Dataset used in the tutorial

[yjgeno]

Hi, excellent work! Could you tell me where the example skin data you showed in the tutorial ('Inference and analysis of cell-cell communication using CellChat') is? It would be great if you could provide me a GEO number thus I can look into the original paper of it Thank you!

[sqjin]

@yjgeno Please check our paper on the application to human skin dataset.

[yjgeno]

Thank you! i found it GSE147424

[yjgeno]

Hi, @sqjin do you also have the processed data with the cell annotations that you used in the paper? Thank you

[sqjin]

@yjgeno Please check the CellChat tutorial on the link of processed data.

[yjgeno]

@yjgeno Please check the CellChat tutorial on the link of processed data.

Hi @sqjin thanks! There was the human skin dataset. I was wondering if I could also get access to your mouse skin dataset you used in Fig.2? The raw data does not contain the annotations of subclusters

[sqjin]

@yjgeno You can download the wound healing data here

[yjgeno]

@yjgeno You can download the wound healing data here

@sqjin Thank you! It helps a lot

[yjgeno]

Hi @sqjin sorry I reopen this issue as wondering if any place I could find the original counts of the human skin data you used in your tutorial? The data downloaded from the provided link only has the normalized data (with cell labels)

Thanks again in advance!

[yjgeno]

Hi @sqjin sorry I reopen this issue as wondering if any place I could find the original counts of the human skin data you used in your tutorial? The data downloaded from the provided link only has the normalized data (with cell labels)

Thanks again in advance!

@sqjin Hi really appreciate it if you could offer the skin dataset with raw counts

[sqjin]

@yjgeno I am sorry I do not have the count data. I think the authors of the original paper did not provide it. You should contact them

[vckraemer]

Hi @sqjin,

I was searching for the annotated mouse data from Supplementary Figure 2 and stumbled upon the issue here. I noticed the Dropbox link from above (June 05 2021) is not active anymore. Do you have the data maybe available as CellChat object as for the E13 and E14 mouse samples on figshare?

Thanks in advance!

[sqjin]

@vckraemer Please download it from https://figshare.com/account/projects/157272/articles/21887559

[vckraemer]

Hi @sqjin,

thanks for your fast response!

If I understand it correctly these are the two CellChat objects for the embryonic development samples that are also available in the Tutorial? I was actually searching for the day 12 adult mouse wound healing stages (Supplementary Figure 2), sorry that i may have expressed myself unclearly there. Do you also have a CellChat object or the normalized data with meta data (especially the cell annotation) for this sample?

Thanks again for your help!

[sqjin]

@vckraemer Please find it at https://figshare.com/account/projects/157272/articles/21896400

On Fri, Jan 13, 2023 at 4:17 PM vckraemer @.***> wrote:

Hi @sqjin https://github.com/sqjin,

thanks for your fast response!

If I understand it correctly these are the two CellChat objects for the embryonic development samples that are also available in the Tutorial? I was actually searching for the day 12 adult mouse wound healing stages (Supplementary Figure 2), sorry that i may have expressed myself unclearly there. Do you also have a CellChat object or the normalized data with meta data (especially the cell annotation) for this sample?

Thanks again for your help!

— Reply to this email directly, view it on GitHub https://github.com/sqjin/CellChat/issues/207#issuecomment-1381463452, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHXF63FLRO3GTRR753PVMU3WSEFSXANCNFSM45OK746A . You are receiving this because you were mentioned.Message ID: @.***>

[vckraemer]

Thanks a lot @sqjin!