The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.
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Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
BiocManager::install("OrganismDbi")TxDb and OrgDb) simultaneously through a single unified interface using select.OrganismDbi meta-packages (like Homo.sapiens) that link genome-centric and gene-centric databases using makeOrganismPackage.transcripts, exons, or cds.transcriptsBy, exonsBy, or cdsBy.OrgDb or TxDb packages available to link together.org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, GO.db).graphData) when building custom packages.select or keys."ENTREZID") provided to select or keys.c("TXNAME", "SYMBOL")) in select, transcripts, or transcriptsBy."gene") used in transcriptsBy."Homo.sapiens") in makeOrganismPackage.makeOrganismPackage.keytypes() and columns() to inspect valid query fields before executing a search.select() method to retrieve multi-database annotations in a single tabular format.transcripts(Homo.sapiens, columns=...) to get GRanges objects pre-annotated with gene metadata.makeOrganismPackage are from the same build (e.g., hg19).TxDb and OrgDb versions. Fix: Ensure the underlying TxDb and OrgDb packages correspond to the same genome assembly and annotation release.columns are unique across ALL of the supporting packages before using makeOrganismPackage.graphData list with multiple pathways between nodes. Fix: Choose exactly one foreign key relationship to connect any two packages in your graph.OrgDb databases.TxDb transcript databases.This skill is the knowledge layer — when, why, and how to use organismdbi. 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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