The PSMatch package helps proteomics practitioners to load, handle and manage Peptide Spectrum Matches. It provides functions to model peptide-protein relations as adjacency matrices and connected components, visualise these as graphs and m
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Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
BiocManager::install("PSMatch")calculateFragments.plotSpectraPTM.makeAdjacencyMatrix.ConnectedComponents to explore shared and unique peptides.Spectra because PSMatch relies on it for raw data representation and extraction.QFeatures because PSMatch focuses on PSM-level filtering and structural relationships.PTMods because PSMatch delegates canonical modification handling to it.PSM object containing columns for peptide sequences (e.g., "sequence") and protein accessions (e.g., "DatabaseAccess").Spectra object for fragment ion visualisation.SummarizedExperiment object with protein groups named by peptide sequences.calculateFragments and plotSpectraPTM to apply carbamidomethylation of cysteines by default.calculateFragments or plotSpectraPTM to apply variable mass modifications.makeAdjacencyMatrix to create a binary matrix instead of counting occurrences.plotAdjacencyMatrix to control protein node colours based on string distances.plotAdjacencyMatrix to colour peptide nodes (e.g., by search engine score).makeAdjacencyMatrix (e.g., ";") to split protein groups into individual proteins.filterPsmDecoy and filterPsmRank before constructing adjacency matrices.Spectra data with PSM identification data using joinSpectraData to enable fragment visualisation.prioritiseConnectedComponents to rank and identify the most interesting connected components (e.g., those with multiple shared peptides).connectedComponents to manually inspect complex protein groups with plotAdjacencyMatrix.plotSpectraPTM locally or adjust the xlim parameter in plotSpectra.joinSpectraData will only keep the last instance if duplicates are found in the key.addCarbamidomethyl = TRUE or explicitly pass modifications via fixedModifications.This skill is the knowledge layer — when, why, and how to use psmatch. 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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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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