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Enes Kemal Ergin edited this page Jul 30, 2022 · 6 revisions

Welcome to Wiki Page of SQuAPP Version 0.28

Simple Quantitative Analysis of Peptides and Proteins (SQuAPP) is a workflow-based web application built on R-Shiny to enable rapid high-level analysis of quantitative proteomics data. SQuAPP provides streamlined and straightforward access to many aspects of typical downstream analysis done with quantitative proteomics data. SQuAPP facilitates combined statistical analysis of multiple levels of proteomics data, including peptide, protein, post-translational modifications and termini modification, and allows for visual comparisons using a variety of plots and table formats.

Mandatory quality control and conscious pre-processing early in the workflow ensure that only robust data are quantitatively evaluated and visualized. The processed datasets can be downloaded for further custom analysis, and the comprehensive report supports record keeping and allows for easy sharing with colleagues and collaborators.

Functionality

SQuAPP is a flexible application, and its functions can be applied in a non-sequential order as long as the requirements for a specific function are met. SQuAPP also can be used to follow a sequential workflow-driven approach.

Help

A detailed tutorial on how to use SQuAPP can be accessed in the respective tabs for section:

Quick Start

You can start exploring the SQuAPP right now using our pre-loaded example data containing protein, phosphorylation and N termini level data comparing primary leukemic cells with matched patient-derived xenografts.(Uzozie et al. 2021)

About SQuAPP

SQuAPP has been developed by Enes Kemal Ergin & Siyuan Chen with contributions from Anuli Uzozie, Ye Su, and Philipp Lange at BC Children’s Hospital & the University of British Columbia.

The source code for SQuAPP is available at SQuAPP Github Page.

For any feedback, comments, and questions, please contact:

Or you can directly submit an issue on SQuAPP's GitHub page.

Change Log

Version 0.28 - August 1st 2022
  • Various bug fixes
  • Updated tutorials with more references, links, descriptions
  • Fixed logical mistake in the custom imputation
Version 0.27 - December 13th 2021
  • Various bug fixes and ui updates
  • Blocking option in statistical testing is disabled
  • Update Global coefficient of variation based QC plot
  • Generate a report section is initialized
Version 0.26 - December 8th 2021
  • Various bug fixes and ui updates
  • More compact protein domain visualization
  • More filtration options for circular network plot
  • Additional combinations to select in circular network plot
  • Customizable colouring for circular network plot
Version 0.25 - December 1st 2021
  • Working version made public
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