「expression」の検索結果

Uses DESeq2 to estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.

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The package CellBarcode performs Cellular DNA Barcode analysis. It can handle all kinds of DNA barcodes, as long as the barcode is within a single sequencing read and has a pattern that can be matched by a regular expression. \code{CellBarcode} can handle barcodes with flexible lengths, with or without UMI (unique molecular identifier). This tool also can be used for pre-processing some amplicon data such as CRISPR gRNA screening, immune repertoire sequencing, and metagenome data.

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Methods to infer clonal tree configuration for a population of cells using single-cell RNA-seq data (scRNA-seq), and possibly other data modalities. Methods are also provided to assign cells to inferred clones and explore differences in gene expression between clones. These methods can flexibly integrate information from imperfect clonal trees inferred based on bulk exome-seq data, and sparse variant alleles expressed in scRNA-seq data. A flexible beta-binomial error model that accounts for stoc

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This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype. For that, users must define a set of guide genes, which are known genes involved in the studied phenotype. Additionally, the mined candidates can be given a score that favor candidates that are hubs and/or transcription factors. The scores can then be used to rank and select the top n most promising genes for downstream experiments.

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This tool uses the label-tree function from HyPhy to annotate a phylogenetic tree. It allows users to select a subset of leaves using either a regular expression or a list of sequence names, and then apply a specified label to these selecte

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Local user-profile maintenance skill for Codex, Claude Code, OpenClaw, OpenCode, and other agent harnesses. Use only when the user explicitly invokes $user-profile-keeper to create, initialize, update, query, correct, delete, export, or audit a local persistent user profile. It can extract durable collaboration preferences, requirement-expression habits, capability boundaries, recurring omissions, risk preferences, privacy boundaries, and typical events from the current session into auditable, confirmable, retractable local profile data. Do not auto-invoke, upload profile data, or replace task-clarifier's normal clarification flow.

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Creates and manages reusable character profiles (Soul IDs) for consistent facial and stylistic identity across multiple image and video generations. Provides identity-vs-motion prompt separation, character sheet creation workflows, micro-expression direction, and Soul Cast AI actor configuration. Use when the user wants to maintain character consistency across multiple generations, asks about Soul ID, creating reusable characters, or generating consistent people across different scenes and shots.

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F# language-specific patterns, Railway-Oriented Programming, and Computation Expressions

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Provides bidirectional translation (Chinese/English), grammar checking, and sentence polishing. Supports specific tense constraints, context-aware tone adjustment, and natural expression optimization. Outputs direct text without formatting.

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Write idiomatic Kotlin 1.9+ with null safety, sealed classes, data classes, extension functions, delegates, collections, inline/reified generics, and expression syntax. Use for Kotlin language constructs, Java-to-Kotlin migration, lazy delegates, data classes, backing properties, or inline/reified generics; keep language constructs in scope even inside response models, and defer coroutine configuration, Android Context/framework, Retrofit/OkHttp client setup, and other library-specific recipes.

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Dart 3.x language feature standards: null safety, records, sealed classes, switch pattern matching, extensions, and async/await. Use when using !, ?., ??, late, sealed classes, record types, switch expressions, or async patterns — and before introducing any new Dart 3.x construct to confirm the modern idiomatic approach.

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Type design analysis — encapsulation, invariant expression, usefulness, and enforcement.

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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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Write, review, or modernize F# code in .NET repositories with functional-first design, algebraic data types, pattern matching, pipelines, async workflows, project ordering, and C# interop. USE FOR: F# .fs/.fsproj code; discriminated unions, records, options, results, pattern matching, computation expressions, or functional domain modeling; strongly typed AI-generated .NET code. DO NOT USE FOR: C# language modernization; FSI-only exploratory scripts with no project changes. INVOKES: inspect .fsproj file order and SDK settings, edit F# source and project files, and run dotnet build/test or dotnet fsi validation commands when changes are made.

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Author and review GitHub Actions workflow YAML safely so syntactically-valid YAML can't ship a workflow that GitHub Actions refuses to run. USE FOR: editing, adding, or reviewing any file under .github/workflows/, writing run-name/name/if/env/run values that contain ${{ }} expressions, diagnosing a run that fails with 'This run likely failed because of a workflow file issue' and no jobs starting, deciding when a workflow scalar must be quoted, validating workflows with actionlint. DO NOT USE FOR: authoring application YAML unrelated to GitHub Actions, Azure Pipelines, GitLab CI, or non-workflow YAML. SCOPE: this skill covers *syntactic/structural* correctness of workflow YAML (quoting, parsing, actionlint); for *semantic and functional* workflow design (what a workflow should do, agentic-workflow behavior), see .github/agents/agentic-workflows.agent.md — the two are complementary. INVOKES: actionlint (downloaded pinned binary) plus git/grep for inspection.

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Calculate mathematical expressions using shell commands. Use when the user asks to perform arithmetic calculations like addition, subtraction, multiplication, division, or powers.

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Use when you need to refactor Java code to adopt modern Java features (Java 8+) — including migrating anonymous classes to lambdas, replacing Iterator loops with Stream API, adopting Optional for null safety, switching from legacy Date/Calendar to java.time, using collection factory methods, applying text blocks, var inference, or leveraging Java 25 features like flexible constructor bodies and module import declarations. This should trigger for requests such as Review Java code for modern Java development; Apply best practices for modern Java development in Java code; Modernize Java code with records pattern matching or switch expressions; Replace legacy idioms with modern Java features; Adopt Java 8+ language features safely. Part of Plinth Toolkit

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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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YouTube thumbnail design with specific dimensions, contrast rules, and mobile preview optimization. Covers safe zones, text placement, face expression psychology, and A/B testing. Use for: YouTube thumbnails, video cover images, click-through optimization. Triggers: youtube thumbnail, thumbnail design, video thumbnail, click through rate, ctr optimization, youtube cover, video cover image, thumbnail maker, thumbnail tips, youtube design, video preview image

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Query CZ CELLxGENE Census (61M+ cells). Filter by cell type/tissue/disease, retrieve expression data, integrate with scanpy/PyTorch, for population-scale single-cell analysis.

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Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

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NCBI GEO access via GEOparse and E-utilities. Search by keyword/organism/platform, download GSE series matrices, parse GPL annotations, extract GSM metadata, load expression matrices into pandas. For single-cell use cellxgene-census; for multi-DB access use gget-genomic-databases.

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NCBI Gene via E-utilities: curated records across 1M+ taxa. Official symbols, aliases, RefSeq IDs, summaries, coordinates, GO, interactions. Use for gene ID resolution and cross-species function queries. For sequences use Ensembl; for expression use geo-database.

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Unified CLI/Python interface to 20+ genomic databases. Gene lookups (Ensembl search/info/seq), BLAST/BLAT, AlphaFold, Enrichr enrichment, OpenTargets disease/drug, CELLxGENE single-cell, cBioPortal/COSMIC cancer, ARCHS4 expression. Spans genomics, proteomics, disease. For batch/advanced BLAST use biopython; for multi-DB Python SDK use bioservices.

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