'flags' 검색 결과

Identifies non-coding RNAs (tRNA, rRNA, snoRNA, snRNA, riboswitches, sRNAs) using Infernal covariance-model search against Rfam, tRNAscan-SE 2.0 for tRNA, barrnap for rRNA, and ARAGORN for tmRNA, plus the small-RNA-seq boundary for miRNA and the transcript-assembly boundary for lncRNA. Covers the structure-conserved-not-sequence-conserved principle (why BLAST fails), GA-threshold and clan-competition correctness, tRNAscan-SE domain modes and pseudogene flags, rDNA copy-number collapse, and why homology annotation is a recall floor. Use when performing genome-wide ncRNA annotation, choosing the right tool for an RNA class, or interpreting ncRNA counts.

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Performs proximity operations on genomic intervals with bedtools (closest, window, flank, slop) and pybedtools - nearest-feature queries with signed/strand-aware distance, fixed-radius window searches, strand-aware promoter construction, and interval extension. Covers the closest -d/-D a/b/ref/-t/-k/-io/-iu/-id flags, the -D ref strand sign-flip, silent chromosome-end clipping in slop/flank, -t all tie double-counting, and the critical distinction between a geometry answer (nearest TSS) and a biology answer (which gene an element regulates). Use when assigning peaks or variants to genes, defining promoters from a gene model, building distance-to-TSS distributions, finding features within a window, or extending intervals - and when deciding whether nearest-gene is a fair prior (GWAS locus) or a trap (distal enhancer).

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Detects TAD boundaries from balanced Hi-C contact matrices via the diamond-window insulation score (cooltools insulation) and HiCExplorer hicFindTADs, returning a continuous log2 insulation track, valley-prominence boundary_strength, and Li/Otsu-thresholded is_boundary flags across a list of window sizes. Covers the multi-scale window sweep (sub-TAD to compartment-domain), why the boundary is reproducible but the domain partition is not, cross-condition comparison via differential SCORE not differential partition, and the insulation-vs-compartment orthogonality. Use when calling TADs or domain boundaries, computing insulation scores, choosing a window size, ranking boundary strength, comparing boundaries across conditions, or annotating CTCF-backed boundaries; route domain rendering to hic-visualization and boundary-feature overlap to genome-intervals.

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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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Analyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct RNA, R10.4.1+) long-read RNA-seq with full-isoform resolution. Tools include FLAIR (correct/collapse/quantify/diffSplice for PacBio + ONT), IsoQuant (de-novo or annotation-guided isoform discovery 2024 SOTA), Bambu (annotation-aware Bayesian discovery + quantification with Novel Discovery Rate), SQANTI3/SQANTI-LR (isoform classification: FSM/ISM/NIC/NNC + artifact flags), rMATS-long (event calling on long-read isoforms), and minimap2 (-ax splice:hq for HiFi; -ax splice -k14 for ONT cDNA; add -uf only for direct RNA or stranded cDNA preps). Solves microexon detection, recursive splicing, complex multi-exon isoforms, and DTU without transcript-quantification uncertainty. Use when short-read AS limitations (anchor length, complex isoforms, microexons, recursive splicing, transcript ambiguity) demand full-isoform resolution.

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Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.

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Use this skill when selecting a Consortium/Third-Party Administrator (C/TPA) for drug + alcohol testing program management. Covers what services they provide, what to look for, and red flags.

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Run the pytest test suite with coverage. Accepts optional filter flags. Use after making changes to verify nothing broke.

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Recipe for THE DOOR LAW (every record the UI names opens; every detected problem ships its fix) and THE INVENTORY LAW. Use before building or fixing a surface that names a record or flags a problem (cell, row, dialog, badge, warning, id, count), or on 'no link to X', 'why can't I click this', 'dead end', EntityRef, peek. NOT for page chrome (use core-route-headers).

