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Spatially-aware quality control (QC) software for both spot-level and artifact-level QC in spot-based spatial transcripomics, such as 10x Visium. These methods calculate local (nearest-neighbors) mean and variance of standard QC metrics (library size, unique genes, and mitochondrial percentage) to identify outliers spot and large technical artifacts. Scales linearly with the number of spots and is designed to be used with 'SpatialExperiment' objects.

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The epistack package main objective is the visualizations of stacks of genomic tracks (such as, but not restricted to, ChIP-seq, ATAC-seq, DNA methyation or genomic conservation data) centered at genomic regions of interest. epistack needs three different inputs: 1) a genomic score objects, such as ChIP-seq coverage or DNA methylation values, provided as a `GRanges` (easily obtained from `bigwig` or `bam` files). 2) a list of feature of interest, such as peaks or transcription start sites, provi

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Provides S4 classes for general nucleases, CRISPR nucleases, CRISPR nickases, and base editors.Several CRISPR-specific genome arithmetic functions are implemented to help extract genomic coordinates of spacer and protospacer sequences. Commonly-used CRISPR nuclease objects are provided that can be readily used in other packages. Both DNA- and RNA-targeting nucleases are supported.

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This R package supports interactive visualization of multi-channel images and segmentation masks generated by imaging mass cytometry and other highly multiplexed imaging techniques using shiny. The cytoviewer interface is divided into image-level (Composite and Channels) and cell-level visualization (Masks). It allows users to overlay individual images with segmentation masks, integrates well with SingleCellExperiment and SpatialExperiment objects for metadata visualization and supports image do

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This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, an

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Mass spectrometry (MS) data backend supporting import and export of MS/MS library spectra from MassBank record files. Different backends are available that allow handling of data in plain MassBank text file format or allow also to interact directly with MassBank SQL databases. Objects from this package are supposed to be used with the Spectra Bioconductor package. This package thus adds MassBank support to the Spectra package.

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A set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files). These tools allow the user to download the genomic locations of transcripts, exons, and CDS, for a given assembly, and

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PhIPData defines an S4 class for phage-immunoprecipitation sequencing (PhIP-seq) experiments. Buliding upon the RangedSummarizedExperiment class, PhIPData enables users to coordinate metadata with experimental data in analyses. Additionally, PhIPData provides specialized methods to subset and identify beads-only samples, subset objects using virus aliases, and use existing peptide libraries to populate object parameters.

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Microbiome time series simulation with generalized Lotka-Volterra model, Self-Organized Instability (SOI), and other models. Hubbell's Neutral model is used to determine the abundance matrix. The resulting abundance matrix is applied to (Tree)SummarizedExperiment objects.

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Graph objects from pathway topology derived from KEGG, Panther, PathBank, PharmGKB, Reactome SMPDB and WikiPathways databases.

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Expert knowledge for Azure Data Api Builder development including troubleshooting, best practices, decision making, limits & quotas, security, configuration, integrations & coding patterns, and deployment. Use when exposing DB objects via REST/GraphQL, tuning paging/timeouts, securing auth/RLS, or deploying DAB to Azure, and other Azure Data Api Builder related development tasks. Not for Azure API Management (use azure-api-management), Azure App Service (use azure-app-service), Azure Functions (use azure-functions), Azure Logic Apps (use azure-logic-apps).

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Transform ordinary snapshots—including daily moments, portraits, objects, pets, food, interiors, streets, architecture, landscapes, travel, and humanistic scenes—into the restrained Shijing Paper Zine visual style. Use when the user wants any real photo turned into a spacious paper-editorial composition with an irregular photographic fragment, simplified source-derived drawing, one structural print color, tactile torn-paper texture, minimal micro-copy, a consistent multi-image series, or a source-to-poster comparison.

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Use when creating mocks, stubbing methods, verifying interactions, registering fallback values, or choosing between mocks, fakes, and real objects (Mocktail).

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Use when generating mocks, stubbing methods, verifying interactions, capturing arguments, or choosing between mocks, fakes, and real objects (Mockito).

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Tactical DDD — aggregate design rules, entities, value objects, domain events, repositories, domain services, and anti-pattern detection

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Use when a user wants Codex to directly operate PowerPoint and reconstruct an entire reference image as editable PowerPoint objects while preserving its full layout, labels, connectors, and visual relationships. Do not use for paper-to-deck generation or VBA-only output.

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Generates Playwright page objects from an executable test plan, one class per screen with ladder-compliant locators and no assertions, wired into a shared fixture. Use when a web scenario needs a page object that does not exist yet, or when locators drift and the page object must be rebuilt.

