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Statial is a suite of functions for identifying changes in cell state. The functionality provided by Statial provides robust quantification of cell type localisation which are invariant to changes in tissue structure. In addition to this Statial uncovers changes in marker expression associated with varying levels of localisation. These features can be used to explore how the structure and function of different cell types may be altered by the agents they are surrounded with.

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This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, En

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Provides large-scale single-cell omics data manipulation using Genomic Data Structure (GDS) files. It combines dense and sparse matrices stored in GDS files and the Bioconductor infrastructure framework (SingleCellExperiment and DelayedArray) to provide out-of-memory data storage and large-scale manipulation using the R programming language.

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Provides basic utility functions for performing single-cell analyses, focusing on simple normalization, quality control and data transformations. Also provides some helper functions to assist development of other packages.

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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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Statistical and computational method to analyze the co-expression of gene pairs at single cell level. It provides the foundation for single-cell gene interactome analysis. The basic idea is studying the zero UMI counts' distribution instead of focusing on positive counts; this is done with a generalized contingency tables framework. COTAN can effectively assess the correlated or anti-correlated expression of gene pairs. It provides a numerical index related to the correlation and an approximate

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The cellxgene data portal (https://cellxgene.cziscience.com/) provides a graphical user interface to collections of single-cell sequence data processed in standard ways to 'count matrix' summaries. The cellxgenedp package provides an alternative, R-based inteface, allowind data discovery, viewing, and downloading.

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Provides R wrappers of several on-target and off-target scoring methods for CRISPR guide RNAs (gRNAs). The following nucleases are supported: SpCas9, AsCas12a, enAsCas12a, and RfxCas13d (CasRx). The available on-target cutting efficiency scoring methods are RuleSet1, Azimuth, DeepHF, DeepCpf1, enPAM+GB, and CRISPRscan. Both the CFD and MIT scoring methods are available for off-target specificity prediction. The package also provides a Lindel-derived score to predict the probability of a gRNA to

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granulator is an R package for the cell type deconvolution of heterogeneous tissues based on bulk RNA-seq data or single cell RNA-seq expression profiles. The package provides a unified testing interface to rapidly run and benchmark multiple state-of-the-art deconvolution methods. Data for the deconvolution of peripheral blood mononuclear cells (PBMCs) into individual immune cell types is provided as well.

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lisaClust provides a series of functions to identify and visualise regions of tissue where spatial associations between cell-types is similar. This package can be used to provide a high-level summary of cell-type colocalization in multiplexed imaging data that has been segmented at a single-cell resolution.

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Provides utilities for identifying drug-target interactions for sets of small molecule or gene/protein identifiers. The required drug-target interaction information is obained from a local SQLite instance of the ChEMBL database. ChEMBL has been chosen for this purpose, because it provides one of the most comprehensive and best annotatated knowledge resources for drug-target information available in the public domain.

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Installs a self-contained conda instance that is managed by the R/Bioconductor installation machinery. This aims to provide a consistent Python environment that can be used reliably by Bioconductor packages. Functions are also provided to e

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epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models. It contains two separate peak callers, one for consensus peaks from biological or technical replicates, and one for differential peaks from multi-replicate multi-condition experiments. In differential peak calling, epigraHMM provides window-specific posterior probabilities associated with every possible combinatorial pattern of read enrichment across conditions.

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This package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated me

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Autonomous compute-reselling agent on Surplus Intelligence - resells free or low-cost provider compute across Bankr, AWS Bedrock, and Google Vertex (GCP) as one skill. Reads the live market + your cost + your usage, auto-lists your models per enabled provider, and reactively prices each offer to win routing within a cost floor, cap, and health guardrails.

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Use when setting up providers, combining requests, managing state disposal, passing arguments, performing side effects, or testing providers (Riverpod).

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Design NestJS module boundaries and provider ownership. Use only when structuring feature/core/shared modules, controller-service boundaries, or provider lifetime; defer JWT/security, caching, and unrelated request-pipeline recipes.

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Implement reactive state management using Riverpod 3.x with code generation in Flutter. Use when defining providers, building AsyncNotifiers, or overriding providers in tests.

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Harden Intent handling, WebView configuration, and FileProvider access in Android apps. Use when securing Intent extras, configuring WebViews, or exposing files via FileProvider; defer manifest export flags and generic Bundle typing to focused Android security guidance.

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Configure DI, inject() usage, and providers in Angular. Use when configuring Angular dependency injection, using inject(), or defining providers.

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Provides design token system and theming framework for consistent, customizable UI styling across all components. Covers complete token taxonomy (color, typography, spacing, shadows, borders, motion, z-index), theme switching (CSS custom properties, theme providers), RTL/i18n support (CSS logical properties), and accessibility (WCAG contrast, high contrast themes, reduced motion). This is the foundational styling layer referenced by ALL component skills. Use when theming components, implementing light/dark mode, creating brand styles, customizing visual design, ensuring design consistency, or supporting RTL languages.

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DO NOT USE when the target already consumes an injected interface or built-in abstraction such as IFileSystem or TimeProvider, even if the request says "generate a wrapper"; no new wrapper is needed. Use only when C# source calls an ambient/static dependency and no injectable seam exists: first-time TimeProvider, IHttpClientFactory, or System.IO.Abstractions adoption; minimal Environment/Console/Process wrappers; IProcessRunner; DI registration; or an ambient seam that preserves a static API. Exclude static detection (detect-static-dependencies), migration to an existing/registered abstraction (migrate-static-to-wrapper), one blocked behavior plus deterministic tests (testability-obstacle), and general interface design.

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Use ManagedCode.Storage when a .NET application needs a provider-agnostic storage abstraction with explicit configuration, container selection, upload and download flows, and backend-specific integration kept. USE FOR: integrating ManagedCode.Storage into a .NET application; reviewing how a project abstracts file or object storage; deciding whether to centralize storage provider. 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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Use when reviewing, designing, or modifying Java enterprise systems from a maintainer-authored or maintainer-sanitized NIS2 engineering evidence inventory. Supports essential or important entities, critical-sector services, managed service providers, supply-chain dependencies, and cybersecurity incident escalation obligations without ingesting raw code, logs, runbooks, tickets, provider documents, or other operational free text. Part of Plinth Toolkit

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