Base Classes and Functions for Mass Spectrometry and Proteomics

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.

Picotti lab data analysis package.

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

Compare different differential abundance and expression methods

Matrix dissimilarity from the differences of Moments and sparsity

Low level infrastructure to handle MS spectra

R-based package for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

An modular and extensible app for visualization of mass spectrometry data and optimization of data acquisition.

Quantitative features for mass spectrometry data

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.

amica: an interactive and user-friendly web-based platform for the analysis of proteomics data

Proteomics Toolset for Integrative Data Analysis

Cell-type Relationship Analysis Workflow Done Across Distances

Single cell proteomics data processing

Tools for normalization, evaluation of outliers, technical biases and batch effects and differential expression analysis.

🍎 Web-based User-friendly Workflow for Metabolomics and Proteomics Data Analysis

Core Utils for Mass Spectrometry Data

A unifying bioinformatics framework for organelle proteomics

feseR: Combining feature selection methods for analyzing omics data