proteomics-data-analysis
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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.
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Jul 11, 2025 - R
Differential Expression Analysis tool box R lang package for omics data
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Jul 9, 2025 - R
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.
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Jul 2, 2025 - R
amica: an interactive and user-friendly web-based platform for the analysis of proteomics data
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Apr 3, 2025 - R
An modular and extensible app for visualization of mass spectrometry data and optimization of data acquisition.
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Mar 17, 2025 - R
Shiny app for making and annotating Volcano plots
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Aug 21, 2024 - R
`sdrf-pipelines` is the official SDRF file validator and converts SDRF to pipeline configuration files
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May 16, 2025 - Python
HistoJS: Web-Based Analytical Tool for Multiplexed Images. Limited Github Online Demo 👇
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Feb 29, 2024 - JavaScript
Initial recommendations for performing, benchmarking, and reporting single-cell proteomics experiments. The code is distributed under an MIT license.
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Apr 5, 2023 - R
Multiplexed data-independent acquisition (plexDIA) for increasing proteomics throughput. The code is distributed by an MIT license.
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Mar 17, 2025 - R
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.
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Apr 11, 2025 - Jupyter Notebook
autoprot provides standardised, fast, and reliable proteomics data analysis while ensuring a high customisability needed to tailor the analysis pipeline to specific experimental strategies.
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Jul 8, 2025 - Python
MaxQuant and Perseus Bug Reporting
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Mar 19, 2025
Python framework for explainable omics analysis
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Jul 23, 2024 - Jupyter Notebook
Visualization of spectral archive
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Jun 11, 2024 - C++
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.
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Jul 27, 2023 - R
An R package providing extended biological annotations for the SomaScan Assay, a proteomics platform developed by SomaLogic Operating Co., Inc.
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Apr 26, 2024 - R
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.
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May 29, 2025 - HTML
R script to perform standard analysis steps for label-free proteomics data
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May 21, 2024
Protein Cleaver is a versatile tool for protein analysis and digestion.
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Apr 9, 2025 - Python
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