「functions」の検索結果

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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Implements a variety of methods for combining p-values in differential analyses of genome-scale datasets. Functions can combine p-values across different tests in the same analysis (e.g., genomic windows in ChIP-seq, exons in RNA-seq) or fo

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This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. Users are given the option to create or extend a reference atlas and,also simulate the desired size of the bulk signature profile of the reference cell types.The package includes the cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can be used in deconvolution. Additionally,we included BS

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This package implements a metabolic network analysis pipeline to identify an active metabolic module based on high throughput data. The pipeline takes as input transcriptional and/or metabolic data and finds a metabolic subnetwork (module) most regulated between the two conditions of interest. The package further provides functions for module post-processing, annotation and visualization.

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Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and off-target search, on-target efficiency scoring, off-target scoring, full gene and TSS contextual annotations, and SNP annotation (human only). It currently support five types of CRISPR modalities (modes of perturbations): CRISPR knockout, CRISPR activation, CRISPR inhibition, CRISPR base editing, and CRISPR knockdown. All types of CRISPR nucleases are supported, including

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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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Manhattan plot and QQ Plot are commonly used to visualize the end result of Genome Wide Association Study. The "ggmanh" package aims to keep the generation of these plots simple while maintaining customizability. Main functions include manhattan_plot, qqunif, and thinPoints.

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The PSMatch package helps proteomics practitioners to load, handle and manage Peptide Spectrum Matches. It provides functions to model peptide-protein relations as adjacency matrices and connected components, visualise these as graphs and m

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Provides S4 data structures and basic functions to deal with flow cytometry data.

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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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Generate SuperSigs (supervised mutational signatures) from single nucleotide variants in the cancer genome. Functions included in the package allow the user to learn supervised mutational signatures from their data and apply them to new data. The methodology is based on the one described in Afsari (2021, ELife).

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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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Functions for plotting genomic data

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Some basic functions for filtering genes.

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Client for the gypsum REST API (https://gypsum.artifactdb.com), a cloud-based file store in the ArtifactDB ecosystem. This package provides functions for uploads, downloads, and various adminstrative and management tasks. Check out the docu

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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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Expert knowledge for Azure Horizondb development including troubleshooting, best practices, decision making, architecture & design patterns, limits & quotas, security, configuration, integrations & coding patterns, and deployment. Use when tuning pgvector, azure_ai SQL functions, LangChain vector stores, Apache AGE graphs, or hybrid search, and other Azure Horizondb related development tasks. Not for Azure Cosmos DB (use azure-cosmos-db), Azure SQL Database (use azure-sql-database), Azure Table Storage (use azure-table-storage).

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Expert knowledge for Azure Event Grid development including troubleshooting, best practices, decision making, architecture & design patterns, limits & quotas, security, configuration, and integrations & coding patterns. Use when configuring Event Grid/MQTT namespaces, securing endpoints, routing events, integrating Functions/Service Bus, or troubleshooting delivery, and other Azure Event Grid related development tasks. Not for Azure Event Hubs (use azure-event-hubs), Azure Service Bus (use azure-service-bus), Azure Notification Hubs (use azure-notification-hubs), Azure Web PubSub (use azure-web-pubsub).

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Transfer code between files with line-based precision. Use when users request copying code from one location to another, moving functions or classes between files, extracting code blocks, or inserting code at specific line numbers.

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Perform bulk code refactoring operations like renaming variables/functions across files, replacing patterns, and updating API calls. Use when users request renaming identifiers, replacing deprecated code patterns, updating method calls, or making consistent changes across multiple locations.

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Train and optimize AI agents using Microsoft's Agent Lightning framework with reinforcement learning. Use when setting up agent training, instrumenting agents with tracing, configuring LightningStore, implementing reward functions, or optimizing prompts with RL/APO algorithms.

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Write maintainable Python with small functions, explicit boundaries, guard clauses, and readable state flow. Use when refactoring Python services, helpers, modules, or async logic for clarity—not generic test writing, tooling setup, or database transaction implementation.

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Write safe, structured concurrent code with Kotlin Coroutines. Use for suspend functions, coroutine scopes, cancellation, and coroutine leaks; defer Java Virtual Threads, Android WorkManager/Fragment lifecycle, Compose state hoisting, and Detekt/tooling configuration.

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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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