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

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

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

Shiny app for making and annotating Volcano plots

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

A repository to convert SDRF proteomics files into pipelines config files

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

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.

Python framework for explainable omics analysis

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

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

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

Visualization of spectral archive

Protein Cleaver is a versatile tool for protein analysis and digestion.

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