205 skills · sorted by relevance
Build and operate LLM applications with guidance on RAG, which uses retrieved documents to inform answers. Covers document indexing, vector database selection, prompt improvement, response evaluation, caching, and estimates of model usage costs.
Run nf-core workflows on local sequencing files or public GEO/SRA datasets to analyze gene expression, genetic variants, or chromatin accessibility. The skill guides environment checks, sample table preparation, workflow configuration, execution, and output verification.
Add purposeful color to monochromatic interfaces so key actions, statuses, and categories are easier to recognize. Refine backgrounds, text, and charts around a consistent palette while checking contrast and avoiding reliance on color alone.
Turn a supplied quote into an animated video-intro scene in a single HTML file. Text appears character by character with a glowing cursor, colored trails, and light flares, with space for a source or chapter label.
Detect chromatin loops and point interactions from Hi-C data using cooltools, chromosight, and HiCCUPS-like methods. Identify CTCF-mediated loops and enhancer-promoter contacts. Use when detecting chromatin loops from Hi-C data.
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Find differentially accessible chromatin regions between conditions using DiffBind or DESeq2. Use when comparing chromatin accessibility between treatment groups, cell types, or developmental stages in ATAC-seq experiments.
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Call accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-specific parameters. Use when identifying open chromatin regions from aligned ATAC-seq BAM files, different from ChIP-seq peak calling.
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Chroma local vector database setup and operations for development and production
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Detects focal chromatin loops (point interactions / corner-dots) in balanced Hi-C and Micro-C contact maps and aggregates/validates a loop set. Covers de-novo calling with cooltools dots (HiCCUPS-style 4-background local enrichment with lambda-chunked FDR), chromosight (template-correlation), and Mustache (scale-space blob detection); aggregate peak analysis (APA) via cooltools pileup for confirmation; the depth/resolution prerequisite (de-novo needs ~5-10kb resolution = hundreds of millions to billions of valid pairs); consensus across callers and convergent-CTCF support as validation; and differential loops via union anchors plus chromosight quantify. Use when calling chromatin loops or dots from a cooler, deciding whether a map is deep enough to call de-novo vs running APA on known CTCF/cohesin anchors, building an aggregate peak pileup, comparing loops across conditions, or validating loop calls. For HiChIP/PLAC-seq/PCHi-C protein-anchored data use FitHiChIP/MAPS, not dots.
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Call accessible chromatin regions from ATAC-seq BAM files using MACS3, MACS2, Genrich, or HMMRATAC. Use when identifying open chromatin from aligned ATAC-seq, choosing between point-source vs HMM peak callers, applying ENCODE-style pseudoreplicate IDR, removing blacklist regions, or fixing 501bp consensus peaks for downstream differential analysis.
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Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR. Use when comparing ATAC-seq accessibility between treatment groups, choosing between consensus-peak vs sliding-window approaches, picking the correct normalization (full library vs reads-in-peaks), correcting batch with SVA/RUVseq, or interpreting log2FC and FDR thresholds in a chromatin context.
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Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL. Use when mapping cis-regulatory genetic variants from heterozygous SNPs, separating cis from trans regulation, building chromatin QTL (caQTL) maps, validating GWAS variant function with allelic imbalance, or detecting reference allele mapping bias before downstream analysis.
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Open-source embedding database for AI applications. Store embeddings and metadata, perform vector and full-text search, filter by metadata. Simple 4-function API. Scales from notebooks to production clusters. Use for semantic search, RAG applications, or document retrieval. Best for local development and open-source projects.
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Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR. Use when comparing ATAC-seq accessibility between treatment groups, choosing between consensus-peak vs sliding-window approaches, picking the correct normalization (full library vs reads-in-peaks), correcting batch with SVA/RUVseq, or interpreting log2FC and FDR thresholds in a chromatin context.
The English summary is being prepared. Showing the original description.
Call accessible chromatin regions from ATAC-seq BAM files using MACS3, MACS2, Genrich, or HMMRATAC. Use when identifying open chromatin from aligned ATAC-seq, choosing between point-source vs HMM peak callers, applying ENCODE-style pseudoreplicate IDR, removing blacklist regions, or fixing 501bp consensus peaks for downstream differential analysis.
The English summary is being prepared. Showing the original description.
Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL. Use when mapping cis-regulatory genetic variants from heterozygous SNPs, separating cis from trans regulation, building chromatin QTL (caQTL) maps, validating GWAS variant function with allelic imbalance, or detecting reference allele mapping bias before downstream analysis.
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SEC (size-exclusion chromatography) analysis with peak detection, oligomer classification, and publication-quality PDF report generation via Typst templates. Triggers on "SEC", "size exclusion", "chromatography", "oligomer analysis", "protein assembly", "SEC report".
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Implement visual regression testing with Playwright screenshots, Chromatic, Percy, and Argos CI. Covers baseline management, diff threshold tuning, dynamic content masking, responsive viewport testing, and review/approval workflows. Use when: "visual test," "screenshot," "visual regression," "pixel diff," "snapshot diff," "update baselines," "Chromatic," "percy snapshot," "argos screenshot." Not for: bulk baseline regeneration after a redesign broke many tests — use selector-drift-recovery; cross-browser rendering matrices — use cross-browser-testing; general Playwright test structure — use playwright-automation. Related: playwright-automation, ci-cd-integration, cross-browser-testing.
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Manage the ChromaDB vector database that stores the ecosystem's persistent memory. Use when user asks to check memory storage, backup memory, search stored entries, delete entries, or reset the vector database. Do NOT use for general question answering about past sessions (use the memory skill for that).
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Spectroscopy, chromatography, titration, elemental analysis, X-ray crystallography, and mass spectrometry for chemical identification and quantitation. Covers UV-Vis and IR spectroscopy, NMR fundamentals, gas and liquid chromatography, gravimetric and volumetric analysis, diffraction methods, separation techniques, and quantitative error analysis. Use when identifying unknown substances, determining purity, measuring concentrations, or interpreting analytical data.
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Design polychromatic ornamental patterns grounded in Alexander Speltz's classical ornament taxonomy. Builds on monochrome structural analysis by adding period-authentic color palettes, color-to-motif mapping, and rendering styles suited to painted, illuminated, and glazed ornament. Use when creating decorative designs where color is integral to the tradition (Islamic tilework, illuminated manuscripts, Art Nouveau), exploring how historical periods used color in ornament, or producing colored reference imagery for design, illustration, or educational materials.
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Chroma vector database -- collection management, automatic embedding, metadata filtering, document storage, query patterns
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Integrate multiple ENCODE data types (RNA-seq, ATAC-seq, Histone ChIP-seq, TF ChIP-seq) for a tissue/cell type to build a comprehensive regulatory landscape. Use when the user wants to answer "what are the enhancers, promoters, and regulatory elements active in my tissue, and which transcription factors control them?" by layering expression, chromatin accessibility, histone marks, and TF binding data. Follows the Mawla et al. 2023 framework for cross-assay integration of islet cell type-specific data. Handles chromatin state annotation (ChromHMM), enhancer-gene linkage, TF motif enrichment, and cell type-specific regulatory element identification. Use for ANY multi-omic analysis, enhancer discovery, regulatory network construction, or epigenomic characterization using ENCODE data.
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Build comprehensive chromatin contact maps by aggregating Hi-C loop calls (BEDPE) across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "what regions are in 3D contact in my tissue?" by creating a union catalog of chromatin loops. Handles resolution-aware anchor matching, cross-lab variation, and Hi-C-specific quality metrics.
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