Web & Frontend

fridrichmethod Bundle

Orchestrates the end-to-end bulk short-read alternative-splicing pipeline from FASTQ to differential splicing, chaining fastp QC, cohort-consistent STAR 2-pass alignment (one shared junction DB), junction QC, event-level differential splicing (rMATS-turbo + leafcutter, optional MAJIQ V3), parallel isoform-level DTU (Salmon -> tximport dtuScaledTPM -> DRIMSeq/DEXSeq -> stageR), and sashimi visualization. Use when committing the annotation GTF and a shared 2-pass junction database for the whole cohort, keeping the analysis at splice-aware resolution (never collapsing to gene), choosing event-level vs isoform-level DTU and reconciling them, applying the stageR two-stage gene->transcript FDR, or off-ramping to splice-variant / outlier / long-read / single-cell splicing. Hands mechanism to the alternative-splicing component skills; not a re-teach of any single step.

fridrichmethod Bundle

End-to-end flow, spectral, and mass cytometry (CyTOF) pipeline from raw FCS files to differentially abundant/expressed cell populations. Orchestrates the read -> compensate/unmix -> transform -> QC -> doublet-removal -> cluster-or-gate -> annotate -> diffcyt DA/DS chain with flowCore/CATALYST/diffcyt, branching on instrument type and on clustering-vs-gating. Use when processing a cytometry experiment end-to-end, deciding the pipeline path for an instrument, or wiring the flow-cytometry component skills into one analysis with valid sample-level statistics.

fridrichmethod Bundle

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.

fridrichmethod Bundle

Detects spatially variable genes, spatial autocorrelation, and cell-type colocalization for spatial transcriptomics using Squidpy with PySAL/esda for local statistics. Use when choosing an SVG method by its null and scaling (SpatialDE/SPARK GP variance-component vs SPARK-X/nnSVG linear vs Moran/Geary graph autocorrelation); separating genes that are spatially variable because of cell-type composition from genes regulated within a cell type; choosing the right autocorrelation statistic (global Moran/Geary vs Getis-Ord hot/cold spots vs local LISA and its FDR trap); and choosing a colocalization null strong enough to defeat the abundance/compartment confound (conditional or toroidal vs the weak Squidpy default permutation).

fridrichmethod Skill

Python library for genomic interval ML. Train/apply region2vec embeddings turning BED regions into vectors, index interval datasets for ML, search embedding space with BEDSpace, and evaluate embedding quality. Use for chromatin accessibility clustering, regulatory element classification, and cross-sample region comparison.

fridrichmethod Bundle

Orchestrates gene regulatory network inference from processed single-cell data to regulons and in-silico perturbation, via pySCENIC (RNA-only GRNBoost2 -> cisTarget -> AUCell), SCENIC+ (multiome cisTopic -> pycistarget -> eGRN), and CellOracle perturbation. Use when recognizing that an inferred GRN is UNDIRECTED by default and reporting only the evidence tier delivered (co-expression vs motif-pruned vs enhancer-resolved vs perturbation), matching species/assembly/namespace across the TF-list + cisTarget DB + motif2TF annotation, feeding RAW counts of the cleaned/doublet-free/batch-controlled cells (never imputed/batch-corrected values), running the cisTarget pruning that buys directionality (modules are not regulons without it), or choosing the RNA-only vs multiome path. Hands mechanism to the gene-regulatory-networks component skills; not a re-teach of any single step.

fridrichmethod Bundle

Orchestrates imaging mass cytometry from raw MCD acquisitions to patient-level spatial analysis, chaining steinbock preprocessing, Mesmer/Cellpose segmentation, single-cell quantification, phenotyping, and squidpy spatial statistics. Use when committing the panel + segmentation frame + pixel size (every per-cell number is a mask-bounded pixel average), compensating channel spillover on PIXELS before segmentation but running REDSEA lateral-spillover on the per-cell table AFTER segmentation, using arcsinh cofactor 1 (not the suspension-CyTOF 5), and aggregating to the PATIENT before any cross-condition test (cells and ROIs from one patient are not independent replicates). Hands mechanism to the imaging-mass-cytometry component skills; not a re-teach of any single step.

fridrichmethod Bundle

Orchestrates bottom-up proteomics from a search engine's output (MaxQuant/FragPipe/DIA-NN) to differential protein abundance with limma/DEqMS/MSstats. Use when committing the search database + acquisition mode (DDA vs DIA) up front, re-controlling FDR at PSM AND peptide AND protein-group level (not just PSM), removing contaminant/reverse rows and inspecting RAW distributions before normalizing, bridging cross-plex TMT with an IRS reference channel, modeling MNAR missingness rather than downshift-imputing on/off proteins, batching as a covariate (not pre-subtracted), and testing with treat()/DEqMS. Hands mechanism to the proteomics component skills; not a re-teach of any single step.

