MSnbase - Base Functions and Classes for Mass Spectrometry and Proteomics
MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.
Last updated 10 days ago
immunooncologyinfrastructureproteomicsmassspectrometryqualitycontroldataimportbioconductorbioinformaticsmass-spectrometryproteomics-datavisualisation
12.80 score 125 stars 35 packages 712 scripts 5.6k downloads
QFeatures - Quantitative features for mass spectrometry data
The QFeatures infrastructure enables the management and processing of quantitative features for high-throughput mass spectrometry assays. It provides a familiar Bioconductor user experience to manages quantitative data across different assay levels (such as peptide spectrum matches, peptides and proteins) in a coherent and tractable format.
Last updated 24 days ago
infrastructuremassspectrometryproteomicsmetabolomicsbioconductormass-spectrometry
11.43 score 25 stars 47 packages 240 scripts 3.3k downloadspRoloc - A unifying bioinformatics framework for spatial proteomics
The pRoloc package implements machine learning and visualisation methods for the analysis and interogation of quantitiative mass spectrometry data to reliably infer protein sub-cellular localisation.
Last updated 24 days ago
immunooncologyproteomicsmassspectrometryclassificationclusteringqualitycontrolbioconductorproteomics-dataspatial-proteomicsvisualisation
10.36 score 15 stars 2 packages 100 scripts 471 downloadsProtGenerics - Generic infrastructure for Bioconductor mass spectrometry packages
S4 generic functions and classes needed by Bioconductor proteomics packages.
Last updated 24 days ago
infrastructureproteomicsmassspectrometrybioconductormass-spectrometrymetabolomics
9.38 score 8 stars 187 packages 4 scripts 19k downloadsrols - An R interface to the Ontology Lookup Service
The rols package is an interface to the Ontology Lookup Service (OLS) to access and query hundred of ontolgies directly from R.
Last updated 24 days ago
immunooncologysoftwareannotationmassspectrometrygo
8.57 score 11 stars 5 packages 84 scripts 722 downloads
MsExperiment - Infrastructure for Mass Spectrometry Experiments
Infrastructure to store and manage all aspects related to a complete proteomics or metabolomics mass spectrometry (MS) experiment. The MsExperiment package provides light-weight and flexible containers for MS experiments building on the new MS infrastructure provided by the Spectra, QFeatures and related packages. Along with raw data representations, links to original data files and sample annotations, additional metadata or annotations can also be stored within the MsExperiment container. To guarantee maximum flexibility only minimal constraints are put on the type and content of the data within the containers.
Last updated 24 days ago
infrastructureproteomicsmassspectrometrymetabolomicsexperimentaldesigndataimport
8.54 score 5 stars 14 packages 108 scripts 2.0k downloadsPSMatch - 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.
Last updated 24 days ago
infrastructureproteomicsmassspectrometrymass-spectrometrypeptide-spectrum-matches
8.18 score 3 stars 37 packages 15 scripts 1.7k downloadsmzID - An mzIdentML parser for R
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 the maintainer with any problems and supply an mzIdentML file so the problems can be fixed quickly.
Last updated 24 days ago
immunooncologydataimportmassspectrometryproteomics
7.81 score 36 packages 32 scripts 4.7k downloadspRolocGUI - Interactive visualisation of spatial proteomics data
The package pRolocGUI comprises functions to interactively visualise spatial proteomics data on the basis of pRoloc, pRolocdata and shiny.
Last updated 24 days ago
proteomicsvisualizationgui
7.02 score 7 stars 3 scripts 234 downloadsqcmetrics - A Framework for Quality Control
The package provides a framework for generic quality control of data. It permits to create, manage and visualise individual or sets of quality control metrics and generate quality control reports in various formats.
Last updated 24 days ago
immunooncologysoftwarequalitycontrolproteomicsmicroarraymassspectrometryvisualizationreportwriting
6.21 score 2 stars 2 packages 237 downloadssynapter - Label-free data analysis pipeline for optimal identification and quantitation
The synapter package provides functionality to reanalyse label-free proteomics data acquired on a Synapt G2 mass spectrometer. One or several runs, possibly processed with additional ion mobility separation to increase identification accuracy can be combined to other quantitation files to maximise identification and quantitation accuracy.
Last updated 24 days ago
immunooncologymassspectrometryproteomicsqualitycontrol
6.03 score 4 stars 5 scripts 316 downloadsrpx - R Interface to the ProteomeXchange Repository
The rpx package implements an interface to proteomics data submitted to the ProteomeXchange consortium.
Last updated 24 days ago
immunooncologyproteomicsmassspectrometrydataimportthirdpartyclientbioconductordatamass-spectrometryproteomexchange
6.00 score 5 stars 20 scripts 496 downloadsCTdata - Data companion to CTexploreR
Data from publicly available databases (GTEx, CCLE, TCGA and ENCODE) that go with CTexploreR in order to re-define a comprehensive and thoroughly curated list of CT genes and their main characteristics.
Last updated 24 days ago
transcriptomicsepigeneticsgeneexpressiondataimportexperimenthubsoftware
5.69 score 1 stars 1 packages 1 scripts 118 downloadshpar - Human Protein Atlas in R
The hpar package provides a simple R interface to and data from the Human Protein Atlas project.
Last updated 24 days ago
proteomicscellbiologydataimportfunctionalgenomicssystemsbiologyexperimenthubsoftware
5.41 score 1 packages 17 scripts 632 downloadsMsDataHub - Mass Spectrometry Data on ExperimentHub
The MsDataHub package uses the ExperimentHub infrastructure to distribute raw mass spectrometry data files, peptide spectrum matches or quantitative data from proteomics and metabolomics experiments.
Last updated 24 days ago
experimenthubsoftwaremassspectrometryproteomicsmetabolomicsbioconductordatamass-spectrometry
4.88 score 1 stars 2 scripts 133 downloadsRforMassSpectrometry - R for MassSpectrometry meta-package
The RforMassSpectrometry meta-package loads and manages the core packages of the R for Mass Spectrometry initiative, that provide efficient, thoroughly documented, tested and flexible R software for the analysis and interpretation of high throughput mass spectrometry assays.
Last updated 11 months ago
4.20 score 16 starsSpectraVis - Visualising and Exploring Spectra Data
This package defines a set of helper function to visualise and explore mass spectrometry data stored as Spectra objects.
Last updated 3 years ago
proteomicsmassspectrometrymetabolomicsvisualizationbioconductormass-spectrometryspectravisualisation
2.30 score 4 stars 1 scriptsMsQuantitation - Mass Spectrometry Quantitation
This package quantitates raw mass spectrometry data contained in Spectra objects into QFeaures instances.
Last updated 2 years ago
2.18 score 3 starsrWSBIM1207 - Companion Package for WSBIM1207 Course
Companion package for the WSBIM1207 course, distributing data and general documentation, and making course administration easier.
Last updated 5 months ago
2.00 score 7 scriptsrWSBIM2122 - Companion Package for WSBIM2122 Course
Companion package for the WSBIM2122 course, distributing data and general documentation, and making course administration easier.
Last updated 2 years ago
1.74 score 11 scriptsrWSBIM1322 - Companion Package for WSBIM1322 Course
Companion package for the WSBIM1322 course, distributing data and general documentation, and making course administration easier.
Last updated 2 years ago
1.70 score 1 scripts