Web & Frontend

holobiomicslab Skill

Use when after identifying pairwise feature connections via correlation and retention-time windowing, when you need to partition the feature space into coherent groups where each feature has sufficient connectivity to its peers.

holobiomicslab Skill

Use when after loading a Metaboprep object containing metabolomic abundance data when you need to: (1) identify samples that are statistical outliers in multivariate metabolite space; (2) determine the number of statistically significant principal components;

holobiomicslab Skill

Use when you have cloned or loaded a deep-learning architecture extension (e.g., chemprop-IR) and need to verify that its feature extraction component can be instantiated and produces correctly shaped feature tensors before integrating it into a larger pipeline or training loop.

holobiomicslab Skill

Use when you have a log2-normalized, zero-mean and unit-variance standardized intensity matrix of metabolite features (rows=metabolites, columns=samples) and need to compute a single activity score per pathway that reflects the coordinated expression behavior of all metabolites assigned to that.

holobiomicslab Skill

Use when after normalizing and log-transforming lipidomics abundance data (e.

holobiomicslab Skill

Use when after preprocessing and aligning 2D chromatogram data (baseline correction, smoothing, peak alignment) and after running m_prcomp multiway PCA on the joined chromatogram matrix.

holobiomicslab Skill

Use when you have a feature list from LC-MS preprocessing (e.g., asari output) and have already identified all pairwise feature matches to isotope and adduct patterns. Apply this skill when you need to separate feature matches into disjoint empirical compounds—i.

holobiomicslab Skill

Use when you have ATAC-seq BAM files aligned to a reference genome, a set of transcription factor motif locations (BED format), and you need to determine which motifs are actually occupied by proteins in your cell type or condition.

holobiomicslab Skill

Use when when reconstructing or validating the ColumnFinder component in mwtab, you need to assess whether the combined NameMatcher.dict_match and ValueMatcher.series_match operations are correctly populating database-ID columns. Apply this skill after defining NameMatcher patterns (e.

holobiomicslab Skill

Use when you have loaded raw Agilent Unknowns Analysis CSV output with required columns (Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, File.

holobiomicslab Skill

Use when you have raw GC-MS output from Agilent Unknowns Analysis (a .CSV with columns Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, File.

holobiomicslab Skill

Use when your input is a normalized, centered gene expression matrix with many genes (e.g., 12,000+) and you need to validate whether reducing to a smaller number of principal components (e.g., 10) preserves pathway enrichment statistics (pathway scores and p-values from geseca or fgsea).

holobiomicslab Skill

Use when you have ATAC-seq BAM alignments with classified motif sites (bound vs. unbound based on chromatin accessibility or binding thresholds) and wish to detect and visualize the characteristic Tn5 insertion depletion signal (footprints) around transcription factor binding sites.

holobiomicslab Skill

Use when you have pre-processed chromatin accessibility data (ATAC-seq or DNAse-seq) with chromVAR deviations already computed for individual cells or bulk samples across multiple cell types or conditions, and you need to identify which transcription factor motifs exhibit significant differential.

diegosouzapw Bundle

Astro Web Framework workflow skill. Use this skill when the user needs Build content-focused websites with Astro — zero JS by default, islands architecture, multi-framework components, and Markdown/MDX support and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

diegosouzapw Bundle

UI Accessibility Audit workflow skill. Use this skill when the user needs Audit a StyleSeed-based component or page for WCAG 2.2 AA issues and apply practical accessibility fixes where the code makes them safe and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

diegosouzapw Bundle

Wiki Q&A workflow skill. Use this skill when the user needs Answer repository questions grounded entirely in source code evidence. Use when user asks a question about the codebase, user wants to understand a specific file, function, or component, or user asks \"how does X work\" or \"where is Y defined\" and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

diegosouzapw Bundle

Astro Web Framework workflow skill. Use this skill when the user needs Build content-focused websites with Astro — zero JS by default, islands architecture, multi-framework components, and Markdown/MDX support and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

tomevault-io Bundle

CIS Controls v8.1 critical security controls for static HTML/CSS websites on GitHub Pages Use when this capability is needed.

