- Cv19caingest - public-lists.sanger.ac.uk

files format to upload our data [EXT]
by Alakwaa, Fadhl 17 Dec '20

17 Dec '20

Hello, How can I submit our rds files, shall you convert it in h5ad format? Regards Fadhl Alakwaa, PhD Michigan Medicine University of Michigan https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_FADHLyemen_… https://urldefense.proofpoint.com/v2/url?u=https-3A__www.linkedin.com_in_fa… ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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CV19 cell atlas publication policy [EXT]
by Avinash Sahu 15 Dec '20

15 Dec '20

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…

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Pre-processing of the raw counts [EXT]
by Ksenia Sokolova 13 Nov '20

13 Nov '20

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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by Yuki Gao 13 Nov '20

13 Nov '20

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[EXT]
by Karen Hope s 13 Nov '20

13 Nov '20

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Imaging mass cytometry data as part of the COVID-19 cell atlas? [EXT]
by Andre Rendeiro 06 Nov '20

06 Nov '20

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>

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Question about publication [EXT]
by Fernando Oneissi Martinez Estrada 29 Oct '20

29 Oct '20

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

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want to report a problem [EXT]
by Gentleman, Robert C. 28 Oct '20

28 Oct '20

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

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Normalization [EXT]
by Gerges, Sherif 28 Oct '20

28 Oct '20

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

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COVID-19 Atlas [EXT]
by Po-Yi Ho 08 Oct '20

08 Oct '20

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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