Base Classes and Functions for Mass Spectrometry and Proteomics
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Updated
Sep 12, 2024 - R
Base Classes and Functions for Mass Spectrometry and Proteomics
Low level infrastructure to handle MS spectra
Olink R package: A collection of functions to facilitate analysis of proteomic data from Olink. The goal of this package is to help users extract biological insights from proteomic data run on the Olink platform.
The SomaDataIO package loads and exports 'SomaScan' data via the 'SomaLogic Operating Co., Inc.' proprietary data file, called an ADAT ('*.adat'). The package also exports auxiliary functions for manipulating, wrangling, and extracting relevant information from an ADAT object once in memory.
Proteomics Toolset for Integrative Data Analysis
COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.
R-based package for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
A unifying bioinformatics framework for organelle proteomics
Core Utils for Mass Spectrometry Data
PGA: a tool for ProteoGenomics Analysis
Compare different differential abundance and expression methods
An modular and extensible app for visualization of mass spectrometry data and optimization of data acquisition.
Analytical R Tools for Mass Spectrometry
Quantitative features for mass spectrometry data
S4 generic functions for Bioconductor mass spectrometry infrastructure
proteoQC: an R package for proteomics data quality assessment.
Tools for normalization, evaluation of outliers, technical biases and batch effects and differential expression analysis.
amica: an interactive and user-friendly web-based platform for the analysis of proteomics data
🍎 Web-based User-friendly Workflow for Metabolomics and Proteomics Data Analysis
R package for easy interop between Perseus and R
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