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 5 months ago

immunooncologyinfrastructureproteomicsmassspectrometryqualitycontroldataimportbioconductorbioinformaticsmass-spectrometryproteomics-datavisualisation

124 stars 12.68 score 126 dependencies 31 dependents

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 19 days ago

infrastructuremassspectrometryproteomicsmetabolomicsbioconductormass-spectrometry

24 stars 11.39 score 98 dependencies 43 dependents

pRoloc - 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 4 months ago

immunooncologyproteomicsmassspectrometryclassificationclusteringqualitycontrolbioconductorproteomics-dataspatial-proteomicsvisualisation

15 stars 10.03 score 218 dependencies 2 dependents

ProtGenerics - Generic infrastructure for Bioconductor mass spectrometry packages

S4 generic functions and classes needed by Bioconductor proteomics packages.

Last updated 2 months ago

infrastructureproteomicsmassspectrometrybioconductormass-spectrometrymetabolomics

7 stars 9.25 score 0 dependencies 178 dependents

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 5 months ago

infrastructureproteomicsmassspectrometrymetabolomicsexperimentaldesigndataimport

5 stars 8.48 score 110 dependencies 13 dependents

rols - 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 5 months ago

immunooncologysoftwareannotationmassspectrometrygo

10 stars 8.37 score 17 dependencies 3 dependents

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.

Last updated 5 months ago

infrastructureproteomicsmassspectrometrymass-spectrometrypeptide-spectrum-matches

3 stars 7.92 score 107 dependencies 34 dependents

mzID - 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 5 months ago

immunooncologydataimportmassspectrometryproteomics

7.77 score 8 dependencies 33 dependents

pRolocGUI - 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 1 months ago

proteomicsvisualizationgui

7 stars 7.02 score 231 dependencies

qcmetrics - 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 5 months ago

immunooncologysoftwarequalitycontrolproteomicsmicroarraymassspectrometryvisualizationreportwriting

2 stars 6.21 score 12 dependencies 2 dependents

rpx - R Interface to the ProteomeXchange Repository

The rpx package implements an interface to proteomics data submitted to the ProteomeXchange consortium.

Last updated 5 months ago

immunooncologyproteomicsmassspectrometrydataimportthirdpartyclientbioconductordatamass-spectrometryproteomexchange

5 stars 6.18 score 43 dependencies

synapter - 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 5 months ago

immunooncologymassspectrometryproteomicsqualitycontrol

4 stars 6.03 score 141 dependencies

CTdata - 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 3 days ago

transcriptomicsepigeneticsgeneexpressiondataimportexperimenthubsoftware

1 stars 5.73 score 60 dependencies 1 dependents

hpar - Human Protein Atlas in R

The hpar package provides a simple R interface to and data from the Human Protein Atlas project.

Last updated 5 months ago

proteomicscellbiologydataimportfunctionalgenomicssystemsbiologyexperimenthubsoftware

5.41 score 60 dependencies 1 dependents

MsDataHub - 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 5 months ago

experimenthubsoftwaremassspectrometryproteomicsmetabolomicsbioconductordatamass-spectrometry

1 stars 4.78 score 60 dependencies

RforMassSpectrometry - 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 10 months ago

15 stars 4.18 score 112 dependencies

SpectraVis - 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

4 stars 2.30 score 115 dependencies

MsQuantitation - Mass Spectrometry Quantitation

This package quantitates raw mass spectrometry data contained in Spectra objects into QFeaures instances.

Last updated 2 years ago

3 stars 2.18 score 109 dependencies

rWSBIM1207 - Companion Package for WSBIM1207 Course

Companion package for the WSBIM1207 course, distributing data and general documentation, and making course administration easier.

Last updated 4 months ago

2.00 score 16 dependencies

rWSBIM2122 - 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 0 dependencies

rWSBIM1322 - 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 28 dependencies