This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.
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Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
BiocManager::install("Rsamtools")DataFrame objects using scanBam.ScanBamParam.BamViews.coverage on imported BAM data.GenomicAlignments (specifically readGAlignments) because Rsamtools provides lower-level list-based outputs.GenomicFiles because it implements higher-level strategies for file iteration.Biostrings or BSgenome instead..bam) and their corresponding index files (.bai).GRanges objects for targeted queries.scanBam.ScanBamParam object determining which genomic coordinates and components to input.GRanges object specifying the genomic ranges to extract.c("rname", "pos", "qwidth")) specifying which BAM record fields to retrieve.scanBamFlag (e.g., isUnmappedQuery=FALSE) to restrict reads.GRanges object defining the genomic rows for a BamViews instance..bai index file is available locally when querying specific ranges with the which argument.what argument in ScanBamParam to minimize memory consumption.BamViews to marshal references to multiple BAM files without loading them immediately into memory.which argument to ScanBamParam requires a BAM index. Fix: Ensure the .bai file exists or create one using indexBam.seqlevels<- to map between naming schemes before querying.GAlignments objects).This skill is the knowledge layer — when, why, and how to use rsamtools. 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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