162건 · 관련도순
Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.
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InterCellar is implemented as an R/Bioconductor Package containing a Shiny app that allows users to interactively analyze cell-cell communication from scRNA-seq data. Starting from precomputed ligand-receptor interactions, InterCellar provides filtering options, annotations and multiple visualizations to explore clusters, genes and functions. Finally, based on functional annotation from Gene Ontology and pathway databases, InterCellar implements data-driven analyses to investigate cell-cell comm
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This package is a implementation of biclustering ensemble method MoSBi (Molecular signature Identification from Biclustering). MoSBi provides standardized interfaces for biclustering results and can combine their results with a multi-algorithm ensemble approach to compute robust ensemble biclusters on molecular omics data. This is done by computing similarity networks of biclusters and filtering for overlaps using a custom error model. After that, the louvain modularity it used to extract biclus
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Own concrete MSBuild ItemGroup and item-expression questions. USE FOR: Include, Remove, Update, item identity and metadata, transforms, filtering, batching, duplicate or overlapping items, and reviews that verify whether those operations are correct. Generated items stay in scope when the central defect is item identity, metadata, batching, duplicate declarations, or glob/Remove/Update semantics. For a generated artifact missing from compilation or output, wrong target timing/path, or FileWrites clean tracking without a broader item-semantics defect, use including-generated-files. The item operation may be broken, suspected, or already correct. Exclude property-only issues, general incrementality with no item question, broad reviews with no concrete item concern, and non-MSBuild systems.
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Use when you need to design, review, or improve REST APIs with Spring Boot — including HTTP methods, resource URIs, status codes, DTOs, versioning, deprecation and sunset headers, content negotiation (JSON and vendor media types), ISO-8601 instants in DTOs, pagination/sorting/filtering, Bean Validation at the boundary, idempotency, ETag concurrency, HTTP caching, error handling, security, contract-first OpenAPI (OpenAPI Generator), controller advice, and problem details for errors. This should trigger for requests such as Review Java code for Spring Boot REST API; Apply best practices for Spring Boot REST API in Java code; Design Spring Boot REST controllers and DTOs; Add Problem Details error responses in Spring Boot REST; Improve pagination validation or idempotency in Spring APIs. Part of Plinth Toolkit
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Managed vector database for production AI applications. Fully managed, auto-scaling, with hybrid search (dense + sparse), metadata filtering, and namespaces. Low latency (<100ms p95). Use for production RAG, recommendation systems, or semantic search at scale. Best for serverless, managed infrastructure.
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Use when writing Playwright tests, fixing flaky tests, debugging failures, implementing Page Object Model, configuring CI/CD, optimizing performance, mocking APIs, handling authentication or OAuth, testing accessibility (axe-core), file uploads/downloads, date/time mocking, WebSockets, geolocation, permissions, multi-tab/popup flows, mobile/responsive layouts, touch gestures, GraphQL, error handling, offline mode, multi-user collaboration, third-party services (payments, email verification), console error monitoring, global setup/teardown, test annotations (skip, fixme, slow), test tags (@smoke, @fast, @critical, filtering with --grep), project dependencies, security testing (XSS, CSRF, auth), performance budgets (Web Vitals, Lighthouse), iframes, component testing, canvas/WebGL, service workers/PWA, test coverage, i18n/localization, Electron apps, or browser extension testing. Covers E2E, component, API, visual, accessibility, security, Electron, and extension testing.
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Read/write SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ. Region queries, pileup, variant filtering, read groups. Python htslib wrapper exposing samtools/bcftools CLI. Use STAR/BWA for alignment; GATK/DeepVariant for variant calling.
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Query the ZINC22 virtual compound library (CartBlanche API, billions of make-on-demand + purchasable molecules). Look up substances by ZINC ID, resolve a SMILES to its ZINC ID (exact match), inspect purchasability/catalogs, and assemble compound sets for docking. Property (MW/logP) filtering is done locally with RDKit. For bioactivity use chembl-database-bioactivity; for approved drugs use drugbank-database-access.
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Out-of-core DataFrame for billion-row data via lazy evaluation and memory-mapped files. Use when data exceeds RAM (10 GB–TB) for fast aggregation, filtering, virtual columns, and visualization without loading. Supports HDF5, Arrow, Parquet, CSV with cloud (S3, GCS, Azure). Built-in ML transformers (scaling, PCA, K-means). In-memory: polars; distributed: dask.
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Fix Gorse 0.5.x recommendation engine silently disabled or degraded due to config incompatibility with 0.4. Use when: (1) Gorse 0.5 recommendations are poor/empty despite having data, (2) collaborative filtering appears disabled even though [recommend.collaborative] section exists, (3) migrating Gorse config from 0.4 to 0.5, (4) old config keys like [recommend.popular], [recommend.neighbors], [recommend.online], [recommend.offline] are being used with Gorse 0.5. Critical: type="mf" must be explicitly set in [recommend.collaborative] or CF is silently disabled (default "none").
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Fix silent video/media processing failures caused by URL extraction code that filters on file extensions (.mp4, .webm, .webp). Use when: (1) Media moderation, transcoding, or analysis silently skips files from Blossom or content-addressed storage servers, (2) URL extraction from Nostr event tags (imeta, r tags) drops URLs without recognized extensions, (3) CDN fallback URLs append .mp4 but the actual server uses extensionless content-addressed paths like /{sha256}. Common in Nostr video events (kind 34236) where different clients use different URL formats.
