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Clinical-trial readout analysis: pull the trial, evaluate the readout with AdCom-style scrutiny (endpoints, statistics, subgroups, missing data, safety, tolerability/persistence), place it in a cross-trial comparison lattice vs SoC and class peers, and size the stock reaction with historical grounding. The judgment core for binary biotech events.
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Generate persistent, explorable 3D worlds/environments with Marble by World Labs — from text, a single image, multiple images, video, or a 360 panorama, plus coarse-structure blocking with Chisel. Use this skill when a task needs a navigable 3D scene, VR/immersive backdrop, virtual-production environment, previz set, game-blockout, or web/engine-ready Gaussian splat or mesh, and you must choose an input mode, a Marble model, an export format, and a plan/API route, then review world quality. Covers the Marble web app and the World API, editing/expansion, output formats and what each supports downstream, import into Unity/Unreal/Blender/Houdini/web, pricing/credits, capability limits, and rights/licensing. Not for flat text-to-image, text-to-video clips, or real-time on-the-fly world models (Marble outputs are downloadable, static 3D environments).
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Generate, reference, and conversationally edit short videos with Google's Gemini Omni Flash through the Gemini Developer API or Gemini Enterprise Agent Platform. Use when a task specifically needs Gemini Omni video, multimodal reference roles, time-directed prompting, audio-aware generation, Interactions API state, or a precise comparison with Veo, Nano Banana, consumer Gemini, or gateway routes.
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Build and operate rights-aware Bria FIBO and FIBO Lite image-generation workflows with structured prompts, reference images, asynchronous status handling, webhooks, cost gates, and safe artifact downloads. Use when a user asks for Bria/FIBO generation, refinement, inspiration, reproducibility, hosted API integration, or a licensed-data image workflow; do not use for FIBO Edit, video, generic image editing, or third-party FIBO gateways.
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Provider-independent workflow for producing terminal, IDE, documentation, browser, desktop, and application demonstration videos. Use when choosing authentic capture, browser automation, synthetic UI, or hybrid treatment; scripting actions and narration; resetting demo state; protecting secrets and personal data; directing cursor/callouts; creating crop variants; and reviewing workflow truth, readability, accessibility, and provenance.
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Use this skill to turn generated, captured, scanned, or modeled 3D output into production-ready standalone assets for DCC, real-time engine, web, or interchange delivery. It covers requirements, topology repair, scale and axes, UVs, PBR baking, LODs, static and skeletal readiness, rig handoff, optimization, glTF/USD/FBX delivery, validation, QA, and rights/provenance. Do not use it for provider-specific generation prompts, full scene/world building, mocap operation, or exact CAD/manufacturing work.
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Facilitate a structured conversation to define requirement standards for a project — epic and feature definitions, scenario structure, AC format, priority notation, status workflow, and naming conventions. Produces a formal requirement-standards.md that the requirement-quality atom reads via config resolution, customising its embedded defaults for the team's product process. Use when setting up a new project, defining product standards, or when the user says 'set up requirement standards', 'define feature standards', 'configure requirement forge', 'define how features should be structured', or 'requirement forge refiner'.
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Architectural thinking partner for an existing repository — scans the codebase, conducts a structured interview, agrees on current architectural state and recommended direction, and produces a shareable insights document. Scoped to one repository, module, or folder. Does not execute transformation — it orients. Use when the user says 'assess my codebase architecture', 'what direction should my codebase go', 'architecture compass', 'understand my architecture', 'audit architecture drift', 'architectural assessment', or 'help me understand what is wrong with my codebase'.
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Writes and executes SQL queries from simple SELECTs to complex multi-table JOINs, aggregations, and subqueries. Use when the user asks to query a database, write SQL, run a SELECT statement, retrieve data, filter records, or generate reports from database tables.
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Computes and interprets treatment effect measures (OR, RR, RD, HR, NNT) with calibrated confidence intervals (Wilson, Newcombe, Miettinen-Nurminen, MOVER, profile likelihood, Bender NNT) and reports marginal vs conditional estimands per FDA 2023 covariate adjustment guidance. Use when reporting treatment effects in confirmatory trials, comparing effect sizes across studies, or constructing forest plots.
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Perform differential expression analysis using edgeR in R/Bioconductor. Use for analyzing RNA-seq count data with the quasi-likelihood F-test framework, creating DGEList objects, normalization, dispersion estimation, and statistical testing. Use when performing DE analysis with edgeR.
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Process Hi-C read pairs using pairtools. Parse alignments, filter duplicates, classify pairs, and generate contact statistics from Hi-C sequencing data. Use when processing raw Hi-C read pairs.
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End-to-end flow cytometry workflow from FCS files to differential analysis. Orchestrates compensation, transformation, gating/clustering, and statistical testing with CATALYST/diffcyt. Use when processing flow or mass cytometry data end-to-end.
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Sequence-based deep learning for ATAC-seq using chromBPNet, BPNet, scBasset, or EnFormer. Use when correcting Tn5 bias with neural networks beyond k-mer models, predicting per-base accessibility profiles, scoring in silico variant effects at GWAS or rare-variant SNPs, discovering motifs via DeepLIFT/TF-MoDISco from a trained model, or generating cell-type-specific accessibility predictions for unobserved cell states.
