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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Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
BiocManager::install("gypsum")saveFile, saveVersion, fetchManifest, and fetchSummary.startUpload, uploadFiles, and completeUpload.cloneVersion and prepareDirectoryUpload.validateMetadata.setPermissions, approveProbation, and setQuota.googleCloudStorageR instead.BiocManager or AnnotationHub instead.BiocFileCache instead.setAccessToken. Read operations are public.startUpload and uploadFiles.cloneVersion.startUpload to deduplicate redundant files on the backend by linking to existing files.uploadFiles, completeUpload) in a tryCatch block and call abortUpload in the error handler to clean up if the upload fails.cloneVersion and prepareDirectoryUpload to expedite the creation of new asset versions by linking unmodified files to their counterparts in the previous version.validateMetadata against the schema fetched by fetchMetadataSchema to ensure downstream databases can index the files.fetchUsage and fetchQuota before initiating large uploads to ensure sufficient storage space.setAccessToken or prompting the user.cloneVersion, modifying a symlinked file directly will alter the linked source; fix this by deleting the symlink and replacing it with a new file before uploading.completeUpload after uploadFiles leaves the upload in a pending state; ensure the full upload sequence is executed.This skill is the knowledge layer — when, why, and how to use gypsum. 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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