fridrichmethod Bundle

Orchestrates an end-to-end long-read structural-variant pipeline - basecalling to minimap2 alignment (platform-matched preset) to Sniffles2/cuteSV/pbsv calling to optional assembly-based calling (dipcall/PAV) to two-step .snf cohort merging to Truvari benchmarking - chaining ONT and PacBio HiFi runs while handing the SV signal mechanism off to the component skills. Use when running a long-read SV workflow from reads to a benchmarked callset, choosing the minimap2 preset and SV caller by platform and goal, deciding when long reads are worth it for the insertions and repeat-mediated SVs short reads physically miss, building a joint-genotyped cohort with the two-step .snf design, or parameterizing a Truvari benchmark against GIAB HG002 Tier 1 plus CMRG. Not for the SV signal mechanism itself (see variant-calling/structural-variant-calling) or short-read SV.

fridrichmethod Bundle

Orchestrates the end-to-end bisulfite/EM-seq methylation pipeline from FASTQ to differentially methylated regions, chaining Trim Galore/fastp QC, Bismark alignment + deduplication, methylation calling, methylKit coverage-filtering/normalization, and selection-aware DMR detection (dmrseq/DSS). Use when gating the run on bisulfite conversion (lambda + pUC19 controls) BEFORE any beta value, committing the genome build + library directionality once, keeping mate-overlap deduplicated (--no_overlap), M-bias-trimming from the plot, filtering coverage before testing, choosing a count model (beta-binomial/DSS) over a bare-beta t-test, or using a region-selection-aware FDR (dmrseq/DSS) rather than raw methylKit tiles. Hands mechanism to the methylation-analysis component skills; not a re-teach of any single step.

fridrichmethod Bundle

Orchestrates VERTICAL bulk multi-omics integration (RNA + protein + methylation on the SAME samples) from harmonization to a validated result, routing to MOFA2 (shared factors), mixOmics/DIABLO (predictive signature), or SNF (patient subtypes). Use when confirming the correspondence is vertical (not horizontal same-features-different-cohorts), joining on a stable sample primary key rather than cbind on assumed row order, normalizing each omic in its OWN space and equalizing block variance BEFORE stacking (or the widest omic hijacks every shared factor), correcting batch ONCE in one place, and validating in a HELD-OUT cohort because in-cohort CV at n<<p is optimistically biased. Hands mechanism to the multi-omics-integration component skills; not a re-teach of any single step.

26zl Bundle

Tests Android inter-process communication (IPC) through intents for vulnerabilities including intent injection, unauthorized component access, broadcast sniffing, pending intent hijacking, and content provider data leakage. Use when assessing Android app attack surface through exported components, testing intent-based data flows, or evaluating IPC security. Activates for requests involving Android intent security, IPC testing, exported component analysis, or Drozer assessment.

paulasilvatech Skill

Apply Salesforce UI component standards for Lightning Web Components, Aura, Visualforce, SLDS 2, WCAG 2.1 AA, secure Apex access, component communication, XSS, CSRF, FLS/CRUD, view state, and Jest tests. Use when building or reviewing Salesforce LWC, Aura components, Visualforce pages, or Apex controllers used by UI components.

paulasilvatech Skill

Design, implement, test, and troubleshoot Backstage permission policies, basic and resource permissions, conditional decisions, rules, frontend authorization, and plugin integration. Use when implementing RBAC, ABAC, resource filtering, action visibility, or fixing authorization failures.

paulasilvatech Bundle

Build production scroll animations and scroll effects in vanilla JS, React, or Next.js using GSAP ScrollTrigger or Framer Motion/Motion v12. Use when asked for scroll-triggered reveals, parallax, pinned sections, horizontal scroll, scrubbed timelines, ScrollSmoother, matchMedia, useScroll, useTransform, useSpring, whileInView, variants, sticky sections, Apple-like scroll, progress bars, entrance animations, or GitHub Copilot prompts for scroll motion.

paulasilvatech Bundle

Plan, architect, scaffold, validate, and prepare custom Backstage plugins and modules using official Backstage documentation. Use when the user asks for new, legacy, or dual frontend plugins, backend plugins, backend modules, catalog processors, entity providers, scaffolder actions, search collators, auth providers, permission policies, TechDocs addons, common packages, node packages, plugin ADRs, architecture, validation, or community publication preparation.

paulasilvatech Skill

Design, edit, validate, and troubleshoot Backstage app configuration, environment overlays, schemas, secrets, integrations, and frontend visibility. Use when working with app-config YAML, BACKSTAGE_ENV, config:check, deployment overrides, or configuration errors.

paulasilvatech Bundle

Create a React Container/Presentation component under src/components with TypeScript, Storybook, SCSS module, ui/features classification, optional Mantine replacement, and validation. Use when explicitly asked for a Container/Presentation component or when running /react-container-presentation-component.

paulasilvatech Skill

Instrument Backstage frontend plugins with meaningful Analytics API events and tests while avoiding duplicate BUI navigation events or UI noise. Use when adding or reviewing captureEvent, AnalyticsContext, event taxonomy, noTrack overrides, or analytics behavior.

paulasilvatech Skill

Add new frontend-system support to an existing Backstage plugin while retaining its legacy entry point. Use when published or shared plugins need dual compatibility, alpha exports, PageBlueprint extensions, route reuse, and both old and new app consumers.

