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Corrects the gene-independent copy-number artifact in CRISPR-Cas9 screens (Aguirre 2016 / Munoz 2016 Cancer Discov) where amplified loci appear essential from DNA-damage burden of simultaneous cuts. Covers the p53-dependent G2-arrest mechanism, CRISPRcleanR (Iorio 2018) unsupervised pre-hoc correction, CERES (Meyers 2017) joint CN + gene-effect model, Chronos (Dempster 2021) DepMap-standard population-dynamics + CN model with lowest residual bias, the decision tree by data availability, the Spearman LFC-vs-CN diagnostic, focal-amplification examples (ERBB2 in HER2+, MYC in colorectal, FGFR1 in head and neck), and CRISPRi/a alternatives that bypass the artifact. Use when screening cancer cell lines, diagnosing essentiality at amplified loci, choosing CRISPRcleanR / CERES / Chronos, deciding whether CN correction is needed before MAGeCK / BAGEL2 / drugZ, or switching from Cas9 to CRISPRi.

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Pull pre-computed ortholog calls from public databases (OrthoDB, Ensembl Compara, OMA browser, eggNOG, PANTHER, KEGG Orthology, HomoloGene) via their REST APIs. Use when orthologs are already curated upstream, when the question is "what is the X ortholog of Y" rather than "how to infer orthology de novo", when batch-mapping gene IDs across species, or when comparing the resources for consensus calls. Encodes confidence-level semantics, 1:1 vs 1:many vs many:many, HomoloGene deprecation, and when to defect to de novo computation.

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Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying variants with allelic effects on TF binding, fine-mapping causal regulatory variants, validating deep-learning variant predictions, or characterizing cis-acting regulatory effects.

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Creates sashimi-style plots showing RNA-seq read coverage and splice junction counts using ggsashimi (general-purpose, condition-grouped overlays), rmats2sashimiplot (rMATS-output-aware), MAJIQ-VOILA (LSV posteriors interactive HTML), leafviz (leafcutter clusters Shiny), Jutils (tool-agnostic heatmaps and sashimi for rMATS/leafcutter/SUPPA2/MAJIQ output), or pyGenomeTracks (multi-track publication figures). Tool choice depends on the upstream differential-splicing tool's output format and the publication vs interactive use case. Use when visualizing specific splicing events, validating differential splicing calls, or producing publication-quality figures.

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Configure an AI agent to send OpenTelemetry traces to Coval. Use when a user wants to add Coval tracing, instrument an agent for simulations or conversation monitoring, make traces show up in Coval, handle SIP/PSTN/WebSocket trace correlation, or replace the one-command wizard with a security-reviewable manual setup.

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A test skill for e2e testing

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Integrate Convex static self hosting into existing apps using the latest upstream instructions from get-convex/self-hosting every time. Use when setting up upload APIs, HTTP routes, deployment scripts, migration from external hosting, or troubleshooting static deploy issues across React, Vite, Next.js, and other frontends.

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Identify all files a specific author contributed to on a branch vs its upstream, tracing code through renames. Use when asked who edited what, what code an author contributed, or to audit authorship before a merge. This skill should be run as a subagent — it performs many git operations and returns a concise table.

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Serves as a reviewer of the codebase with instructions on looking for Apple App Store optimizations or rejection reasons.

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[BETA] AEM Cloud Service expert skill — add explicit connect/read/socket timeouts to outbound HTTP clients constructed without one (Apache HttpClient 4.x/5.x, OkHttp, JDK java.net.http.HttpClient), including the JDK per-request read timeout on HttpRequest. Use for "add HTTP timeouts", "this external/outbound call has no timeout", or a scan that flags a timeout-less client. Highest-frequency CSO outage cause: a client on default (effectively infinite) timeouts holds request threads on a slow upstream until the Jetty pool saturates and the site goes down. The analyzer locates timeout-less construction sites; mechanical per-library remediation applies CSO-backed default timeouts (recipe.md). This skill is in beta. Verify all outputs before applying them to production projects.

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Hunt Host Header Injection — password reset poisoning → ATO, web cache poisoning via unkeyed Host/X-Forwarded-Host, routing-based SSRF (Host picks upstream → cloud metadata/internal services), path-override SSRF/ACL-bypass (X-Original-URL/X-Rewrite-URL), OAuth redirect_uri/issuer poisoning, and absolute-URL link poisoning in emails. High to Critical when it reaches ATO or mass cache poisoning. Built on public Host-header research (PortSwigger 'Practical web cache poisoning' + James Kettle, and the classic password-reset-poisoning class). Use on any forgot-password flow, CDN/reverse-proxy-fronted app, OAuth/OIDC endpoint, or absolute-URL-in-email feature.

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Social engineering attack techniques beyond email phishing for authorized red team and physical penetration testing engagements. Covers pretexting methodology (persona creation, authority and urgency psychological triggers, rapport building), vishing (voice phishing via caller ID spoofing, IVR system exploitation, VoIP infrastructure setup with Twilio/Asterisk), smishing (SMS-based phishing, carrier gateway abuse, short code impersonation), physical social engineering (tailgating and piggybacking, RFID badge cloning with Proxmark3, lock picking and bypass, dumpster diving for sensitive documents), USB drop attacks (Rubber Ducky keystroke injection, Bash Bunny multi-vector payloads, O.MG cable covert implants, BadUSB firmware attacks), watering hole attack planning and execution, and OSINT-driven targeting (LinkedIn harvesting, organizational chart reconstruction, employee pattern analysis). Integrates with the Social Engineering Toolkit for attack automation, Proxmark3 for RFID/NFC cloning, USB Rubber Duc...

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Comprehensive offensive methodology for software supply chain attacks covering the full kill chain from reconnaissance through exploitation. Addresses dependency confusion across npm, PyPI, and NuGet ecosystems where internal registry override allows an attacker to inject malicious packages that shadow private dependencies. Covers typosquatting techniques for popular packages, compromised package injection via maintainer account takeover or social engineering, and build system attacks through Makefile injection, setup.py install hooks, and npm postinstall scripts. Extends into CI/CD artifact tampering where build outputs are replaced or modified in transit, code signing abuse through stolen or self-signed certificates, upstream repository compromise via commit injection or force-push to trusted repos, and container image supply chain attacks including base image trojaning and registry confusion. Maps to MITRE ATT&CK T1195.001 (Supply Chain Compromise: Compromise Software Dependencies and Development Tools...

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Fetch, preview, merge, and test GitHub PRs locally. Great for trying upstream PRs before they're merged.

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Efficiently bring upstream NanoClaw updates into a customized install, with preview, selective cherry-pick, and low token usage.

日本語の概要は準備中です。原文の説明を表示しています。

Check for and apply updates to installed skill branches from upstream.

日本語の概要は準備中です。原文の説明を表示しています。