'chroma' 검색 결과

Machine learning toolkit for genomic interval (BED) data; use it when you need to tokenize BED collections and train embeddings for regions/cells/labels, build consensus peak universes, or run similarity search and downstream ML on chromatin accessibility datasets.

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INVOKE THIS SKILL when building ANY retrieval-augmented generation (RAG) system. Covers document loaders, RecursiveCharacterTextSplitter, embeddings (OpenAI), and vector stores (Chroma, FAISS, Pinecone).

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Assemble a viral iOS "AirDrop" notification-carousel video ad (≈6–8s, 9:16) from a brand line plus 6–16 real product photos — a native AirDrop share-sheet card ("Brand would like to share a ___ · Decline / Accept") springs up and its preview window CYCLES through the products, landing on a range/lineup payoff with an Accept tap; a chime + soft per-swap ticks track the swaps. DETERMINISTIC assembly — an HTML card (real DOM text) rendered to PNG via headless Chrome, chroma-keyed, its magenta window refilled per-product in PIL, then animated + audio-synthed with FFmpeg. FREE (no paid model calls); the recipe supplies the brand line, product images, and payoff and gates the only optional paid step (a hero shot when the brand has NO usable photo → create-image-fal). Use for the airdrop-notification-carousel format.

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Turns Hi-C/Micro-C FASTQ into a deduplicated, filtered .pairs file with pairtools and decides whether the library worked. Covers the bwa mem -SP5M / bwa-mem2 / chromap --preset hic alignment idiom (mates mapped as independent single-end reads), pairtools parse vs parse2 and the walks-policy choice (5unique pairwise vs all for Pore-C/Micro-C concatemers), pair-type classification (keep UU and rescued UC), dedup (PCR vs optical/by-tile), select by pair_type/MAPQ/distance, restriction-fragment handling (restrict, Arima dual-enzyme, Micro-C/DNase fragment-free), and allele-specific phasing (pairtools phase to two coolers). The library-QC decision uses % long-range cis as the one-number quality metric, trans as the noise floor, orientation balance as fragment-map-free dangling-end/self-circle QC, and % duplicates as a complexity proxy. Use when processing Hi-C/Micro-C/Omni-C reads into pairs, judging library quality, handling multi-enzyme or restriction-agnostic protocols, or generating allele-specific contacts.

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Detects A/B chromatin compartments from balanced Hi-C contact matrices via eigenvector decomposition of the distance-normalized, Pearson-correlated cis matrix with cooltools (eigs_cis), then orients (phases) the compartment eigenvector against a GC or gene-density track so the active (A) sign is not arbitrary. Covers the eigenvector-is-a-choice problem (per-arm view_df to remove the centromere gradient; picking the eigenvector by max correlation with activity, not by eigenvalue), GC phasing with bioframe.frac_gc, resolution choice (100kb-1Mb), saddle plots and saddle_strength for compartmentalization strength, the cohesin-loss-strengthens-compartments result, subcompartments (SNIPER/Calder/dcHiC), and cross-condition compartment switching. Use when calling A/B compartments, computing E1/eigenvectors, phasing the eigenvector, building saddle plots, choosing a compartment resolution, quantifying compartment strength, or comparing compartmentalization across conditions.

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Designs and analyzes pooled prime-editor (PE) screens for installing precise genetic variants without bystander confounding. Covers pegRNA design with PRIDICT and PRIDICT2 for predicting per-pegRNA editing efficiency, pegRNA architecture (spacer + scaffold + PBS + RTT), PE2/PE3/PE3b/PEmax variants, MOSAIC in situ saturation mutagenesis, the PRIME pooled-screen methodology (Ren 2023; ~3,699 ClinVar variant screens), chromatin context as a major locus-level determinant of PE efficiency, scaffold-incorporation and indel byproduct quantification with CRISPResso2, and the cross-modal validation strategy of PE + base-editor screens for variant function. Use when designing a pegRNA library for variant installation, choosing between BE and PE for a specific edit, predicting pegRNA efficiency before library synthesis, analyzing PE screen output, distinguishing intended-edit from scaffold-incorporation, or scaling PE screens to thousands of variants.

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Analyzes single-cell pooled CRISPR screens (Perturb-seq, CROP-seq, Perturb-CITE-seq, ECCITE-seq, multiome) where each cell carries an sgRNA and a scRNA-seq / surface-protein / chromatin readout. Covers experimental design (direct-capture Perturb-seq Dixit 2016 vs CROP-seq 3'UTR-barcoded Datlinger 2017 vs ECCITE-seq vs Multiome), MOI for sgRNA assignment, escaper-cell filtering (Mixscape, Papalexi 2021), SCEPTRE NB GLM + permutation for low-MOI (Barry 2024 Genome Biol 25:124), the Pertpy framework, factor decomposition, genome-scale Perturb-seq (Replogle 2022 Cell, 2.5M cells), and per-perturbation single-cell DE. Use when running a single-cell CRISPR screen, choosing direct-capture vs CROP-seq architecture, filtering escaper cells, performing single-cell DE, integrating Perturb-seq with pathway analysis, scaling to GW CRISPRi via Replogle protocol, or analyzing multi-omics screens.