holobiomicslab Skill

Use when you have completed LC–MS/MS feature detection and annotation (via MZmine2/3 and GNPS/SIRIUS/CANOPUS), have compiled a taxonomically annotated metadata table, and need to rank extracts by their likelihood of containing novel chemistry.

holobiomicslab Skill

Use when you have sparse, single-cell or bulk ATAC/DNAse-seq data from multiple cell types or conditions (e.g., GM vs H1 cell lines), pre-filtered and GC-bias-corrected, with motif-to-peak matches already computed.

holobiomicslab Skill

Use when after instantiating a specXplore dashboard session layer with a loaded session data object from disk, before conducting visual exploration of LC-MS/MS spectral data.

diegosouzapw Bundle

Rayden Code Skill workflow skill. Use this skill when the user needs Generate React code with Rayden UI components using correct props, tokens, and premium layout patterns and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

diegosouzapw Bundle

UI Component workflow skill. Use this skill when the user needs Generate a new UI component that follows StyleSeed Toss conventions for structure, tokens, accessibility, and component ergonomics and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

diegosouzapw Bundle

UI Review workflow skill. Use this skill when the user needs Review UI code for StyleSeed design-system compliance, accessibility, mobile ergonomics, spacing discipline, and implementation quality and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

diegosouzapw Bundle

UI Tokens workflow skill. Use this skill when the user needs List, add, and update StyleSeed design tokens while keeping JSON sources, CSS variables, and dark-mode values in sync and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

diegosouzapw Bundle

Functional Programming in React workflow skill. Use this skill when the user needs Practical patterns for using fp-ts with React - hooks, state, forms, data fetching. Works with React 18/19, Next.js 14/15 and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

diegosouzapw Bundle

UI Review workflow skill. Use this skill when the user needs Review UI code for StyleSeed design-system compliance, accessibility, mobile ergonomics, spacing discipline, and implementation quality and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

diegosouzapw Bundle

UI Tokens workflow skill. Use this skill when the user needs List, add, and update StyleSeed design tokens while keeping JSON sources, CSS variables, and dark-mode values in sync and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

diegosouzapw Bundle

Astro Performance Playbook workflow skill. Use this skill when the user needs Astro-specific performance optimizations for 95+ Lighthouse scores. Covers critical CSS inlining, compression, font loading, and LCP optimization. Use when optimizing Astro site performance, improving Astro Lighthouse scores, or configuring astro-critters. Do NOT use for non-Astro sites (use perf-web-optimization or core-web-vitals) or running Lighthouse audits (use perf-lighthouse) and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

diegosouzapw Bundle

UI Accessibility Audit workflow skill. Use this skill when the user needs Audit a StyleSeed-based component or page for WCAG 2.2 AA issues and apply practical accessibility fixes where the code makes them safe and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

diegosouzapw Bundle

Wiki Q&A workflow skill. Use this skill when the user needs Answer repository questions grounded entirely in source code evidence. Use when user asks a question about the codebase, user wants to understand a specific file, function, or component, or user asks \"how does X work\" or \"where is Y defined\" and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

diegosouzapw Bundle

Development Workflow Bundle workflow skill. Use this skill when the user needs Comprehensive web, mobile, and backend development workflow bundling frontend, backend, full-stack, and mobile development skills for end-to-end application delivery and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

diegosouzapw Bundle

Functional Programming in React workflow skill. Use this skill when the user needs Practical patterns for using fp-ts with React - hooks, state, forms, data fetching. Works with React 18/19, Next.js 14/15 and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

holobiomicslab Skill

Use when after identifying differentially accessible peaks (via tl.

holobiomicslab Skill

Use when you have paired scATAC-seq and scRNA-seq data from the same cells (multiome experiment) and want to perform integrated analysis that leverages both chromatin accessibility and gene expression signals.