Infrastructure to support 'views' used to classify Bioconductor packages. 'biocViews' are directed acyclic graphs of terms from a controlled vocabulary. There are three major classifications, corresponding to 'software', 'annotation', and '
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Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
BiocManager::install("biocViews")genReposControlFiles and writeRepositoryHtml.extractVignettes.BiocViews objects for specific top-level terms (e.g., "Software") using getBiocSubViews.graphNEL object using getSubTerms.BiocCheck or devtools instead because biocViews focuses on repository HTML and vocabulary generation.BiocPkgTools instead because biocViews generates static HTML views.src/contrib) and binary packages (bin/windows/contrib, bin/macosx/contrib).biocViewsVocab.dot) which is converted to a graphNEL object.getSubTerms.writeBiocViews.src/contrib and bin directories before running genReposControlFiles.extractVignettes before generating the repository HTML.getBiocSubViews with a valid graphNEL vocabulary object (like biocViewsVocab) to categorize packages.writeBiocViews pointing to a dedicated output directory.genReposControlFiles without the correct contribPaths names. Fix: Ensure the contribPaths vector has exact names like "source", "win.binary", and "mac.binary".dot2gxl from graphviz is installed and on your PATH.This skill is the knowledge layer — when, why, and how to use biocviews. 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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