This tool fetches microarray data directly from GEO database, based on the GEOQuery R package. Given a GSE accession ID, it returns an Rdata object containing the data and a text file (.cond file) summarizing the conditions of the experimen
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Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
BiocManager::install("GEOquery")ExpressionSet using getGEO.searchGEO and searchFieldsGEO.getRNASeqData..mtx or .h5 files, BED files) attached to GEO records using getGEOSuppFiles.DropletUtils (e.g., read10xCounts) directly on your local files instead of routing through GEOquery."GSE2553"): The primary GEO accession string passed to getGEO or getGEOSuppFiles.TRUE): Forces getGEO to use the faster, tab-delimited GSEMatrix files instead of the legacy SOFT format.TRUE): Automatically includes GPL (Platform) annotation when retrieving GSE records.TRUE): When set to FALSE in getGEOSuppFiles, it lists available supplementary files without downloading them.getGEOSuppFiles to download only specific file types (e.g., 'txt').TRUE): Applies a log2 transformation when converting a GDS object to an ExpressionSet using GDS2eSet.GSEMatrix = TRUE (the default) when downloading GSEs, as parsing is 10-100x faster and memory usage is more efficient than legacy SOFT files.hasRNASeqQuantifications before attempting to download and process raw RNA-seq supplementary files.GDS2eSet (for ExpressionSet) or GDS2MA (for limma's MAList).getGSEDataTables to extract additional metadata tables that might not be captured in the standard GSE structure.getGEO returns a list of ExpressionSet objects because a single GSE can contain experiments from multiple platforms; fix this by indexing the list (e.g., gse[[1]]).getGEOSuppFiles on a large GSE can download gigabytes of unwanted data; fix this by running with fetch_files = FALSE first to inspect the file list..mtx file without barcodes and features; fix this by downloading the full tarball or all related supplementary files, then using DropletUtils::read10xCounts on the extracted prefix.DropletUtils: For reading the actual 10x single-cell files (read10xCounts) after GEOquery has downloaded them.limma: For downstream differential expression analysis of the ExpressionSet or MAList objects generated by GEOquery.This skill is the knowledge layer — when, why, and how to use geoquery. 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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