Problems with metadata upload about immunarch

[annecar]

Dear Eugene the Metadata import worked perfectly! Thanks again. Another thing: i tried to install 0.5.2 via CRAN as suggested on GitHub, but i get a teh waring : in install.packages : package ‘immunarch’ is not available (for R version 3.6.1) So i installed it as you suggested. May be you would like to check back what is happening there. Best Anne Anne Eugster, PhD Scientist AG Bonifacio CRTD - Center for Regenerative Therapies TU Dresden Fetscherstr. 105 01307 Dresden Tel: [phone] Fax: [phone] Email: [email protected]<mailto:[email protected]> Webpage: www.crt-dresden.de<http://www.crt-dresden.de> On 20. Nov 2019, at 13:26, Eugene Rumynskiy <[email protected]<mailto:[email protected]>> wrote: Hi @annecar<https://github.com/annecar> We fixed the metadata problem in 0.5.2 version. 1. Update your package to 0.5.2. Get the latest version from master branch. * https://github.com/immunomind/immunarch/blob/master/immunarch.tar.gz 2. Just apply repLoad(...) to your data folder again and it will load the metadata file. tmp = repLoad("path/to/your/data") tmp$meta names(tmp$data) [image]<https://user-images.githubusercontent.com/20778038/69238622-7ba4d500-0ba9-11ea-89a3-4692732d883e.png> Hope we solved your problem :) @vadimnazarov<https://github.com/vadimnazarov> Will mail you about IMMREP20 and rarefaction in one of the next days. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#27?email_source=notifications&email_token=AIM7QPR2OZCZR7HIVJ7WSOLQUUUF5A5CNFSM4JGZAOXKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEERZ4HQ#issuecomment-555982366>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIM7QPUUPNLSEEQMLEWXF4TQUUUF5ANCNFSM4JGZAOXA>.

[vadimnazarov]

Hi, thank you, we will look into it! We will have a new release at the beginning of the next week, so it should be fixed there. However, if you want to speed up things, can you please remove quotes " from the sample names, and try again?

[annecar]

Hi vadim! Thanks, For your quick answer. I am sorry to bother you... I will try again, though I am not aware of the quotes. Otherwise I will wait for the new release! Best Anne On 31. Oct 2019, at 10:01, Vadim Nazarov <[email protected]<mailto:[email protected]>> wrote: Hi, thank you, we will look into it! We will have a new release at the beginning of the next week, so it should be fixed there. However, if you want to speed up things, can you please remove quotes " from the sample names, and try again? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#27?email_source=notifications&email_token=AIM7QPRQ3QHYUEZYR47WSXTQRKLDTA5CNFSM4JGZAOXKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOECW6RJA#issuecomment-548268196>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIM7QPTYDX5NOOVCJ5FSXPLQRKLDTANCNFSM4JGZAOXA>.

[annecar]

Hi, i had tried without before and it did not work either. thanks for your help Anne Anne Eugster, PhD Head Single Cell Unit/ Scientist AG Bonifacio Technische Universität Dresden DFG-Center for Regenerative Therapies Dresden Cluster of Excellence Fetscherstr. 105 01307 Dresden Tel: [phone] Fax: [phone] Email: [email protected] Webpage: www.crt-dresden.de

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On 31. Oct 2019, at 09:43, Vadim Nazarov ***@***.***> wrote: Hi, thank you, we will look into it! We will have a new release at the beginning of the next week, so it should be fixed there. However, if you want to speed up things, can you please remove quotes " from the sample names, and try again? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[vadimnazarov]

Hi, thank you, it should be fixed in todays release, we will message you here or by email when its ready!

[annecar]

Hi Vadim one more question: do you plan to ingrate the Shannon diversity index in your pipeline? That would be quite good. Thanks!! Anne CRTD Anne Eugster, PhD Head Single Cell Unit/ Scientist AG Bonifacio Technische Universität Dresden DFG-Center for Regenerative Therapies Dresden Cluster of Excellence Fetscherstr. 105 01307 Dresden Tel: [phone] Fax: [phone] Email: [email protected] Webpage: www.crt-dresden.de

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On 4. Nov 2019, at 09:32, Vadim Nazarov ***@***.***> wrote: Hi, thank you, it should be fixed in todays release, we will message you here or by email when its ready! — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[vadimnazarov]

Can you provide a link to it please? Wikipedia, a publication, anything you find useful.

