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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Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
BiocManager::install("ExperimentHub")ExperimentHub web service.SummarizedExperiment, ExpressionSet, or GAlignmentPairs directly into your session.BiocHubsShiny.AnnotationHub because ExperimentHub is focused exclusively on experimental data.TRUE in ExperimentHub to use only the local cache and avoid internet queries.FALSE in removeCache to bypass interactive prompts when deleting the cache.rappdirs::user_cache_dir to specify the package name (e.g., "ExperimentHub").tools::R_user_dir to specify the directory type (e.g., "cache").query to search for specific strings and filter the ExperimentHub object before downloading.snapshotDate and use possibleDates to ensure reproducibility with older versions of a snapshot.tools::R_user_dir or by setting the EXPERIMENT_HUB_CACHE environment variable.EXPERIMENT_HUB_PROXY environment variable or using setExperimentHubOption.BiocFileCache.sqlite and BiocFileCache.sqlite.LOCK to g+rw.tools::R_user_dir location or setting EXPERIMENT_HUB_CACHE.This skill is the knowledge layer — when, why, and how to use experimenthub. To run this analysis on your own data with managed compute, automated QC, and reproducible outputs, use BioMate — free to start.
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The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.
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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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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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apeglm provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients.
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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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AUCell allows to identify cells with active gene sets (e.g. signatures, gene modules...) in single-cell RNA-seq data. AUCell uses the "Area Under the Curve" (AUC) to calculate whether a critical subset of the input gene set is enriched with
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