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Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS, Sequenza, and other callers. Covers genome-wide and per-chromosome log2 scatter plots, B-allele-frequency/minor-allele-fraction tracks, ideograms, cohort heatmaps, circos views, and caller-native plots. Use when creating publication CNV figures, choosing which plot answers a given question, diagnosing a wrong diploid baseline visually, displaying loss of heterozygosity, or deciding what depth-only plots cannot reveal.

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Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DTL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signals (STRIDE / Williams 2017 ALE-rooting), counting DTL events per branch, refining noisy gene trees against a species tree, modeling WGD events jointly with DTL, or producing publication-grade gene-family histories for phylogenomic / comparative analyses.

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Runs cis-pQTL Mendelian randomization for drug-target validation using UKB-PPP (Olink), deCODE (SomaScan), Fenland, INTERVAL, ARIC, and FinnGen-PPP proteomes plus colocalization triangulation, phenome-wide on-target adverse-effect scans, cross-platform Olink/SomaScan replication, and PAV (protein-altering variant) sensitivity. Use when nominating or de-risking a drug target from plasma-proteome GWAS, mimicking pharmacological inhibition via cis-pQTL instruments, separating shared-causal from LD-confounded signal under the Schmidt 2020 cis-MR framework, screening on-target adverse phenotypes pheWAS-style, or producing publication-grade STROBE-MR plus PP.H4 evidence for a target gene.

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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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Maps GWAS-implicated loci to candidate effector (causal) genes by integrating variant-to-gene (V2G) features via Open Targets L2G (Mountjoy 2021), MAGMA gene-based association (de Leeuw 2015), FUMA SNP2GENE, cS2G combined SNP-to-gene scores (Gazal 2022), Polygenic Priority Scores (PoPS, Weeks 2023), FLAMES, INQUISIT, DEPICT, and enhancer-gene predictors (ABC, ENCODE-rE2G). Use when narrowing a GWAS lead locus to a candidate causal gene, picking between proximity, eQTL-based, and similarity-based prioritizers, integrating multi-evidence streams (fine-mapping, colocalization, ABC enhancer-gene, distance, chromatin), reconciling discordant L2G vs PoPS calls, prioritizing tissue-specific eQTL evidence, or triangulating across at least three independent lines of evidence for a publication-grade effector-gene nomination.

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Estimate SNP heritability and partition it across functional annotations, cell types, and loci from GWAS summary statistics or individual-level genotypes. Implements LDSC, stratified LDSC with the baseline-LD model, Finucane 2018 cell-type prioritization, LDAK SumHer, HDL, HESS local heritability, BOLT-REML, GCTA-GREML, graphREML, and Popcorn cross-population genetic correlation. Use when computing total h2_SNP from summary stats, partitioning heritability across functional categories, prioritizing trait-relevant tissues or cell types from ENCODE/Roadmap chromatin marks, reconciling LDSC vs LDAK enrichment estimates, computing local heritability with HESS, estimating genetic correlation between traits, or producing publication-grade enrichment with calibrated sensitivity to model assumptions.

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Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven track plots), Gviz (R browser-style), EnrichedHeatmap (ComplexHeatmap-based), ChIPseeker tag heatmaps, and IGV batch screenshots. Handles bigWig normalization choices (CPM, BPM, RPGC, spike-in scaled), bamCompare operations (log2 ratio, subtract, SES), k-means clustering of heatmaps for biological subgrouping, and spike-in-scaled tracks for global-shift experiments. Use when generating publication-quality ChIP-seq signal heatmaps, profile plots, genome-browser tracks, or comparing samples visually.

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When the user requests to add academic papers to a BibTeX bibliography file while maintaining format consistency and sourcing from appropriate repositories. This skill handles 1) Reading existing BibTeX files to understand formatting conventions, 2) Searching for academic papers across multiple sources (OpenReview for conference papers, arXiv for preprints), 3) Extracting proper BibTeX metadata from conference pages or arXiv entries, 4) Determining appropriate citation format (@article vs @inproceedings) based on publication venue, 5) Appending new entries while preserving existing file structure and formatting. Triggers include requests to 'add to ref.bib', 'update bibliography', 'cite papers', or when working with academic reference files.

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Use when you need to apply Java concurrency best practices — including thread safety fundamentals, ExecutorService thread pool management, concurrent design patterns like Producer-Consumer, asynchronous programming with CompletableFuture, immutability and safe publication, deadlock avoidance, virtual threads and structured concurrency, scoped values, backpressure, cancellation discipline, and observability for concurrent systems. Part of the skills-for-java project

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Use this skill when the user requests to review, analyze, critique, or summarize academic papers, research articles, preprints, or scientific publications. Supports comprehensive structured reviews covering methodology assessment, contribution evaluation, literature positioning, and constructive feedback generation. Trigger on queries involving paper URLs, uploaded PDFs, arXiv links, or requests like "review this paper", "analyze this research", "summarize this study", or "write a peer review".

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Generates professional infographics with 21 layout types and 20 visual styles. Analyzes content, recommends layout×style combinations, and generates publication-ready infographics. Use when user asks to create "infographic", "信息图", "visual summary", "可视化", or "高密度信息大图".

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Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with decision algorithms). Supports GRADE evidence grading, statistical analysis (hazard ratios, survival curves, waterfall plots), biomarker integration, and regulatory compliance. Outputs publication-ready LaTeX/PDF format optimized for drug development, clinical research, and evidence synthesis.

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Start AEM Workflows on AEM as a Cloud Service using all available triggering mechanisms. Use when starting workflows manually via the Timeline UI, programmatically via WorkflowSession.startWorkflow(), via the HTTP Workflow API, through Manage Publication, or passing initial metadata and payload to a workflow instance.

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Publish, deactivate, and delete AEM content programmatically via the Cloud Service Replication API (com.day.cq.replication). Covers single-path and bulk activation, preview-tier targeting with AgentFilter, synchronous/async options, ReplicationStatus checks, permission validation, workflow process steps, and replication event handling. Use when the user needs to publish pages, activate or deactivate content, check replication status, build workflow steps that replicate content, listen to replication events, query batch publication state, or work with Replicator, ReplicationOptions, or ReplicationStatusProvider in AEM Cloud Service.

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Use when publishing, unpublishing, replicating, or activating/deactivating content in AEM 6.5 LTS. Covers Quick Publish, Manage Publication, tree activation, bulk content activation, package replication, workflow-based approval, scheduled activation/deactivation (on/off time), dispatcher flush, and the programmatic Replication Java API for AEM publish instances.

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Use when a Spark branch or pull request needs final diff hygiene, validation selection, commit scope, remote topology, and readiness checked before publication.

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Use when coding interviews, focus groups, or open-ended responses with AI assistance, when a codebook needs building or auditing, when intercoder reliability must be computed, or when qualitative quotes need integrity checks before publication.

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Monitor competitor blogs and industry publications to surface content opportunities

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