Organise and run a tidyomics workshop/demo for BioC, BioC Asia, EuroBioC, at your institute, etc.

[mikelove]

@stemangiola and I can provide materials and advice

[TobiErges]

How do I participate? I'm interested please

[stemangiola]

How do I participate? I'm interested please

Hello @TobiErges. You can organise a date and a place for the seminar/workshop with your Institute. We can provide an abstractas example and we have plenty of material that you can use to deliver your workshop, depending on how long it is going to be.

@TobiErges please post here a little biography of yourself.

[TobiErges]

Hello @stemangiola Thanks for your response

I am a first-year Ph.D. student in the Dept of Biochem and Molecular Bio, I'm working on prostate cancer, and I have some bioinformatics/programming skills, R, Bash, rnaseq, and some materials I am still studying, however, I am looking for a community that I can join/volunteer for, use my skills for them and also learn more in the process.

I assumed what this project needed was for me to try it out on my end not to organize a workshop, however, I might be able to do that from next year... Thanks

[stemangiola]

Thanks @TobiErges, I made the description more clear :)

There are many ways to contribute. For example

• Some "good first issues" for plyranges https://github.com/orgs/tidybiology/projects/1#:~:text=any%20of%20the%20plyranges%20%22good%2Dfirst%2Dissue%22%20issues

• Or improving the documentation of tidybulk where new eyes, with few years of experience, can make the difference. For example, all functions and arguments should be absolutely clear to everybody and very simple to understand.

In this case, you can assign yourself here https://github.com/orgs/tidybiology/projects/1/views/1#:~:text=Improve%20the%20documentation%20for%20tidybulk

Each challenge can be contributed by more than one person.

[iza-mcac]

A question,Could this workshops be in the format of a class?
I could propose this as a class for graduate and pos graduate level for next semester at my university in Brasil (Federal University of Minas Gerais)

[stemangiola]

A question,Could this workshops be in the format of a class? I could propose this as a class for graduate and pos graduate level for next semester at my university in Brasil (Federal University of Minas Gerais)

For sure!

[iza-mcac]

That's perfect then. Are the basic materials the published vignettes? I can start on translating then for portuguese and think about the main requirements for the class

[stemangiola]

Sure, the workshop we delivered is here, https://github.com/tidybiology/tidyomicsWorkshopBioc2023

But we have many workshop templates, including genomic objects or transcriptomic objects (single cell, pseudobulk or bulk), depending on what you are more interested in.

You can teach one of the ready workshops or compose yours. I pasted a few more, Please @mikelove feel free to add a few workshops of yours.

https://github.com/tidytranscriptomics-workshops

[mikelove]

Another one is fluentGenomics which Stuart and I gave a while back. It got longer and became a paper but you could cut it halfway.

I think tidy transcriptomics probably make the best intro though, because many students want to learn RNA-seq or single cell.

[iza-mcac]

I will probably use the transcriptomics one.
Also will add some introductory classes about general transcriptomics pipeline and the wetlab procedure for sequencing since the public will be diverse with people with statistics, computer science and biology/biotec undergrad as background. I am planning for a 15 hour class to be taught between march and april next year.

[stemangiola]

I will probably use the transcriptomics one. Also will add some introductory classes about general transcriptomics pipeline and the wetlab procedure for sequencing since the public will be diverse with people with statistics, computer science and biology/biotec undergrad as background. I am planning for a 15 hour class to be taught between march and april next year.

Amazing! As soon as you have details about the event feel free to share it here.

[paupaiz]

I am also interested in organizing a workshop/demo. It is too late for EuroBioC? I am at Stanford could ask around how to organize one here?

[stemangiola]

I am also interested in organizing a workshop/demo. It is too late for EuroBioC? I am at Stanford could ask around how to organize one here?

Amazing! Please ask the BiocEurope organising committee from the conference website. Organising at your institution would be great, to keep things concrete, please share here where and when the workshop will be given once you have been given approval, and info about how people could attend if it's open.

You can like your material (github page) with the community, and we will put into the home page of tidyomics. As written above, there is a lot of material you can use, and modify.

[iza-mcac]

I will probably use the transcriptomics one. Also will add some introductory classes about general transcriptomics pipeline and the wetlab procedure for sequencing since the public will be diverse with people with statistics, computer science and biology/biotec undergrad as background. I am planning for a 15 hour class to be taught between march and april next year.

Amazing! As soon as you have details about the event feel free to share it here.

