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概要と使いどころ
The sva package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. Specifically, the sva package contains functions for the identifying and building surrogate variables for high-dimensi
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standR is an user-friendly R package providing functions to assist conducting good-practice analysis of Nanostring's GeoMX DSP data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. standR allows data inspection, quality control, normalization, batch correction and evaluation with informative visualizations.
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Tools for LiP peptide and protein significance analysis. Provides functions for summarization, estimation of LiP peptide abundance, and detection of changes across conditions. Utilizes functionality across the MSstats family of packages.
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performing all the steps of gene expression meta-analysis considering the possible existence of missing genes. It provides the necessary functions to be able to perform the different methods of gene expression meta-analysis. In addition, it contains functions to apply quality controls, download GEO datasets and show graphical representations of the results.
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Provides functionalities to visualize and contextualize CRISPR guide RNAs (gRNAs) on genomic tracks across nucleases and applications. Works in conjunction with the crisprBase and crisprDesign Bioconductor packages. Plots are produced using the Gviz framework.
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This package implements functions to find influential TF and target based on different input type. It have five module: Multi-peak multi-gene annotaion(mmPeakAnno module), Calculate regulation potential(calcRP module), Find influential Target based on ChIP-Seq and RNA-Seq data(Find influential Target module), Find influential TF based on different input(Find influential TF module), Calculate peak-gene or peak-peak correlation(peakGeneCor module). And there are also some other useful function lik
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The BloodGen3Module package provides functions for R user performing module repertoire analyses and generating fingerprint representations. Functions can perform group comparison or individual sample analysis and visualization by fingerprint grid plot or fingerprint heatmap. Module repertoire analyses typically involve determining the percentage of the constitutive genes for each module that are significantly increased or decreased. As we describe in details;https://www.biorxiv.org/content/10.11
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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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hoodscanR is an user-friendly R package providing functions to assist cellular neighborhood analysis of any spatial transcriptomics data with single-cell resolution. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. The package can result in cell-level neighborhood annotation output, along with funtions to perform neighborhood colocalization analysis and neighborhood-based ce
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This package supports functional characteristics of both coding and non-coding genomics data for thousands of species with up-to-date gene annotation. It provides a univeral interface for gene functional annotation from a variety of sources
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This package builds on existing tools and adds some simple but extremely useful capabilities for working wth ChIP-Seq data. The focus is on detecting differential binding windows/regions. One set of functions focusses on set-operations retaining mcols for GRanges objects, whilst another group of functions are to aid visualisation of results. Coercion to tibble objects is also implemented.
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Functions that are needed by many other packages or which replace R functions.
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Expert knowledge for Azure Static Web Apps development including troubleshooting, decision making, limits & quotas, security, configuration, integrations & coding patterns, and deployment. Use when wiring SWA APIs to Azure DBs, configuring custom domains/backends, Entra auth, CI/CD, or plan limits, and other Azure Static Web Apps related development tasks. Not for Azure App Service (use azure-app-service), Azure Functions (use azure-functions), Azure Container Apps (use azure-container-apps), Azure Logic Apps (use azure-logic-apps).
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Expert knowledge for Azure Spring Apps development including troubleshooting, best practices, decision making, architecture & design patterns, limits & quotas, security, configuration, integrations & coding patterns, and deployment. Use when configuring ASA networking/security, Tanzu tools, observability/APM, CI/CD deployments, or blue‑green releases, and other Azure Spring Apps related development tasks. Not for Azure App Service (use azure-app-service), Azure Container Apps (use azure-container-apps), Azure Kubernetes Service (AKS) (use azure-kubernetes-service), Azure Functions (use azure-functions).
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Expert knowledge for Azure Stream Analytics development including troubleshooting, best practices, decision making, architecture & design patterns, limits & quotas, security, configuration, integrations & coding patterns, and deployment. Use when building ASA jobs with Event Hubs/Kafka, Cosmos/SQL outputs, ML/UDF queries, autoscale, or IoT Edge clusters, and other Azure Stream Analytics related development tasks. Not for Azure Synapse Analytics (use azure-synapse-analytics), Azure Data Factory (use azure-data-factory), Azure Event Hubs (use azure-event-hubs), Azure Functions (use azure-functions).
