Dear all,
We, computational scientists, are developing new statistical methods for the analysis of single-cell data. The application of these methods to COVID-19 data has revealed novel findings in terms of its biology, which would also impact its treatment. We are gearing towards the submission of these findings. Could you let us know regarding the policy of publication manuscripts that leverage COVID19 cell atlas data? We will be happy to accommodate researchers who had generated the data as co-authors in the manuscript as deemed necessary.
Avinash Sahu
Research Fellow
asahu(a)ds.dfci.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__connects.catalyst.harv…
Hello,
I had a question about the pre-processing of the datasets hosted on the covid19cellatlas.org<http://covid19cellatlas.org>. I am sorry if I reached out on a wrong address, and I would be grateful if you could forward me to the right person.
Specifically, I am interested in the information on the normalization/processing of the raw expression values, used to generate the .h5ad files for the healthy donors. I noted on the data ingestion information that the raw counts are always pre-processed, but no information on what that processing is or for what datasets that affected. So, I would be grateful if you could clarify this.
Sincerely yours,
Ksenia Sokolova
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Hello,
We've recently generated spatially-resolved single-cell data of
post-mortem lung tissue of COVID-19 patients and other lung infections
(https://urldefense.proofpoint.com/v2/url?u=https-3A__www.medrxiv.org_conten… ).
Would there be interest in adding this dataset to the COVID-19 portal of
the HCA?
We already provide a h5ad file with the single-cell data
(https://urldefense.proofpoint.com/v2/url?u=https-3A__zenodo.org_record_4139… ), but
perhaps this could help researchers having a one-stop place for COVID-19
single cell data?
Of importance, our features do not represent gene expression but protein
abundance for 36 selected proteins, so this is in contrast to most other
datasets which I believe are scRNA-seq.
Best wishes,
Andre
--
*André Rendeiro, Ph.D.
*Postdoctoral Associate, Elemento Lab
Englander Institute for Precision Medicine
Institute for Computational Biomedicine
*Weill Cornell Medicine
*1305 York Ave., Y13.13
New York, NY (USA) 10021
afr4001(a)med.cornell.edu <mailto:afr4001@med.cornell.edu>
Good afternoon:
I am finding your Covid19 cell atlas very useful.
Can we publish snapshots of the data?
What is the best way to use it for publications?
I am happy to share our paper draft where I believe some of your data could be very complimentary.
If I could extract data for roc curves it would be amazing.
Thank you in advance
Fernando Martinez
Hi
Sorry to send to this address but I could not find out where to report problems. I wanted to download and use this file
https://urldefense.proofpoint.com/v2/url?u=https-3A__hosted-2Dmatrices-2Dpr…
Which is supposed to be an R data set, unfortunately it is not and is corrupted or otherwise not valid (could be they used a very old version of R, but no information is provided on your website).
It would be helpful to provide md5 checksums or other tools to help
validate downloads etc.
Robert
Hi!
I hope this email finds you well! I have a question about the normalized
expression for the datasets on covidatlas.
How are the data normalized? Are gene expression values comparable across
cell types?
Best wishes,
Sherif
--
Sherif Gerges
PhD Candidate
Harvard Medical School | Broad Institute of Harvard and M.I.T | Analytic &
Translational Genetics Unit, MGH
Institute for Applied Computational Science | Harvard John A. Paulson
School of Engineering and Applied Sciences
Hey,
I am very interested in this website and would like to be added to it.
Thank you,
Po-Yi
--
*Po-Yi Ho, Ph.D.*
ORISE Fellow
Molecular Epidemiology & Bioinformatics Team
Division of Viral Hepatitis, Centers for Disease Control and Prevention
(CDC)
1600 Clifton Rd NE, Building 18, Room 4-110, MS H18-4, Atlanta, GA 30329
Tel: 678-559-2413, Email: poyiho.ph(a)gmail.com
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