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PSMatch:Handling and Managing Peptide Spectrum Matches
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 make informed decision about shared peptide filtering. The package also provides functions to calculate and visualise MS2 fragment ions.
Maintained by Laurent Gatto. Last updated 5 months ago.
infrastructureproteomicsmassspectrometrymass-spectrometrypeptide-spectrum-matches
3 stars 8.40 score 15 scripts 39 dependentsbioc
ReducedExperiment:Containers and tools for dimensionally-reduced -omics representations
Provides SummarizedExperiment-like containers for storing and manipulating dimensionally-reduced assay data. The ReducedExperiment classes allow users to simultaneously manipulate their original dataset and their decomposed data, in addition to other method-specific outputs like feature loadings. Implements utilities and specialised classes for the application of stabilised independent component analysis (sICA) and weighted gene correlation network analysis (WGCNA).
Maintained by Jack Gisby. Last updated 3 months ago.
geneexpressioninfrastructuredatarepresentationsoftwaredimensionreductionnetworkbioconductor-packagebioinformaticsdimensionality-reduction
3 stars 4.13 score 8 scripts