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Calculate read depth and coverage across genomic intervals using bedtools genomecov and coverage. Generate bedGraph files, compute per-base depth, and summarize coverage statistics. Use when assessing sequencing depth, creating coverage tracks, or evaluating target capture efficiency.
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Per-CpG differential methylation testing from bisulfite sequencing count data or beta-value matrices. Covers beta and M-value computation, coverage filtering, statistical tests (Welch t-test, Mann-Whitney, limma, DSS beta-binomial), multiple testing correction, and effect size calculation. Use when comparing methylation at individual CpG sites between experimental groups from WGBS, RRBS, or targeted bisulfite sequencing.
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Perform differential expression analysis of miRNAs between conditions using DESeq2 or edgeR with small RNA-specific considerations. Use when identifying miRNAs that change between treatment groups, disease states, or developmental stages.
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Designs and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiplex (enCas12a, DeWeirdt 2021), in4mer 4-guide-array Cas12a (Esmaeili Anvar N et al 2024 Nat Commun 15:3577) and the Inzolia paralog-pair library, paralog-buffering detection (Dede 2020 Genome Biol; Thompson 2021 Cell Reports 36:109597), genetic-interaction (GI) scoring as observed_double_LFC minus expected_additive_double_LFC, synthetic-lethal and synthetic-rescue interaction interpretation, the half-of-essentiality buffered by paralogs phenomenon, multiplex screen statistical analysis with MAGeCK MLE interaction terms, and the relationship to single-cell combinatorial Perturb-seq. Use when designing a paralog or pathway-pair screen, choosing between paired-Cas9 (Big Papi) and Cas12a multiplex (Inzolia), interpreting genetic interaction scores, identifying synthetic-lethal targets for drug development, or scaling beyond single-gene CRISPR screens.
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Test whether two or more traits share a causal variant at a locus using Bayesian colocalization (coloc.abf, coloc.susie, HyPrColoc, moloc, eCAVIAR, SMR/HEIDI, PWCoCo, SharePro). Use when integrating GWAS with eQTL/sQTL/pQTL/mQTL, distinguishing shared causal variants from LD-driven coincidence, handling allelic heterogeneity, choosing between single-causal vs multi-causal methods, picking PP.H4 thresholds, running sensitivity over p12, or harmonising summary statistics for colocalization.
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Detect somatic and germline copy number variants from targeted, exome, and whole-genome sequencing with CNVkit, a read-depth caller that combines on-target and off-target (antitarget) coverage. Covers panel-of-normals construction, flat-reference tumor-only calling, hybrid/amplicon/WGS modes, CBS vs HMM segmentation selection, purity-aware integer calling, and reconciliation against GATK and allele-specific callers. Use when calling CNVs from hybrid-capture panels or exomes, deciding whether CNVkit (depth-only) is the right tool versus an allele-specific caller, building a panel of normals, diagnosing flat-reference false positives, or interpreting log2 ratios into copy-number states.
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Performs time-to-event analysis for clinical trials including Cox proportional hazards regression with PH diagnostics, restricted mean survival time (RMST) under non-PH, competing risks via Fine-Gray vs cause-specific Cox, weighted log-rank and MaxCombo for non-proportional hazards, recurrent events (Andersen-Gill, PWP, WLW), and interval-censored data. Use when analyzing time-to-event endpoints (OS, PFS, DOR, TTR, TTNT) in oncology or other clinical trials.
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Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. Use when identifying unknown sequences, finding homologs, picking the correct BLAST program (blastn/blastp/blastx/tblastn/tblastx/psiblast/megablast/dc-megablast), interpreting Karlin-Altschul E-values, avoiding the max_target_seqs trap (Shah 2019), choosing composition-based statistics, or limiting searches by organism. Covers RID lifecycle, database choice (nt/nr/refseq_select/swissprot), word-size and CBS taxonomy.
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End-to-end post-GWAS causal inference pipeline orchestrating heritability partitioning, genetic correlation, Mendelian randomization with CHP-aware sensitivity (CAUSE / LHC-MR), colocalization, fine-mapping with SuSiE / FOCUS, mediation, TWAS triangulation, cis-pQTL drug-target MR, effector-gene prioritization (L2G / PoPS / cS2G), and GenomicSEM common-factor GWAS. Use when triangulating causal inference across multiple complementary methods, prioritizing tissues via stratified LDSC, nominating or de-risking drug targets, mapping a lead SNP to a candidate effector gene, modeling shared genetic architecture across correlated traits, or producing a STROBE-MR-compliant publication-grade evidence battery from GWAS summary statistics.
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Reads, validates, and prepares CDISC SDTM and ADaM clinical trial data for analysis. Covers SDTM domain joins (DM, AE, EX, VS, LB, DS), ADaM architecture (ADSL, BDS, OCCDS, ADTTE) with traceability, treatment-emergent AE conventions, baseline derivation, SUPPQUAL/NSV handling, Define-XML 2.1, and Pinnacle 21 / CORE validation. Use when working with clinical trial datasets in CDISC SDTM/ADaM format, preparing analysis-ready data, or validating for regulatory submission.
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