly with SQL, reducing or profiling large data before MATLAB analysis, creating portable development databases, or installing DuckDB extensions. Triggers on: DuckDB, duckdb(), large CSV/Parquet/JSON, file too large for readtable, filter/aggregate at source, deduplicate, reduce before analysis, profile large file, persistent file import, analytical engine, SQL on CSV, SQL on Parquet, SQL on JSON, query CSV with SQL, query Parquet with SQL, run SQL on files, SQL queries on files, query files directly, SQL without database, in-process SQL.

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