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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, applies the Patel et al 2024 *Nat Biotechnol* failure-mode framework, and validates that normalization is 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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Analyzes CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data. Handles SEACR vs MACS2 peak calling (with the btaf375 2025 benchmark guidance), pA-MNase vs pA-Tn5 vs pAG-Tn5 chimera differences, E. coli spike-in carryover normalization, IgG-only control logic (no input), characteristic fragment-size signatures (25-75 bp for CUT&Tag), and lower depth requirements (5M reads typical vs 25M for ChIP). Use when calling peaks from CUT&RUN/CUT&Tag, scaling by E. coli spike-in carryover, choosing SEACR norm mode, or comparing CUT&RUN/Tag results to traditional ChIP.

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Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC, ATACseqQC, DANPOS3, or scprinter. Use when characterizing nucleosome organization at promoters and enhancers, calling +1/-1 nucleosomes flanking NFRs, generating V-plots for chromatin structure visualization, or comparing nucleosome positioning between conditions.

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Estimates SNP heritability and partitions 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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Infer cis-regulatory connections (peak-to-peak co-accessibility) from scATAC-seq using Cicero, ArchR getCoAccessibility, or SCENIC+. Use when linking enhancer accessibility to promoter accessibility, identifying enhancer-gene pairs from chromatin alone (without paired RNA), running gene-regulatory inference combining ATAC + RNA, or comparing predicted regulatory contacts against Hi-C/Micro-C ground truth.

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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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Use when editing footage that already exists on Scenario through MCP with a tool model instead of a new generation: 3D LUT grading, color correction, film grain, vignette, blur, sharpen, glow, tint, desaturate, posterize, solarize, cubism, crystallize, oilify, chromatic aberration or dodge and burn on a clip; trimming to a time range, splitting at cut points, reversing, resizing, re-encoding, frame extraction, image sequences, background removal, segmentation masks, subjects as layers.

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Use when editing an existing image on Scenario through MCP with a tool model, not a new generation: upscale or enhance to 2x, 4K, 8K, super resolution, 3D LUT color grade, color correction, posterize, solarize, vignette, film grain, blur, sharpen, glow, chromatic aberration, oilify, cubism, crystallize, dodge and burn, tint, desaturate, expand or uncrop, reframe an aspect ratio, resize to exact pixels, slice tiles, contact sheet, split into layers, remove a background or watermark, vectorize.

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RAG-specific best practices for LlamaIndex, ChromaDB, and Celery workers. Covers ingestion, retrieval, embeddings, and performance.

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Use when the user sends or generates an image, screenshot, video, audio or file and wants it saved, or asks to find past media (that diagram, the mockup from last week). Ingests and searches with local ChromaDB embeddings.

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Vector database implementation for AI/ML applications, semantic search, and RAG systems. Use when building chatbots, search engines, recommendation systems, or similarity-based retrieval. Covers Qdrant (primary), Pinecone, Milvus, pgvector, Chroma, embedding generation (OpenAI, Voyage, Cohere), chunking strategies, and hybrid search patterns.

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Security-first SOP for multi-tenant RAG systems. Activate when a calling agent is building, reviewing, or debugging any retrieval pipeline whose vector store is shared across more than one user, organisation, workspace, customer, or permission scope. Encodes the single non-negotiable rule — **filter at the vector store query, never after retrieval / never after rerank** — together with the per-vendor query-time filter APIs (Pinecone namespaces + `$eq`/`$in`, Weaviate `multiTenancyConfig` + tenant handle, Qdrant `is_tenant` payload index + `Filter.must`, Chroma `where`, pgvector RLS), and the cross-framework adapters (LlamaIndex `MetadataFilters`, LangChain `filter=` dict). Frame the work as preventing CVE-2024-41892 / EchoLeak / Slack-AI-class cross-tenant leakage, not as "adding a filter for relevance".

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ENCODE Portal REST API for regulatory genomics: TF ChIP-seq, ATAC-seq/DNase-seq peaks, histone marks, and RNA-seq across 1000+ cell types. Search experiments by assay/biosample/target; download BED/bigWig; retrieve SCREEN cCREs by region or gene. Use to annotate variants with regulatory tracks, find open chromatin in a cell type, or fetch peak files for ChIP/ATAC analysis. For regulatory variant scoring use regulomedb-database; for GWAS associations use gwas-database.

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Query RegulomeDB v2 GET REST API to score variants for regulatory function and retrieve overlapping evidence (TF binding, histone marks, DNase peaks, footprints, motifs, eQTLs, chromatin state). Scores range 1a (strongest) to 7 (none). Use for GWAS hit prioritization, regulatory variant annotation, cis-regulatory discovery. Use clinvar-database for pathogenicity; gwas-database for trait associations.

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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.

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Implement semantic vector search for construction data. Build AI-powered search using embeddings and vector databases (Qdrant, ChromaDB) for intelligent querying of specifications, standards, and project documents.

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Add strategic color to monochromatic or dull interfaces using oklch for perceptually uniform palettes. Generates harmonious color systems with automatic light/dark variants and accessible contrast ratios.

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