For now I am forking and translating the workshop repositories you guys provided. Meanwhile doing some introductory slides for transcriptomics analyses and what we expect to gain from them, my public will be grads and undergrads from biology, medicina, biomed, computer science and statistics; so a very variable public to say the least.

[ryumh]

Hi @mikelove @stemangiola. I am a postdoc fellow at Brigham and Women's Hospital, Channing Division of Network Medicine. I saw you two present at BioC2023 and wanted to reach out to organize a workshop at Channing. I've got an approval for 1-hour presentation slot in the division-wide "Multiple Omics" meeting on October 18. The title of my presentation is “Tidyomics: A Tool for Multiple Omics Analysis?". The audience is researchers (mostly postdocs and faculties) in pulmonary medicine in computational labs. The goal of the presentation is to showcase computational tools that would aid in doing multiple omics data analysis - which I think tidyomics is poised to do well. Could you point me to resources that will help me prepare for this workshop? Any more example of analyzing multiple omics, other than the one you presented at BioC2023? Maybe CITE-seq? Our meeting is hybrid, so doing an online demo (via zoom) while presenting in person would be ideal. Also, depending on how well this is received, I can have follow-up workshop too, so the contents don't necessarily have to all fit into 1-hr slot.

Thank you very much and looking forward to hearing from you!

[mikelove]

I have only done multiple omics in terms of genomic overlap (as in the fluentGenomics pub, or the workshop at BioC2023).

But if you have measurements on the same cell for the same gene (RNA / protein or RNA / promoter accessibility), you can easily do interesting things with tidySingleCellExperiment. You would have both assays to manipulate / compute on. E.g. you could use purrr to do some computation like correlation of the omics within feature, etc.

I don't think any material exists on this just yet.

@stemangiola the paradigm would be the following?

se <- se %>%
  nest(data = -.feature) %>%
  mutate(rho = map_dbl(data, 
    ~myFunction(
      pull(.x, omic_assay_one), 
      pull(.x, omic_assay_two)
    ))) %>%
  unnest(data)

There may be more optimized ways to do this, e.g. just using mutate() without nesting.

[iza-mcac]

It has been a while but I finally got administrative approval here in Universidade Federal de Minas Gerais Brazil for the course. Here is the general program that was just approved, translated into english, remembering the public will be mostly grad students into biochemistry or bioinformatics phd courses:

Course Name: Introduction to Tidy Single-Cell Data Analysis

Duration: 15 hours

Syllabus: Single-cell sequencing, questions addressed by single-cell analysis, examples of single-cell projects, tidy data analysis methods, single-cell sequencing alignment, data input into R, data processing methods, visualization methods, hypothesis testing in a single-cell dataset, pseudotime/rna velocity, key challenges, and the rationale for using tidy methods.

Instructors: Izabela Mamede

Number of Seats: 20

Start Date: Second half of May 2024

End Date: Second half of May 2024

Days of the Week: Condensed format (exact days not specified)

Class Schedule: Condensed format (exact times not specified)

Prerequisite: None (students are expected to have some basic knowledge of R and molecular biology)

[stemangiola]

Hi @mikelove @stemangiola. I am a postdoc fellow at Brigham and Women's Hospital, Channing Division of Network Medicine. I saw you two present at BioC2023 and wanted to reach out to organize a workshop at Channing. I've got an approval for 1-hour presentation slot in the division-wide "Multiple Omics" meeting on October 18. The title of my presentation is “Tidyomics: A Tool for Multiple Omics Analysis?". The audience is researchers (mostly postdocs and faculties) in pulmonary medicine in computational labs. The goal of the presentation is to showcase computational tools that would aid in doing multiple omics data analysis - which I think tidyomics is poised to do well. Could you point me to resources that will help me prepare for this workshop? Any more example of analyzing multiple omics, other than the one you presented at BioC2023? Maybe CITE-seq? Our meeting is hybrid, so doing an online demo (via zoom) while presenting in person would be ideal. Also, depending on how well this is received, I can have follow-up workshop too, so the contents don't necessarily have to all fit into 1-hr slot.

Thank you very much and looking forward to hearing from you!

Amazing @ryumh, sorry I was on holiday and with a lot of backlog. How did the workshop go? Do you have a video, or material of it?