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Fix HTTP 500 / ClickHouse "column not found" errors when filtering by a MATERIALIZED column through a VIEW that doesn't expose it. Use when: (1) a WHERE clause references alias.column on a view but the column is MATERIALIZED on the underlying table, (2) the query works on the raw table but fails through the view, (3) adding a new filter param to an API causes 500 even though the column exists in the base table. Fix by using a subquery against the base table instead of referencing the column directly on the view. Applies to ClickHouse views over tables with MATERIALIZED or ALIAS columns.
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Build recommendation systems with collaborative filtering, matrix factorization, hybrid approaches. Use for product recommendations, personalization, or encountering cold start, sparsity, quality evaluation issues.
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Extract, filter, annotate, and export differential expression results from DESeq2 or edgeR. Use for identifying significant genes, applying multiple testing corrections, adding gene annotations, and preparing results for downstream analysis. Use when filtering and exporting DE analysis results.
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Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate removal using fgbio. Applies cfDNA-specific quality thresholds and fragment length filtering. Use when processing plasma cfDNA sequencing data before downstream analysis.
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Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extraction, adapter trimming, length filtering, and post-alignment PCR-duplicate collapse. Use when raw CLIP FASTQ must be turned into deduplicated, crosslink-preserving BAM input for peak calling; choosing between two-pass and single-pass adapter trimming; deciding minimum read length; or mapping UMI patterns to specific eCLIP/iCLIP/iCLIP2/iCLIP3 library preps.
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Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.
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Predicts ADMET properties using ADMETlab 3.0 (119 endpoints with uncertainty), ADMET-AI, DeepChem MolNet, and chemprop D-MPNN with explicit handling of OECD QSAR principles, applicability domain assessment, calibration, hERG/CYP/AMES gold-standard endpoints, and PAINS / Lipinski / Ro5 / Veber / BBB druglikeness filters. Use when filtering compounds for drug-likeness, prioritizing leads by predicted safety, or building an in-house ADMET QSAR model.
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Nexscope Ozon keyword reverse lookup: reverse-looks up Ozon (and Wildberries) search keywords by a list of product SKUs (up to 20), returning which search terms those products appear under (organic/ad search terms), with multi-dimensional filtering by search volume, growth, product count, seller count, competitor count, natural rank, ad rank, exposure, conversion, cart-add conversion, etc. Each keyword carries monthly search volume, growth, market space, competitor/seller counts, average price, cart-add conversion, top products, and organic/ad channel, rank, exposure, and conversion (dimension) market profiles. Use for Ozon keyword reverse lookup, listing keyword optimization, competitor traffic word mining, and ad keyword analysis. Trigger when the user mentions Ozon keyword reverse lookup, Ozon reverse keyword search, Ozon SKU keyword reverse, Ozon product traffic keywords, Ozon competitor ranking keywords, Ozon organic/ad keyword reverse lookup, Nexscope Ozon, Ozon keyword back search, Ozon reverse keyword lookup, Ozon SKU keyword reverse. Also trigger when the intent is to reverse-lookup Ozon search keywords by product SKU and view market profiles, even without explicitly mentioning Nexscope.
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Use when writing Playwright tests, fixing flaky tests, debugging failures, implementing Page Object Model, configuring CI/CD, optimizing performance, mocking APIs, handling authentication or OAuth, testing accessibility (axe-core), file uploads/downloads, date/time mocking, WebSockets, geolocation, permissions, multi-tab/popup flows, mobile/responsive layouts, touch gestures, GraphQL, error handling, offline mode, multi-user collaboration, third-party services (payments, email verification), console error monitoring, global setup/teardown, test annotations (skip, fixme, slow), test tags (@smoke, @fast, @critical, filtering with --grep), project dependencies, security testing (XSS, CSRF, auth), performance budgets (Web Vitals, Lighthouse), iframes, component testing, canvas/WebGL, service workers/PWA, test coverage, i18n/localization, Electron apps, or browser extension testing. Covers E2E, component, API, visual, accessibility, security, Electron, and extension testing.
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Work with the @upstash/search TypeScript/JavaScript SDK, a serverless full-text and semantic search database with built-in reranking. Use when adding search to an app or site, creating a search index, upserting documents with searchable content and filterable metadata, running keyword, semantic, or hybrid search queries, reranking results, filtering with SQL-like or structured filter syntax, paginating with range, fetching or deleting documents, resetting an index, or checking index info. Also use when the user asks for site search, product, document, or knowledge-base search, or a managed search service that needs no cluster to run.
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Work with the @upstash/vector TypeScript/JavaScript SDK, a serverless vector database for embeddings, similarity search, semantic search, and RAG (retrieval-augmented generation). Use when upserting, querying, fetching, ranging, or deleting vectors, upserting raw text against an index with a built-in embedding model, choosing dense, sparse, or hybrid indexes, filtering by metadata, organizing data with namespaces, running resumable queries, or connecting Upstash Vector to an AI or LLM application. Also use when the user asks for a vector store, vector search, nearest-neighbor or kNN search, embeddings storage, semantic cache, recommendations or similarity features, or a hosted vector index that needs no infrastructure.
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Process multimedia files with FFmpeg (video/audio encoding, conversion, streaming, filtering, hardware acceleration) and ImageMagick (image manipulation, format conversion, batch processing, effects, composition). Use when converting media formats, encoding videos with specific codecs (H.264, H.265, VP9), resizing/cropping images, extracting audio from video, applying filters and effects, optimizing file sizes, creating streaming manifests (HLS/DASH), generating thumbnails, batch processing images, creating composite images, or implementing media processing pipelines. Supports 100+ formats, hardware acceleration (NVENC, QSV), and complex filtergraphs.
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