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Find and identify the CCSPlayerController_Respawn virtual function in CS2 binary using IDA Pro MCP. Use this skill when reverse engineering CS2 server.dll or libserver.so to locate the Respawn vfunc slot by RTTI-walking the CCSPlayerController vtable and confirming the candidate's decompiled body performs a full controller-state reset (networked flags, per-round fields, comeback/damage-info bookkeeping) rather than any other lifecycle vfunc. Trigger: CCSPlayerController_Respawn

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Runs a session's fan-out — splits a large request into tiered, recoverable units, dispatches and reconciles them against the repo. Trigger when work needs many agents or spans many repos or files (rebuild, re-architect, sweep, migrate, 'do all of this'); when subagents would launch with no model or effort set; for the plan table (units, models, tokens, meters) before launch; to resume a unit that died or hit a usage limit; when units would share a repo; or say dispatchwright (plan, dispatch, resume, audit, refresh). Tiers come from its own table (scoutwright flags it stale); pacing, pacewright's; hooks, rigwright's; schedules, agentwright's.

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The science of learning through controlled experimentation. A/B testing isn't about picking winners—it's about building a culture of validated learning and reducing the cost of being wrong. This skill covers experiment design, statistical rigor, feature flagging, analysis, and building experimentation into product development. The best experimenters know that every test, positive or negative, teaches something valuable. Use when "a/b test, experiment, hypothesis, statistical significance, sample size, feature flag, variant, control, treatment, p-value, conversion rate, test winner, split test, experimentation, testing, statistics, feature-flags, hypothesis, growth, optimization, learning, validation" mentioned.

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Centralized configuration management with feature flags and dynamic refresh.

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Azure App Configuration SDK for Java. Centralized application configuration management with key-value settings, feature flags, and snapshots.

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Azure App Configuration SDK for Python. Use for centralized configuration management, feature flags, and dynamic settings.

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Legal contract analysis using CUAD dataset (41 risk categories). Supports NDA, SaaS, M&A, employment, payment/merchant, and finder/broker agreements. Identifies red flags, suggests redlines, compares to market standards.

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86 peer-reviewed behavioral frameworks applied to every Maxim output. The flagship moat.

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Use when you need to check feature flag states, compare channels, or debug why a feature behaves differently across release channels.

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Guide for Private and Internal member testing strategies. Use when you need to test private or internal members, configure InternalsVisibleTo, or evaluate testability design. Covers design-first thinking, reflection testing, strategy pattern refactoring, AbstractLogger pattern, and decision frameworks. Keywords: private method testing, internal testing, InternalsVisibleTo, reflection testing, GetMethod BindingFlags, Meziantou.MSBuild.InternalsVisibleTo, testability design, strategy pattern refactoring, testability

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Configures Options pattern, user secrets, and feature flags. IOptions<T>, FeatureManagement.

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Flags agent mistakes in .NET code -- async misuse, NuGet errors, deprecated APIs, DI.

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Detect abuse of elevation control mechanisms including UAC bypass, sudo exploitation, and setuid/setgid manipulation by monitoring registry modifications, process elevation flags, and unusual parent-child process relationships.

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Performs statistical analysis of Zeek conn.log connection intervals to detect C2 beaconing patterns. Uses the ZAT library to load Zeek logs into Pandas DataFrames, calculates inter-arrival time standard deviation, and flags periodic connections with low jitter. Use when hunting for command-and-control callbacks in network data.

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[BETA] AEM Cloud Service expert skill — handle an explicitly-unbounded query (`p.limit=-1` predicate or JCR `setLimit(-1)`): bound it when capping is provably safe, otherwise flag it for human pagination. Use for "bound my query", "unbounded query", "query causing OOM", or a scan that flags `p.limit=-1`. Top CSO OOM cause: an unbounded result set traversed in a loop fills the heap and saturates the instance. The analyzer locates the explicit markers; the recipe triages each by how the result is consumed — single-result → 1, already-bounded list → N, iterate-all on the request path → escalate. Never silently cap a result the caller reads in full. This skill is in beta. Verify all outputs before applying them to production projects.

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