「express」の検索結果

Given a matrix of counts (e.g. from featureCounts) and optional information about the genes, this tool performs differential expression (DE) using the limma Bioconductor package and produces plots and tables useful in DE analysis. Interacti

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mastR is an R package designed for automated screening of signatures of interest for specific research questions. The package is developed for generating refined lists of signature genes from multiple group comparisons based on the results from edgeR and limma differential expression (DE) analysis workflow. It also takes into account the background noise of tissue-specificity, which is often ignored by other marker generation tools. This package is particularly useful for the identification of g

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ASURAT is a software for single-cell data analysis. Using ASURAT, one can simultaneously perform unsupervised clustering and biological interpretation in terms of cell type, disease, biological process, and signaling pathway activity. Inputting a single-cell RNA-seq data and knowledge-based databases, such as Cell Ontology, Gene Ontology, KEGG, etc., ASURAT transforms gene expression tables into original multivariate tables, termed sign-by-sample matrices (SSMs).

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Estimates differential gene expression for short read sequence count using methods appropriate for count data. If you have paired data you may also want to consider Tophat/Cufflinks. Input must be raw count data for each sequence arranged i

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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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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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This package provides the visualization of bayesian network inferred from gene expression data. The networks are based on enrichment analysis results inferred from packages including clusterProfiler and ReactomePA. The networks between pathways and genes inside the pathways can be inferred and visualized.

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Implements a variety of methods for batch correction of single-cell (RNA sequencing) data. This includes methods based on detecting mutually nearest neighbors, as well as several efficient variants of linear regression of the log-expression

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Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data fr

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Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA) provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP and Copy number variation data. It's easy to download data from TCGA using the gdc tool, but processing these data into a format suitable for bioinformatics analysis requires more work. This R package was developed to handle these data.

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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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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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Connect new gene expression profile with the relevant information from the existing databases, such as previous publications, MeSH terms, and gene sets.

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Volcano plots represent a useful way to visualise the results of differential expression analyses. Here, we present a highly-configurable function that produces publication-ready volcano plots. EnhancedVolcano will attempt to fit as many po

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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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Expert knowledge for Azure Dedicated HSM development including troubleshooting, decision making, architecture & design patterns, security, integrations & coding patterns, and deployment. Use when configuring ExpressRoute IP SKUs, migrating Dedicated HSMs, securing HSM networks, or scripting HSM provisioning, and other Azure Dedicated HSM related development tasks. Not for Azure Cloud Hsm (use azure-cloud-hsm), Azure Key Vault (use azure-key-vault), Azure Payment Hsm (use azure-payment-hsm).

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Expert knowledge for Azure Enclave development including troubleshooting, best practices, decision making, architecture & design patterns, limits & quotas, security, configuration, and deployment. Use when building DMZ/AVD/AKS enclave apps, configuring RBAC/CMK, deploying via Bicep/ARM, or setting up ExpressRoute/VPN, and other Azure Enclave related development tasks. Not for Azure Confidential Computing (use azure-confidential-computing), Azure Attestation (use azure-attestation), Azure Dedicated HSM (use azure-dedicated-hsm), Azure Cloud Hsm (use azure-cloud-hsm).

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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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Design and build expressive 3D scenes, explainers and interactive models with grounded subject knowledge. Use for 3D creation or edits, including scientific visualization and spatial puzzles.

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Write a brand manifesto — a bold, belief-driven declaration of what the brand stands for, fights against, and exists to change. Use when the user says "brand manifesto", "manifesto", "what we believe", "brand declaration", "brand belief statement", "rally the team around the brand", "inspire the team", "internal brand document", "culture document", "why we exist statement", "brand credo", "brand creed", or wants to write something that goes beyond a mission statement to express the brand's conviction and worldview.

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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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Use when a designer needs hands-on production direction inside a tool — Canva, Figma, or Adobe Express: which template to start from, the operating order, element-by-element mapping, grid and spacing, brand kit colors and fonts, export checklist, and the dos and do-nots. Trigger on 'Canva brief', 'Figma brief', 'production direction', 'how do I build this in Canva', 'layout direction for the designer', 'the junior designer needs step by step'. Not for — the creative concept for a static, see `42-image-brief-global`; the concept for a slide sequence, see `43-carousel-brief-global`; the brand rules being applied, see `46-brand-guideline-global`; adapting one master into every size, see `50-asset-resize-global`.

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Helps users discover and install agent skills when they ask questions like "how do I do X", "find a skill for X", "is there a skill that can...", or express interest in extending capabilities. This skill should be used when the user is looking for functionality that might exist as an installable skill.

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