Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/imp
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Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
BiocManager::install("rtracklayer")GRanges objects using import and export.browserSession.track<- function.ucscTableQuery and getTable.GenomicRanges instead.GenomicAlignments or Rsamtools instead, as rtracklayer is designed for annotation tracks.GRanges in R.import or export.browserSession.GRanges object specifying the genomic segment to view or download.ucscTableQuery.ucscTableQuery.GRangesForUCSCGenome to formally associate interval data with a UCSC genome build and validate bounds before uploading.GRanges tracks before uploading or viewing (e.g., targetTrack[1:10]) to avoid overwhelming the browser session.export and import which derives the format from the file extension.GRanges use 1-based coordinates, while formats like BED use 0-based. Fix: rtracklayer handles this automatically during import/export, so avoid manual coordinate shifting.browseGenome to load tracks and set the view in a single call.This skill is the knowledge layer — when, why, and how to use rtracklayer. 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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