[stemangiola]

It has been a while but I finally got administrative approval here in Universidade Federal de Minas Gerais Brazil for the course. Here is the general program that was just approved, translated into english, remembering the public will be mostly grad students into biochemistry or bioinformatics phd courses:

Course Name: Introduction to Tidy Single-Cell Data Analysis

Duration: 15 hours

Syllabus: Single-cell sequencing, questions addressed by single-cell analysis, examples of single-cell projects, tidy data analysis methods, single-cell sequencing alignment, data input into R, data processing methods, visualization methods, hypothesis testing in a single-cell dataset, pseudotime/rna velocity, key challenges, and the rationale for using tidy methods.

Instructors: Izabela Mamede

Number of Seats: 20

Start Date: Second half of May 2024

End Date: Second half of May 2024

Days of the Week: Condensed format (exact days not specified)

Class Schedule: Condensed format (exact times not specified)

Prerequisite: None (students are expected to have some basic knowledge of R and molecular biology)

Maravilha Isabela,

if you open the workshop repo (feel free to fork one of our workshops) I will send you the invitation to the paper.

[ryumh]

@stemangiola Thanks for checking in. I hope you had a good time off. The workshop went well.
The slides I used below are mostly adapted from your BioC2023 workshop.
https://docs.google.com/presentation/d/1KwpWVqOcWwKJaYse-yf-_Y0-c04gHARfWBk286Bjka0/edit?usp=sharing
No recording though. It was well attended with ~20 people on site/online.

[iza-mcac]

It has been a while but I finally got administrative approval here in Universidade Federal de Minas Gerais Brazil for the course. Here is the general program that was just approved, translated into english, remembering the public will be mostly grad students into biochemistry or bioinformatics phd courses:
Course Name: Introduction to Tidy Single-Cell Data Analysis
Duration: 15 hours
Syllabus: Single-cell sequencing, questions addressed by single-cell analysis, examples of single-cell projects, tidy data analysis methods, single-cell sequencing alignment, data input into R, data processing methods, visualization methods, hypothesis testing in a single-cell dataset, pseudotime/rna velocity, key challenges, and the rationale for using tidy methods.
Instructors: Izabela Mamede
Number of Seats: 20
Start Date: Second half of May 2024
End Date: Second half of May 2024
Days of the Week: Condensed format (exact days not specified)
Class Schedule: Condensed format (exact times not specified)
Prerequisite: None (students are expected to have some basic knowledge of R and molecular biology)

Maravilha Isabela,

if you open the workshop repo (feel free to fork one of our workshops) I will send you the invitation to the paper.

Hey! I had already done that, but decided to organize it better this morning since now I have an approved program for the class, I hope it is not a problem sinc emost of it will be in portuguese: https://github.com/iza-mcac/analises-de-dados-de-celula-unica-de-forma-tidy, I already added your markdowns as reference, and will start translating next month since I have some time until the class itself

[stemangiola]

@ryumh @iza-mcac please add your authorship details here

https://docs.google.com/spreadsheets/d/19XqhN3xAMekCJ-esAolzoWT6fttruSEermjIsrOFcoo/edit?usp=sharing

[mikelove]

Great to hear about these workshops being run at Channing by @ryumh and planned to run at Universidade Federal de Minas Gerais Brazil by @iza-mcac!

[iza-mcac]

Hello all, it has been a while,

Anyway I have 22 enrolled for the in person workshop and over 50 enrolled online. The classes will start on mid May and it will be a two week, condensed course.
I decided to send some forum like activities to check general knowledge in sequencing techniques and how sequencing result are presented and asked the students to choose their own dataset to analyze using a general "How to explore SRA/GEO" tutorial.
I already finished translating everything to Portuguese, just waiting for a friend to check before putting on github, but if anyone has interest on the translations before just send me a message and will share asap.

Here is the general look of my teaching forum inside the university website for the course:

[stemangiola]

Maravilha Izabela!

We find that package the workshop as R package, with github pages of the workshop makes it very easy for participants. (.g. https://github.com/tidyomics/tidyomicsWorkshopBioc2023).

In any case if you have chance take video, and photos so we can share, and promote your work!

[ryumh]

I am interested in submitting an abstract and presenting a short talk or demo showcasing tidyomics at EuroBioC 2024. Is anyone else going and also interested? @stemangiola

[stemangiola]

Hello @ryumh, great timing!

I was for submitting that workshop, but I am more than happy for you to deliver it. Maybe you can put me down as a facilitator/assistant.

I will pivot to a workshop on sccomp used for atlas-size compositional analyses.

[ryumh]

Great! I will definitely put you down as a facilitator/assistant. I will work on this next week and email you the abstract draft for a quick look. Thanks. Min.