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Expert knowledge for Azure Logic Apps development including troubleshooting, best practices, decision making, architecture & design patterns, limits & quotas, security, configuration, integrations & coding patterns, and deployment. Use when building Logic Apps with AI/OpenAI, SAP/B2B, private endpoints, DevOps deployments, or DR/multi-region designs, and other Azure Logic Apps related development tasks. Not for Azure Functions (use azure-functions), Azure App Service (use azure-app-service), Azure Service Bus (use azure-service-bus), Azure Data Factory (use azure-data-factory).
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Expert knowledge for Azure Operator Service Manager development including troubleshooting, best practices, security, configuration, and integrations & coding patterns. Use when onboarding CNFs/VNFs, designing config groups, managing ACR artifacts, using ARM/CLI, or securing with Private Link, and other Azure Operator Service Manager related development tasks. Not for Azure Operator Nexus (use azure-operator-nexus), Azure Operator Insights (use azure-operator-insights), Azure Network Function Manager (use azure-network-function-manager), Azure Networking (use azure-networking).
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Expert knowledge for Azure Firewall Manager development including best practices, decision making, security, and configuration. Use when configuring DDoS plans, DNS proxy, FQDN/IP groups, WAF policies, or secured virtual hubs, and other Azure Firewall Manager related development tasks. Not for Azure Firewall (use azure-firewall), Azure Virtual Network Manager (use azure-virtual-network-manager), Azure Network Function Manager (use azure-network-function-manager), Azure Web Application Firewall (use azure-web-application-firewall).
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Expert knowledge for Azure Durable Task development including best practices, decision making, architecture & design patterns, limits & quotas, configuration, integrations & coding patterns, and deployment. Use when choosing Durable storage backends, versioning orchestrations, using fan-out/fan-in, human approvals, or instance APIs, and other Azure Durable Task related development tasks. Not for Azure Functions (use azure-functions), Azure Logic Apps (use azure-logic-apps), Azure App Service (use azure-app-service), Azure Service Fabric (use azure-service-fabric).
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Expert knowledge for Azure Health Bot development including best practices, security, configuration, and integrations & coding patterns. Use when wiring Teams/SMS/WhatsApp channels, embedding web chat, calling external APIs, configuring handoff, or enforcing consent, and other Azure Health Bot related development tasks. Not for Azure AI Bot Service (use azure-bot-service), Azure Communication Services (use azure-communication-services), Azure Functions (use azure-functions).
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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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Expert knowledge for Azure App Configuration development including troubleshooting, best practices, decision making, limits & quotas, security, configuration, integrations & coding patterns, and deployment. Use when using feature flags, dynamic config refresh, snapshots, Key Vault integration, or CI/CD config sync, and other Azure App Configuration related development tasks. Not for Azure App Service (use azure-app-service), Azure Key Vault (use azure-key-vault), Azure Functions (use azure-functions).
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Expert knowledge for Azure App Service development including troubleshooting, best practices, decision making, architecture & design patterns, limits & quotas, security, configuration, integrations & coding patterns, and deployment. Use when configuring App Service plans/slots, VNet integration, managed identity/Key Vault, CI/CD deployments, or diagnostics, and other Azure App Service related development tasks. Not for Azure Functions (use azure-functions), Azure Static Web Apps (use azure-static-web-apps), Azure Spring Apps (use azure-spring-apps), Azure Container Apps (use azure-container-apps).
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Expert knowledge for Azure AI Bot Service development including troubleshooting, decision making, limits & quotas, security, configuration, integrations & coding patterns, and deployment. Use when using Direct Line 3.0, configuring Teams/Web Chat channels, setting App Service bots, CI/CD, or App Insights, and other Azure AI Bot Service related development tasks. Not for Azure Health Bot (use azure-health-bot), Azure Functions (use azure-functions), Azure App Service (use azure-app-service).
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