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.

Differential Expression Analysis tool box R lang package for omics 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.

`sdrf-pipelines` is the official SDRF file validator and converts SDRF to pipeline configuration files

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

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

Shiny app for making and annotating Volcano plots

HistoJS: Web-Based Analytical Tool for Multiplexed Images. Limited Github Online Demo 👇

CLI toolkit for fast analysis of DIA proteomics experiments and in silico library prediction

Search- and quantification-engine agnostic biological interpretation of proteomics data

Initial recommendations for performing, benchmarking, and reporting single-cell proteomics experiments. The code is distributed under an MIT license.

This repository contains the code to reproduce our exploratory analysis of a pan-cancer plasma proteomics dataset, including differential expression analysis and disease classification (https://doi.org/10.1038/s41467-023-39765-y). The data can be explored in the Human Protein Atlas: www.proteinatlas.org/humanproteome/disease.

Multiplexed data-independent acquisition (plexDIA) for increasing proteomics throughput. The code is distributed by an MIT license.

A resource for biomedical students and researchers. Includes proteomics software tools like FragPipe, MaxQuant, PDV, SearchGUI, ThermoRawFileParser, and PeptideShaker. Offers a user-friendly interface, automated identification and quantification, comprehensive data analysis, and lightweight clone feature for optimized storage.

MaxQuant and Perseus Bug Reporting

autoprot provides standardised, fast, and reliable proteomics data analysis while ensuring a high customisability needed to tailor the analysis pipeline to specific experimental strategies.

GRaph-based Analysis of Subcellular/Spatial Proteomics

Visualization of spectral archive

Python framework for explainable omics analysis

An R package providing extended biological annotations for the SomaScan Assay, a proteomics platform developed by SomaLogic Operating Co., Inc.

QuantQC is a package for quality control (QC) of single-cell proteomics data. It is optimized to work with nPOP, a method for massively parallel sample preparation on glass slides.

📊 User-friendly mass spectrometry and chromatography data analysis app with native UI, graphing, quantification, MS/MS and data export capabilities

Code accompanying batch effects processing workflow for "omic" data, mainly targeted for proteomics

R script to perform standard analysis steps for label-free proteomics data

Cell Permeability analysis

Inspecting the quality of isobaric labeling proteomic data in a Jupyter notebook. Data output from Proteome Discoverer.

Annotation and processing of peptides from FragPipe search results

A highly specialized suite of standardized plotting routines based on the "Grammar of Graphics" framework of mapping variables to aesthetics used in 'ggplot2'. Graphics types are biased towards visualizing SomaScan (proteomic) data.

R package and Shiny app for the dowstream analysis of quantitative proteomic data

WeSA (Weighted SocioAffinity): a tool for improving affinity proteomics data.