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zhangzlab / covid_balf

R script for the covid balf data analysis
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balf_1.txt #7

Closed maximilianh closed 3 years ago

maximilianh commented 4 years ago

Hi, we're trying to run your seurat_integration script but it requires a file balf_1.txt which is not in the Github repository. Could you add this file?

thanks!

polojacky commented 4 years ago

Please refer to meta.txt.

maximilianh commented 4 years ago

many thanks for the quick reply!

Another question: we're trying to run your analysis script, but while removing all the obstacles and fighting against R packages, I was wondering: couldn't you provide the final Seurat.rds file with the raw and integrated dataset? That may be easier for most users, like me, to get the full dataset, rather than us having to download .h5, R and .txt files. I imagine you have this Seurat object on your disk, possibly as a data file already... you could copy a dropbox or similar link into the README file and possibly this would save a lot of questions in Github...?

zhangzlab commented 4 years ago

Yes, that's a good idea. I'll try to find an option since the file is too big to be included in Github repo. Dropbox is not available, maybe OneDrive.

maximilianh commented 4 years ago

We could also host it for you. Email mspeir@ucsc.edu and/or me, you can upload the file via an sftp account here that we create for you and we can provide the file through our servers under a normal URL instead of a free cloud something account. We are building an interactive browser for your data and can attach any supplemental files there. Also other big files you may have (images, etc)

On Fri, Jul 10, 2020 at 2:34 PM zhangzlab notifications@github.com wrote:

Yes, that's a good idea. I'll try to find an option since the file is too big to be included in Github repo. Dropbox is not available, maybe OneDrive.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/zhangzlab/covid_balf/issues/7#issuecomment-656652738, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TPMENW3V56FDOBAT4TR24DFVANCNFSM4ONSPRMQ .

maximilianh commented 4 years ago

Hi!

Yes, happy to host it. Let us know, we can set up sftp for you to upload the data and we can host your dataset visualization through our site.

Matthew Speir

UCSC Cell Browser, Quality Assurance and Data Wrangler

Human Cell Atlas, User Experience Researcher

UCSC Genome Browser, User Support

UC Santa Cruz Genomics Institute http://genomics.ucsc.edu/

Revealing life’s code.

On Fri, Jul 10, 2020 at 6:14 AM Maximilian Haeussler maximilianh@gmail.com wrote:

We could also host it for you. Email mspeir@ucsc.edu and/or me, you can upload the file via an sftp account here that we create for you and we can provide the file through our servers under a normal URL instead of a free cloud something account. We are building an interactive browser for your data and can attach any supplemental files there. Also other big files you may have (images, etc)

On Fri, Jul 10, 2020 at 2:34 PM zhangzlab notifications@github.com wrote:

Yes, that's a good idea. I'll try to find an option since the file is too big to be included in Github repo. Dropbox is not available, maybe OneDrive.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/zhangzlab/covid_balf/issues/7#issuecomment-656652738, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TPMENW3V56FDOBAT4TR24DFVANCNFSM4ONSPRMQ .

zhangzlab commented 4 years ago

Please send the account info to jack.liu9@outlook.com.