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alphadia

alphapeptstats

Python Package for the downstream analysis of mass-spectrometry-based proteomics data

do-ms

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

ewce

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

ggstatsplot

Enhancing {ggplot2} plots with statistical analysis 📊📣

glycresoft

An LC-MS/MS glycan and glycopeptide search engine

informed-proteomics

Top down / bottom up, MS/MS analysis tool for DDA and DIA mass spectrometry data

iq

An R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics

ksear

omiclearn

🧪 🖥 Transparent exploration of machine learning for biomarker discovery from proteomics and omics data

pnnl.dia.utils

**WORK IN PROGRESS** misc. functions for DIA proteomics data analysis and parsing to MSnSet objects

proteomicsvisualization

This is a collection of minimal code to visualize various aspects of proteomics data.

pyopenms-docs

pyOpenMS readthedocs documentation, additional utilities, addons, scripts, and examples.

pythondatasciencehandbook

Python Data Science Handbook: full text in Jupyter Notebooks

qireshape

Merge Qualitative and Quantitative Metabolomics Data exported from Progenesis QI software

quality-control-of-the-plasma-proteome

quantms

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.

venn-diagram-plotter

The Venn Diagram Plotter draws correctly proportioned and positioned two and three circle Venn diagrams (aka Euler diagrams) whose colors can be customized and the diagrams copied to the clipboard or saved to disk.