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cox_tdp43-fingerprinting

This repository contains the code associated with the MND TDP43 single-molecule pulldown project, conducted at the University of Cambridge and led by Dr. Dezerae Cox.

https://github.com/dezeraecox-manuscripts/cox_tdp43-fingerprinting

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 14 DOI reference(s) in README
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    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
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    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.4%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

This repository contains the code associated with the MND TDP43 single-molecule pulldown project, conducted at the University of Cambridge and led by Dr. Dezerae Cox.

Basic Info
  • Host: GitHub
  • Owner: dezeraecox-manuscripts
  • License: mit
  • Language: Python
  • Default Branch: master
  • Size: 10.5 MB
Statistics
  • Stars: 0
  • Watchers: 0
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Created over 1 year ago · Last pushed over 1 year ago
Metadata Files
Readme License Citation

README.md

DOI DOI

COX_TDP43-fingerprinting

This repository contains the analysis code associated with the MNDTDP single-molecul pulldown project, led by Dr Dezerae Cox. This manuscript has been submitted for publication under the title Fingerprinting disease-derived protein aggregates reveals unique signature of Motor Neuron Disease.

This manuscript has been submitted as a preprint via BioRxiv here. A link to the final version will be provided upon publication.

Prerequisites

This analysis assumes a standard installation of Python3 (=> 3.8). For specific package requirements, see the environment.yml file, or create a new conda environment containing all packages by running conda create -f environment.yml.

Raw data

The proteomics .RAW files have been deposited via the PRIDE1 partner repository to the ProteomeXchange Consortium2 under the dataset identifier PXD061429. In addition, preprocessed data (including identification and quantitation for proteomics, and property summaries for microscopy data; hereon termed raw data) have also been uploaded as an open-access Zenodo dataset. These data can be collected automatically using the raw_data.py script in each of the respective src analysis folders.

Workflow

Raw data were preprocessed using either MaxQuant3 or smma4. Individual scripts to produce each visualisation from the resulting summary data are presented within the src folder, alongside some utilities scripts for statistical testing, imputing or visualisation.

References

  1. Perez-Riverol, Yasset, Attila Csordas, Jingwen Bai, Manuel Bernal-Llinares, Suresh Hewapathirana, Deepti J Kundu, Avinash Inuganti, et al. The PRIDE Database and Related Tools and Resources in 2019: Improving Support for Quantification Data. Nucleic Acids Research 47, no. D1 (January 8, 2019): D44250. https://doi.org/10.1093/nar/gky1106.

  2. Deutsch, Eric W., Attila Csordas, Zhi Sun, Andrew Jarnuczak, Yasset Perez-Riverol, Tobias Ternent, David S. Campbell, et al. The ProteomeXchange Consortium in 2017: Supporting the Cultural Change in Proteomics Public Data Deposition. Nucleic Acids Research 45, no. Database issue (January 4, 2017): D11001106. https://doi.org/10.1093/nar/gkw936.

  3. Tyanova, Stefka, Tikira Temu, and Juergen Cox. The MaxQuant Computational Platform for Mass Spectrometry-Based Shotgun Proteomics. Nature Protocols 11, no. 12 (December 2016): 230119. https://doi.org/10.1038/nprot.2016.136.

  4. SMMA: Single Molecule Microscopy Analysis (SMMA) Module Containing Analysis Functions for Single-Molecule Data. Last accessed February 24, 2025. https://github.com/dezeraecox/smma.

Owner

  • Name: manuscripts
  • Login: dezeraecox-manuscripts
  • Kind: organization

Citation (citation.cff) 

cff-version: 0.1.0
message: "If you use this respository, please cite the manuscript alongside the following:"
authors:
  - family-names: Cox
    given-names: Dezerae
    orcid: https://orcid.org/0000-0002-5345-8360
title: "Source code for *Fingerprinting disease-derived protein aggregates reveals unique signature of Motor Neuron Disease*"
version: 1.0
doi: 
date-released:

GitHub Events

Total
  • Release event: 1
  • Public event: 1
  • Push event: 2
  • Create event: 1
Last Year
  • Release event: 1
  • Public event: 1
  • Push event: 2
  • Create event: 1

Dependencies

environment.yml pypi
  • statannotations *