KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essenti
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BiocManager::install("KEGGgraph")graphNEL objects using parseKGML2Graph.subGraphByNodeType) or specific neighborhoods (using subKEGGgraph).mergeGraphs.brandes.betweenness.centrality from RBGL) on biological pathways.KGML-ED instead.SPIA instead.ggplot2-based visualization of KEGG pathways, use ggkegg instead because KEGGgraph relies on Rgraphviz for rendering.retrieveKGML.parseKGML2Graph; if TRUE, non-gene nodes (like compounds or maps) are removed from the graph.parseKGML2Graph or KEGGpathway2Graph; if TRUE, nodes representing multiple homologues are topologically expanded.retrieveKGML.retrieveKGML.expandGenes=TRUE when parsing to ensure that nodes representing multiple gene products (homologues) are expanded into individual nodes.mergeGraphs to union related pathways together, which helps resolve disconnected nodes that lack edges in a single specific disease pathway.translateGeneID2KEGGID to map Entrez Gene IDs from microarray data to KEGG IDs before performing graph operations.subKEGGgraph to divide and conquer large pathways, maintaining KEGG information while subsetting the graph.mergeGraphs to combine linked pathways.expandGenes=TRUE during parsing.translateGeneID2KEGGID or translateKEGGID2GeneID.This skill is the knowledge layer — when, why, and how to use kegggraph. 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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