Dear COVID-19 Cell Atlas maintainer,
I downloaded haniffa21.processed.h5ad from you website twice as follows
$ wget https://covid19.cog.sanger.ac.uk/submissions/release1/haniffa21.processed.h… )
And both times
$ md5sum haniffa21.processed.h5ad
while you provide md5 checksum
Since all other files of COVID-19 PBMC Ncl-Cambridge-UCL release 1.0 matched your md5 checksums perfectly, I suspect you provide wrong checksum for haniffa21.processed.h5ad
Daniil Sarkisyan, Bioinformatician
Department of Immunology, genetics and pathology, BMC B11:406b
mobile: +46 70 885 9883, email: daniil.sarkisyan(a)igp.uu.se
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No problem at all and I too am excited to see the data on the covid19atlas,
which is an awesome community resource. I'm cc'ing that team here to
hopefully help with the modifications that you've pointed out.
All good things,
On Tue, Apr 6, 2021 at 11:55 AM Tsang, John (NIH/NIAID) [E] <
> Hi Jonah,
> Thanks so much! It has been such a pleasure working with you and Pablo on
> this and we are very grateful for your support. Excited that our dataset is
> now on the human covid19 atlas site!
> I noticed a couple of minor items that would benefit from small textual
> changes if possible:
> 1) title of the dataset -> "Blood PBMCs from COVID-19 patients over time"
> would be a better title as most of our patients were not fatal.
> 2) lab name - there are quite a few labs in the Laboratory of Immune
> Systems Biology (as it's a department). Easiest to put "Tsang Lab" like the
> others would be most consistent.
> Thanks again!
> *From:* Jonah Cool <jcool(a)chanzuckerberg.com>
> *Sent:* Tuesday, April 6, 2021 2:40 PM
> *To:* Tsang, John (NIH/NIAID) [E] <john.tsang(a)nih.gov>; Lau, William
> (NIH/NIAID) [E] <lauwill(a)mail.nih.gov>
> *Subject:* your data on covid19cellatlas
> John & William,
> Hope all is well and you've been getting lots of positive feedback on the
> paper. I wanted to quickly confirm that your data is now available (think
> it has been for a few days, actually:)) on the covid19cellatlas site
> <https://www.covid19cellatlas.org/index.patient.html> under the "patient"
> Thanks again for working with us on this and looking forward to connecting
> again soon.
> All good things,
Thank you for making the data available for download. I have downloaded some data (https://covid19.cog.sanger.ac.uk/submissions/release1/20200804_NasalSwab_Br…), however I have been unable to open it
I get errors like this:
Warning: Unknown file type: h5ad
Warning: 'assay' not set, setting to 'RNA'
Creating h5Seurat file for version 22.214.171.12400
Adding X as data
Adding X as counts
Error: Cannot find feature names in this H5AD file
error #001: c:/msys64/home/Jeroen/hdf5-1.8.16/src/H5Dio.c in H5D__read(): line 551: can't read data
minor: Read failed
error #002: c:/msys64/home/Jeroen/hdf5-1.8.16/src/H5Dchunk.c in H5D__chunk_read(): line 1875: unable to read raw data chunk
major: Low-level I/O
minor: Read failed
error #003: c:/msys64/home/Jeroen/hdf5-1.8.16/src/H5Dchunk.c in H5D__chunk_lock(): line 2905: data pipeline read failed
major: Data filters
minor: Filter operation failed
error #004: c:/msys64/home/Jeroen/hdf5-1.8.16/src/H5Z.c in H5Z_pipeline(): line 1347: required filter 'lzf' is not registered
major: Data filters
minor: Read failed
There are many message boards that have listed possible solutions, but I have not been able to get any of them to work. Could you provide some guidance as to what programs are used to open/manipulate these files please?
I previously contributed data to the COVID-19 Cell Atlas. I now have an updated/finalized Fetal Cerebellum dataset that I would like to replace for the dataset that is currently hosted: https://www.covid19cellatlas.org/index.healthy.html
What is the best way to transfer the updated .rds?
Kimberly A Aldinger, PhD (she/her)
Center for Integrative Brain Research (CIBR)
Seattle Children's Research Institute
Member, Brotman Baty Institute for Precision Medicine
OFFICE Center for Integrative Brain Research, Seattle Children's Research Institute, 1900 9th Avenue, Seattle, WA 98101
MAIL 1900 9th Avenue, M/S JMB-10, Seattle, WA 98101
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Hi Ni and COVID-19 Cell Atlas Team,
I hope you are doing well. I'm writing to request some guidance on updating
our group's previous submission to the COVID-19 Cell Atlas Portal (current
data and viewer is "Nasal Epithelia":
We just submitted our manuscript and are in the process of uploading this
manuscript as a preprint to biorxiv. We would love to supply the data link
for the expanded and updated object. How would you like us to proceed? I
can provide an updated h5ad, though I had some difficulties in formatting
this properly before (I generally work in R/Seurat).
Thanks in advance!
Carly G. K. Ziegler
Harvard/MIT MD-PhD Program
Hope you are doing well!
Following on my previous email, as they tend to slip through the cracks,
I wanted to see if you’re looking to expand your business globally?
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Thank you so much!
I am having trouble downloading single cell expression data from your website. After following the download link below,
I am brought to a page stating:
Could you recommend a solution for me?
Thank you in advance,
If it is possible, we would like to upload our COVID-19 patient data to the COVID-19 Cell Atlas web portal.
Please let us know how we can begin this process. The data is currently unpublished.
Many thanks and best wishes,
M3.121 Leech Building
Faculty of Medical Sciences
Happy New Year
My name is Aaron Wilk from the Blish lab at Stanford University. Your cell atlas is currently hosting our early COVID-19 scRNA-seq immune profiling work, and I am excited to tell you that we have now posted a preprint expanding that initial work to many more patients across a wider range of disease severity: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.biorxiv.org_conten…
Would you be able to host Seurat .rds and .h5ad for this dataset as well?
Please let me know if you have any questions.
All the best,