Results for “complexity”

Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair tracking, antibody-lot metadata recording, replicate concordance via deepTools multiBamSummary + plotCorrelation, IP enrichment QC via plotFingerprint and per-transcript IP/input ratio distributions, library-complexity saturation curves via PreSeq c_curve / lc_extrap, and the explicit do-NOT-deduplicate convention for standard non-UMI MeRIP. Use when preparing paired IP and input BAM files for exomePeak2 / MeTPeak / MACS3 peak calling, evaluating MeRIP replicate concordance and IP enrichment, deciding whether to deduplicate (standard MeRIP typically NOT — see Tips), choosing genome-vs-transcriptome alignment for downstream peak vs m6Anet workflows, recording antibody clone and lot metadata for downstream cross-batch reconciliation, detecting failed IPs via saturation curves and IP/input distribution shape, or generating IP-over-Input bigWig tracks for downstream visualisation.

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Quality control for pooled CRISPR screens covering library representation, Gini index, log-skew, replicate Pearson and Spearman concordance, essentialome precision-recall AUC against CEGv2 (Hart 2017), Cas9 cut-toxicity diagnostics, copy-number amplicon detection (Aguirre 2016 / Munoz 2016), bottleneck propagation through plasmid pool, infection, selection, and endpoint stages, MOI verification, and DepMap-style screen-quality scoring. Use when assessing screen quality before hit calling, deciding whether to repeat or rescue a screen, diagnosing low-confidence hits, choosing between MAGeCK / BAGEL2 / Chronos based on quality grade, picking a normalization strategy from QC signatures, or evaluating whether an in-vivo screen retained adequate library complexity.

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Comprehensive quality control for CLIP-seq libraries (eCLIP, iCLIP, iCLIP2, PAR-CLIP) covering library complexity (preseq), FRiP, IDR replicate reproducibility, read-distribution metagene, SMInput vs IgG control rationale, rRNA / snoRNA contamination, fragment-length distribution, and ENCODE-compliance thresholds. Use when assessing whether a CLIP library passed, deciding lenient vs stringent peak thresholds, comparing replicates with IDR rescue and self-consistency ratios, or distinguishing failed IP from over-amplified library.

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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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Introduce people to AI, agentic AI, and AI skills with appropriate pedagogy for any audience. Covers LLM analogies, progressive complexity paths, aha-moment demos, audience-tailored explanations, workshop design, and overcoming emotional barriers to AI adoption. Activate on 'explain AI', 'introduce AI', 'AI workshop', 'AI demo', 'teach AI', 'AI literacy', 'onboard to AI', 'AI evangelism', 'explain agentic', 'explain skills to', 'AI training session', 'AI onboarding'. NOT for teaching ML engineering (use ai-engineer), not for building AI features (use ai-engineer), not for prompt engineering (use prompt-engineer), not for building training data pipelines.

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Use when a Spark implementation needs an evidence-based review for correctness, ownership, compatibility, failure handling, maintainability, and unnecessary complexity.

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Strip designs to their essence by removing unnecessary complexity. Great design is simple, powerful, and clean. Use when the user asks to simplify, declutter, reduce noise, remove elements, or make a UI cleaner and more focused.

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Cost optimization patterns for LLM API usage — model routing by task complexity, budget tracking, retry logic, and prompt caching.

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Analyze chatmode or prompt files and recommend optimal AI models based on task complexity, required capabilities, and cost-efficiency

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Build self-serve acquisition and expansion motions. Use when deciding PLG vs sales-led, optimizing activation, driving freemium conversion, building growth equations, or recognizing when product complexity demands human touch. Includes the parallel test where sales-led won 10x on revenue.

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Analyze a screen recording of a manual process and produce targeted, working automation scripts. Extracts frames and audio narration from video files, reconstructs the step-by-step workflow, and proposes automation at multiple complexity levels using tools already installed on the user machine.

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Route a task by complexity and run the gated Forge pipeline (research → plan → implement → ship). Use when the user runs /forgemaster or wants the full guided feature pipeline.

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Simplify a bounded code area when the user explicitly requests behavior-preserving refactoring or a named complexity/readability problem is the accepted task; do not trigger automatically after implementation, during every review, for adjacent cleanup, or when behavior may change.

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Use when a Spark implementation needs an evidence-based review for correctness, ownership, compatibility, failure handling, maintainability, and unnecessary complexity.

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Advanced API exploitation methodology focused on business logic abuse and sophisticated attack patterns that bypass traditional security controls. Covers business logic bypass through API call chaining and workflow manipulation. Addresses GraphQL-specific attacks including batching for credential brute-force, query depth exploitation, and introspection abuse. Includes pagination exploitation for data exfiltration, webhook hijacking for SSRF and data interception, and resource exhaustion through algorithmic complexity attacks. Covers race conditions in API transactions using parallel request techniques. Provides comprehensive JWT manipulation including algorithm confusion, kid injection, jku/x5u abuse, and claim tampering. Details API key leakage detection across source repositories, client-side code, and error messages. Covers undocumented endpoint discovery through predictable naming, debug routes, and source map analysis. Tooling includes Arjun, ParamSpider, jwt_tool, and GraphQL Voyager. Designed for a...

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Gmail, Calendar, Drive, Docs, Sheets — NO Google Cloud Console required. Just OAuth sign-in. Zero setup complexity vs traditional Google API integrations.

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Firebase gives you a complete backend in minutes - auth, database, storage, functions, hosting. But the ease of setup hides real complexity. Security rules are your last line of defense, and they're often wrong. Firestore queries are limited, and you learn this after you've designed your data model. This skill covers Firebase Authentication, Firestore, Realtime Database, Cloud Functions, Cloud Storage, and Firebase Hosting. Key insight: Firebase is optimized for read-heavy, denormalized data. I

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