[English workshop]: Single-cell proteomics data analysis using QFeatures and scp

PeteHaitch commented 3 years ago

Abstract

Mass spectrometry (MS)-based single-cell proteomics (SCP) is an emerging field that requires a dedicated computational environment. QFeatures along with its extension scp allow for standardized analysis of SCP data. The workshop will start by introducing the QFeatures class and its functions to perform generic proteomics data analysis. We will then move to SCP and present how scp extends QFeatures to single-cell applications. The remainder of the workshop will be a hands-on session where attendees will be guided through the reproduction of a real-life analysis of published SCP data. Along the reproduction exercise, we will point out to current challenges that still need to be tackled computationally. This workshop is meant for inexperienced users that want to learn how to perform current state-of-the-art analysis of SCP data as well as experienced developers interested in contributing to an emerging and exciting single-cell technology.

This workshop is provided as two vignettes. The first vignette provides a general introduction to the QFeatures class in the general context of MS-based proteomics data manipulation. The second vignette focuses on single-cell application and introduces the scp package as an extension of QFeatures. This second vignette also provides exercises that give the attendee the opportunity to apply the learned concepts to reproduce a published analysis on a subset of a real data set.

Language used in the workshop

English

Convenient day for your Long workshop.

@lgatto Please let us know your preference

Contact Details

laurent.gatto@uclouvain.be

Comment field

Submitted on behalf of Laurent Gatto (@lgatto). Workshop will be a re-run of a workshop presented at BioC 2021 (https://lgatto.github.io/QFeaturesScpWorkshop2021/).

Checklist

[X] This workshop has a Bioconductor focus or interest to Bioconductor users/developers.
[X] I checked and confirmed the BioC Asia 2021 Code of Conduct.
[X] I understood that it would be desirable for the workshop to be based on this template project.

kozo2 commented 3 years ago

@lgatto Thank you for the abstract. I accepted it. You can see the schedule at https://biocasia2021.bioconductor.org/workshops/ . Thank you again.

lgatto commented 3 years ago

Could you also add @cvanderaa's name, please. Thanks!

kozo2 commented 3 years ago

@lgatto I added @cvanderaa 's name to https://biocasia2021.bioconductor.org/workshops/ . Sorry for being late to do that.

cvanderaa commented 3 years ago

What would you expect from us?

A workshop where we provide hands-on exercises to attendees, or
A demonstration that attendees can later on reproduce at their own pace through Orchestra

We personally prefer option 2 due to time constrains, are you fine with that?

kozo2 commented 3 years ago

Yes, option 2 is fine. As you say, it will be 2 due to time constraints.

Bioconductor / BiocAsia2021