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
autoprot provides standardised, fast, and reliable proteomics data analysis while ensuring a high customisability needed to tailor the analysis pipeline to specific experimental strategies.
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
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.
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
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.
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
Routinely used R scripts in statistical analysis of proteomic experiment results with figure and plot generation
This is Loan Robinson Github Page, which includes all tutorials for education purpose.
Workflow to perform interference modeling and interference correction for MS2-based multiplex proteomics data
WeSA (Weighted SocioAffinity): a tool for improving affinity proteomics data.
Pipeline y shiny app para el análisis de datos de proteómica cuantitativa label free
Data analysis on relationship between neurodegenerative diseases and plasma/CSF protein expression levels.
Mass spectrometry Perseus Data analysis