A parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less 'pretty' output than a vendor specific parser. Please contact th
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Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
BiocManager::install("mzID")mzIdentML (.mzid) files containing peptide and protein identification results using the mzID() function.data.frame objects using the flatten() function.mzR instead because mzID only parses identification files.MSnbase instead because mzID is strictly a barebones parser for identification data.mzIdentML (.mzid) files conforming to the HUPO-PSI schema.mzID object contains slots for parameters, psm, peptides, evidence, and database.mzID()).flatten() function immediately after parsing to convert the complex S4 mzID object into a flat data.frame for standard R operations.names()), as ambiguity can arise (e.g., length refers to the nucleotide sequence coding for the protein, not the peptide length).nchar() and substr() on the sequence columns to verify you are working with the expected string lengths.length column in a flattened data.frame refers to the peptide sequence length. Fix: Inspect the content using flatResults$length and verify it refers to the protein's nucleotide sequence length.This skill is the knowledge layer — when, why, and how to use mzid. 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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