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Use ManagedCode.Communication when a .NET application needs explicit result objects, structured errors, and predictable service or API boundaries instead of exception-driven control flow. USE FOR: integrating ManagedCode.Communication into services or APIs; replacing exception-driven result handling with explicit results; reviewing service boundaries that return. DO NOT USE FOR: unrelated stacks; generic tasks that do not need this specific guidance. INVOKES: inspect the repository context, edit targeted files, and run relevant build, test, lint, or validation commands when changes are made.

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Removes unwanted visual elements from videos using AI-powered inpainting via Volcengine LAS. Video watermark removal, subtitle removal, logo removal, and text overlay removal — erases and cleans up watermarks, hardcoded subtitles, logos, text, and other fixed-region artifacts and obstructions from video footage. Video inpainting, video repair, video restoration, and video cleanup. Supports specifying exact bounding boxes for targeted removal and erasure. Handles videos up to 4 hours and 30GB. Use this skill when the user wants to remove watermarks from videos, erase hardcoded subtitles/captions, delete logo or text overlays, clean up video footage by removing unwanted objects, repair or restore videos by removing obstructions, do video inpainting on fixed regions, or remove visual artifacts from video content.

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Converts audio objects stored in Volcengine TOS into PCM-oriented WAV output through TOS data-process async jobs. Use this skill when the user needs to convert audio to PCM or WAV, resample audio to 16k, convert to mono, change sample format, normalize audio for ASR pipelines, or prepare TOS audio files for speech recognition — even if they don't explicitly mention 'PCM' or 'audio conversion'.

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Transforms and inspects image objects stored in Volcengine TOS. Use this skill only when the task explicitly involves a TOS bucket/object key, TOS image processing, TOS-to-TOS save-as output, or Volcengine TOS image process syntax such as image/info, image/resize, image/format, image/watermark, image/draw, image/blindwatermark, or image/understanding. Do not use this skill for ordinary uploaded screenshots, local images, UI screenshot analysis, generic OCR, face detection, or visual question answering unless the user clearly says the image is a TOS object or asks to process/save it through TOS.

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Use when you need to apply functional programming principles in Java — including writing immutable objects and Records, pure functions, functional interfaces, lambda expressions, Stream API pipelines, Optional for null safety, function composition, higher-order functions, pattern matching for instanceof and switch, sealed classes/interfaces for controlled hierarchies, Stream Gatherers for custom operations, currying/partial application, effect boundary separation, and concurrent-safe functional patterns. This should trigger for requests such as Improve the code with Functional Programming; Apply Functional Programming; Refactor the code with Functional Programming; Refactor Java code to use streams or Optionals safely; Improve immutability and pure functions in Java. Part of Plinth Toolkit

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Read from a UModel object-graph semantic layer with the `umctl` CLI (MCP alternative noted). Three kinds of read: (1) entities & relationships / topology (`.entity`, `.topo`) and (2) the model itself (`.umodel`, and `.entity_set` methods, including entity-linked `list_skills`) return real rows; (3) metrics & logs (`get_metrics` / `get_logs`) return an executable *plan* — PromQL / Elasticsearch DSL with the entity id pre-substituted — that you run against the backend. Against a PaaS endpoint the same calls return data rows instead of a plan. Use to query or read UModel entities, relations, topology, or model metadata; to read a service's metrics or logs; to look up services and dependencies; or to discover what objects, datasets, and methods exist. For root-cause analysis on top of these reads, see the `umodel-rca` skill. Triggers: UModel, object graph, .entity / .topo / .umodel / .entity_set, query entities, read topology, read metrics / logs, get_metrics / get_logs, list services / dependencies / datasets / skills, 实体查询, 关系/拓扑查询, 读模型, 读指标, 读日志, 查指标, 查日志, 查服务依赖.

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Create animated, explorable editorial diagrams in 45 types (architecture, flowchart, sequence, state, ER, DB schema, UML class, swimlane, timeline, gantt, journey, tree, org chart, nested, venn, quadrant, fishbone, wardley, bar, line, scatter, sankey, treemap, heatmap, 3D isometric objects, floor plans and exploded views) as standalone HTML from a short JSON spec. Use when the user asks to draw, diagram, chart or visualize a system, codebase, flow, process, API call sequence, hierarchy, data or a physical object (a chair); to convert Mermaid, Graphviz/DOT, PlantUML, D2, draw.io, Excalidraw, SQL or CSV into a clean diagram; or to export a diagram as PNG, JPEG, SVG, GIF or MP4. Also for everyday plans: trips, moves, job hunts, approvals, budgets, where money goes.

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