Annotate variants, compute amino acid coding changes, predict coding outcomes.
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Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
BiocManager::install("VariantAnnotation")readVcf() and ScanVcfParam().locateVariants().predictCoding().SnpMatrix object for downstream GWAS analysis using genotypeToSnpMatrix().TxDb object) matching the VCF's genome assembly.BSgenome or fasta file) matching the VCF's assembly for computing codon changes.GRanges or ScanVcfParam object passed to readVcf() to restrict import to specific genomic coordinates or VCF fields.ScanVcfParam() specifying which INFO fields (e.g., "LDAF", "RSQ") to extract.ScanVcfParam() specifying which FORMAT/genotype fields (e.g., "GT", "DS", "GL") to extract.locateVariants() specifying the region of interest (e.g., CodingVariants(), AllVariants()).BSgenome object passed to predictCoding() to retrieve reference sequences.FALSE): Logical in genotypeToSnpMatrix() indicating whether to use posterior probabilities (GL/GP) instead of called genotypes.ScanVcfParam() to read only the necessary info and geno fields, or use TabixFile() with a GRanges object to stream specific genomic coordinates.TxDb (e.g., using seqlevels(vcf) <- "chr22") before running locateVariants().bgzip and tabix (or indexTabix()) to enable fast, random-access querying.PolyPhen.Hsapiens.dbSNP131 or SIFT.Hsapiens.dbSNP132 to query pre-computed damage predictions for non-synonymous variants identified by predictCoding().TabixFile and use ScanVcfParam to process the file in chunks or subsets.seqlevels().predictCoding() returns frameshifts for all variants. Fix: Ensure the BSgenome reference matches the exact assembly version (e.g., hg19) used to call the variants in the VCF.genotypeToSnpMatrix().This skill is the knowledge layer — when, why, and how to use variantannotation. 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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