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https://github.com/const-ae/proda-paper

https://github.com/const-ae/proda-paper

Science Score: 36.0%

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    Found 1 DOI reference(s) in README
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    Links to: biorxiv.org
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    Low similarity (7.7%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: const-ae
  • Language: HTML
  • Default Branch: master
  • Size: 66.3 MB
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Created about 7 years ago · Last pushed about 6 years ago
Metadata Files
Readme

README.md

proDA-Paper

Currently available as a preprint:

Constantin Ahlmann-Eltze and Simon Anders: proDA: Probabilistic Dropout Analysis for Identifying Differentially Abundant Proteins in Label-Free Mass Spectrometry. biorXiv 661496 (Jun 2019)

This repository contains the code to reproduce the figures for the paper describing the proDA R package.

Data

There are two datasets that are used for demonstration:

  • Data on the phosphorylation dynamics from a study by Erik de Graaf et al.1
  • Data studying the interaction landscape of Ubiquitin signalling by Xiaofei Zhang et al.2

Both can be found in the data/ folder.

Analysis

There are three additional folders that contain R markdown notebook that were used to generate the plots for the paper:

  • approach_intuition contains the code to give an overview of the ideas underlying proDA
  • compare_performance contains the code to run DEP, QPROT, Perseus, DAPAR, EBRCT, Triqler and proDA on the de Graaf data and make the validation and comparison plots
    • Null comparison on the de Graaf data set notebook
    • de Graaf semi-synthetic dataset performance comparison notebook
  • ubiquitination contains the code that was used to analyze the Ubiquitination data

Sources

1. de Graaf, E. L., Giansanti, P., Altelaar, A. F. M. & Heck, A. J. R. Single-step Enrichment by Ti4 + -IMAC and Label-free Quantitation Enables In-depth Monitoring of Phosphorylation Dynamics with High Reproducibility and Temporal Resolution . Mol. Cell. Proteomics 13, 2426–2434 (2014).

2. Zhang, X. et al. An Interaction Landscape of Ubiquitin Signaling. Mol. Cell 65, 941–955.e8 (2017).

Owner

  • Name: Constantin
  • Login: const-ae
  • Kind: user
  • Location: Heidelberg, Germany
  • Company: EMBL

PhD Student, Biostats, R

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