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theislab / single-cell-tutorial

Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"
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Package versions in .yml file #74

Closed lefterov closed 3 years ago

lefterov commented 3 years ago

It is rather a question, not an issue:

in the .yml file some of the packages are listed with older than most recent versions:

the most recent and installed are: -python=3.9.7 -cmake=3.21.2

there should not be a problem, right?

nice day,

Iliya

LuckyMD commented 3 years ago

Hey!

I can't imagine there would be a problem with cmake updates. For python, I'm not sure... but I don't think there should be backwards compatibility issues there either. Sorry I can't give you a more detailed answer.

lefterov commented 3 years ago

Absolute and excellent answer.

Have a great day!

-I.

Iliya Lefterov Professor, School of Public Health University of Pittsburgh

+1 412 449 9195 (mobile, USA) @.***

From: MalteDLuecken @.> Date: Tuesday, September 7, 2021 at 6:10 AM To: theislab/single-cell-tutorial @.> Cc: Lefterov, Iliya @.>, Author @.> Subject: Re: [theislab/single-cell-tutorial] Package versions in .yml file (#74)

Hey!

I can't imagine there would be a problem with cmake updates. For python, I'm not sure... but I don't think there should be backwards compatibility issues there either. Sorry I can't give you a more detailed answer.

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lefterov commented 3 years ago

at this time I have no problem with the newest versions. I don't know if it is worth changing the content of the .yml file. for more experienced users, such a question would not have existed.

LuckyMD commented 3 years ago

I'm trying to stick to the docker rather than the yaml file for the moment. But could you add this as a comment on the PR #58 ? Then I can try to add it there when i get around to it.

lefterov commented 3 years ago

Posted.

Thanks, Malte. What if I permit myself in the near future to send questions directly… 😊?

Nice evening.

-I.

-- Iliya Lefterov, MD, PhD Professor, Graduate School of Public Health Department of Environmental & Occupational Health University of Pittsburgh, Public Health, 130 De Soto Str., Rm 4134 Pittsburgh, PA 15261

Tel. office: 412 383 6906 Lab: 412 6248662 Email: @.**@.>

From: MalteDLuecken @.> Date: Wednesday, September 8, 2021 at 12:10 PM To: theislab/single-cell-tutorial @.> Cc: Lefterov, Iliya @.>, Author @.> Subject: Re: [theislab/single-cell-tutorial] Package versions in .yml file (#74)

I'm trying to stick to the docker rather than the yaml file for the moment. But could you add this as a comment on the PR #58https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ftheislab%2Fsingle-cell-tutorial%2Fpull%2F58&data=04%7C01%7Ciliyal%40pitt.edu%7C04f4da66208747fa177e08d972e33c2d%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637667142580490401%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=xg1NDGZcv883sdoglkIC3ialKX%2FCYqgH1Cndw82%2F0R0%3D&reserved=0 ? Then I can try to add it there when i get around to it.

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LuckyMD commented 3 years ago

Thanks. I'm usually quite responsive on github as well ;).

dturaev commented 3 years ago

Here is some additional information:

lefterov commented 3 years ago

👍

Beginning Monday, I am moving full speed again… means I will let you know how it works and, definitely – will have more questions… :-)

Cheers, and nice weekend.

-I.

Iliya Lefterov Professor, School of Public Health University of Pittsburgh

+1 412 449 9195 (mobile, USA) @.***

From: DT @.> Date: Saturday, September 18, 2021 at 4:57 PM To: theislab/single-cell-tutorial @.> Cc: Lefterov, Iliya @.>, Author @.> Subject: Re: [theislab/single-cell-tutorial] Package versions in .yml file (#74)

Here is some additional information:

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LuckyMD commented 2 years ago

@dturaev Thanks so much for that! This is really useful!

lefterov commented 1 year ago

@LuckyMD: We have finally moved to diffxpy and are trying to move faster...

quick question: to compare two groups (each comprised of 2 biological replicates), is it sufficient to supply the h5ad files written after we ranked the genes using Wilcoxon method?

Thanks in advance.