paulasilvatech Bundle

Migrate Backstage app or plugin UI from Material-UI to Backstage UI with version-checked component mappings, CSS setup, accessibility, analytics, styling, and visual validation. Use when replacing @material-ui imports, MUI icons, makeStyles, or adopting BUI.

paulasilvatech Skill

Fully migrate a Backstage frontend plugin to the new frontend system and remove legacy support. Use when performing internal or intentionally breaking migrations from createPlugin to createFrontendPlugin, new route refs, blueprints, PageLayout, and legacy dependency removal.

paulasilvatech Skill

Choose and implement Backstage framework extension points, core backend services, frontend blueprints, service refs, modules, lifecycle, auth, permissions, schedulers, tracing, metrics, and generated API references. Use when designing plugin architecture or selecting supported framework APIs.

paulasilvatech Bundle

Create a personal daily focus board in a browser canvas from a self-contained HTML template. Use when the user wants to plan their day, get organized, stay focused, kick off a work session, track task progress, add counters for pages/pomodoros/reps, use Focus mode, or save an end-of-day recap with localStorage persistence.

paulasilvatech Skill

Embed before/after screenshots and annotated images in pull request descriptions so reviewers can inspect visible changes quickly. Use this skill when a PR changes layout, styling, CSS, charts, dashboards, data visualizations, UI components, forms, modals, error messages, CLI output, or log formatting.

paulasilvatech Skill

Prepare a structured HTML day-prep file for tomorrow or a requested date by pulling Outlook calendar details through WorkIQ, classifying meetings, detecting conflicts and day-fit issues, cross-referencing workspace tasks, finding learning and deep-work slots, and producing productivity recommendations. Use this skill when the user says "prepare me for tomorrow", "prep me for Friday", asks what a date looks like, or requests weekly planning.

paulasilvatech Skill

Design, implement, review, and package Power Apps Component Framework code components for model-driven apps, canvas apps, and Power Pages. Use when the user asks about PCF manifests, lifecycle APIs, dataset or field controls, React platform libraries, PAC CLI tooling, ALM, performance, accessibility, security, testing, or deployment.

paulasilvatech Skill

This skill should be used when the user asks to "test this website", "run exploratory testing", "check for accessibility issues", "verify the login flow works", "find bugs on this page", or requests automated QA testing. Triggers on web application testing scenarios including smoke tests, accessibility audits, e-commerce flows, and user flow validation using ScoutQA CLI. Use this skill proactively after implementing web application features to verify they work correctly.

paulasilvatech Bundle

Convert Markdown files to HTML similar to `marked.js`, `pandoc`, `gomarkdown/markdown`, or similar tools; or writing custom script to convert markdown to html and/or working on web template systems like `jekyll/jekyll`, `gohugoio/hugo`, or similar web templating systems that utilize markdown documents, converting them to html. Use when asked to "convert markdown to html", "transform md to html", "render markdown", "generate html from markdown", or when working with .md files and/or web a templating system that converts markdown to HTML output. Supports CLI and Node.js workflows with GFM, CommonMark, and standard Markdown flavors.

paulasilvatech Skill

Prevent generic web and iOS interfaces by extracting product-specific design decisions from repository evidence and UIZZE's public catalogue of 800,000+ real web and iOS screens. Use this skill when building, refactoring, or reviewing UI, when asked to browse https://uizze.com before choosing a layout, or when the user wants a hard finish gate against interchangeable dashboard cards, filler metrics, vague headings, and generic calls to action.

paulasilvatech Bundle

Toolkit for interacting with and testing local web applications using Playwright. Use when verifying frontend functionality, debugging rendered UI behavior, capturing screenshots, inspecting browser logs, or automating a local web workflow.

paulasilvatech Bundle

Build web-based game engines and games with HTML5 Canvas, WebGL, SVG, CSS, and JavaScript. Use when creating 2D or 3D games, implementing game loops, physics, collision detection, sprites, tilemaps, controls, audio, multiplayer with WebRTC or WebSockets, optimization, or publishing workflows.

paulasilvatech Bundle

Migrate React string refs, ref="name" assignments, and this.refs.name access to React.createRef(), callback refs, or child ref forwarding. Use this skill when migrating React 18.3.1 warnings or React 19 removals involving single refs, multiple refs, list refs, callback refs, or refs passed to child components.

paulasilvatech Skill

Design, implement, test, and troubleshoot Backstage permission policies, basic and resource permissions, conditional decisions, rules, frontend authorization, and plugin integration. Use when implementing RBAC, ABAC, resource filtering, action visibility, or fixing authorization failures.

paulasilvatech Skill

Design, edit, validate, and troubleshoot Backstage app configuration, environment overlays, schemas, secrets, integrations, and frontend visibility. Use when working with app-config YAML, BACKSTAGE_ENV, config:check, deployment overrides, or configuration errors.

paulasilvatech Bundle

Instrument Backstage frontend plugins with meaningful Analytics API events and tests while avoiding duplicate BUI navigation events or UI noise. Use when adding or reviewing captureEvent, AnalyticsContext, event taxonomy, noTrack overrides, or analytics behavior.