There are 8 repositories under proteomics-data-analysis topic.
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.
Shiny app for making and annotating Volcano plots
A repository to convert SDRF proteomics files into pipelines config files
Initial recommendations for performing, benchmarking, and reporting single-cell proteomics experiments. The code is distributed under an MIT license.
autoprot provides standardised, fast, and reliable proteomics data analysis while ensuring a high customisability needed to tailor the analysis pipeline to specific experimental strategies.
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.
Python framework for explainable omics analysis
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.
MaxQuant and Perseus Bug Reporting
Visualization of spectral archive
R script to perform standard analysis steps for label-free proteomics data
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
Exploring correlations in an isobaric labeling mass spectrometry-based proteomic data set
Performance of Julia and Python for reading and matching mass spectrometry data
Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.
WeSA (Weighted SocioAffinity): a tool for improving affinity proteomics data.
Pipeline and shiny app for the downstreaming analysis of quantitative proteomic data
An R package providing extended biological annotations for the SomaScan Assay, a proteomics platform developed by SomaLogic Operating Co., Inc.
Code accompanying batch effects processing workflow for "omic" data, mainly targeted for proteomics
Code of the R Shiny App of the PRONE R Package.
This is Loan Robinson Github Page, which includes all tutorials for education purpose.
Data analysis on relationship between neurodegenerative diseases and plasma/CSF protein expression levels.
Mass spectrometry Perseus Data analysis