P.S. Todays release postponed to the middle of the week, sorry for that!

[annecar]

Dear Vadim for example used in this paper, there is also the original reference. ok, i wait to see the release… Something else: about IMMREP20: we should talk about a workshop or tool demo, as you said you would be interested to do some. Would you like to think about this and then i could arrange a call wit the other organisers? Thanks for all! Anne CRTD Anne Eugster, PhD Head Single Cell Unit/ Scientist AG Bonifacio Technische Universität Dresden DFG-Center for Regenerative Therapies Dresden Cluster of Excellence Fetscherstr. 105 01307 Dresden Tel: [phone] Fax: [phone] Email: [email protected] Webpage: www.crt-dresden.de

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On 4. Nov 2019, at 21:29, Vadim Nazarov ***@***.***> wrote: Can you provide a link to it please? Wikipedia, a publication, anything you find useful. P.S. Todays release postponed to the middle of the week, sorry for that! — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[EugeneRumynskiy]

Hi @annecar
We fixed the metadata problem in 0.5.2 version.

1. Update your package to 0.5.2. Get the latest version from master branch.
   • https://github.com/immunomind/immunarch/blob/master/immunarch.tar.gz
2. Just apply repLoad(...) to your data folder again and it will load the metadata file.
   tmp = repLoad("path/to/your/data")
   tmp$meta
   names(tmp$data)
   
   Hope we solved your problem :)

@vadimnazarov Will mail you about IMMREP20 and rarefaction in one of the next days.

[annecar]

Thanks a lot, Eugene! I will give it a try asap. @vadim: talks for getting back to me, that would be great. Best Anne Anne Eugster, PhD Scientist AG Bonifacio CRTD - Center for Regenerative Therapies TU Dresden Fetscherstr. 105 01307 Dresden Tel: [phone] Fax: [phone] Email: [email protected]<mailto:[email protected]> Webpage: www.crt-dresden.de<http://www.crt-dresden.de> On 20. Nov 2019, at 13:26, Eugene Rumynskiy <[email protected]<mailto:[email protected]>> wrote: Hi @annecar<https://github.com/annecar> We fixed the metadata problem in 0.5.2 version. 1. Update your package to 0.5.2. Get the latest version from master branch. * https://github.com/immunomind/immunarch/blob/master/immunarch.tar.gz 2. Just apply repLoad(...) to your data folder again and it will load the metadata file. tmp = repLoad("path/to/your/data") tmp$meta names(tmp$data) [image]<https://user-images.githubusercontent.com/20778038/69238622-7ba4d500-0ba9-11ea-89a3-4692732d883e.png> Hope we solved your problem :) @vadimnazarov<https://github.com/vadimnazarov> Will mail you about IMMREP20 and rarefaction in one of the next days. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#27?email_source=notifications&email_token=AIM7QPR2OZCZR7HIVJ7WSOLQUUUF5A5CNFSM4JGZAOXKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEERZ4HQ#issuecomment-555982366>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIM7QPUUPNLSEEQMLEWXF4TQUUUF5ANCNFSM4JGZAOXA>.

[annecar]

Hi ! Happy new year to the crew! I have a question regarding downsampling: how can i get “data’ attached to my downsampled batch? when i downsample now, using dsP1 = repSample(immdata$data, "downsample") I do not have a $data slot. Thanks a lot for your help! Anne Anne Eugster, PhD Scientist AG Bonifacio CRTD - Center for Regenerative Therapies TU Dresden Fetscherstr. 105 01307 Dresden Tel: [phone] Fax: [phone] Email: [email protected]<mailto:[email protected]> Webpage: www.crt-dresden.de<http://www.crt-dresden.de> On 4. Dec 2019, at 14:56, Vadim Nazarov <[email protected]<mailto:[email protected]>> wrote: Closed #27<#27>. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#27?email_source=notifications&email_token=AIM7QPX54NMHGBEX2J7TPV3QW6ZKRA5CNFSM4JGZAOXKYY3PNVWWK3TUL52HS4DFWZEXG43VMVCXMZLOORHG65DJMZUWGYLUNFXW5KTDN5WW2ZLOORPWSZGOVIO5EQQ#event-2854081090>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIM7QPTVLU2HZQTKRZVVEUDQW6ZKRANCNFSM4JGZAOXA>.