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User: berry

gravatar for berry
berry • 30
Reputation:
30
Status:
New User
Location:
Belgium
Last seen:
1 week, 3 days ago
Joined:
2 years, 5 months ago
Email:
g**********@gmail.com

Posts by berry

<prev • 22 results • page 1 of 3 • next >
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Comment: C: Count matrices correction before integrating single-cell RNA-seq datasets
... From different papers. They all used GRCh38 but I don't know about the GTF files. ...
written 6 weeks ago by berry • 30
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Comment: C: Count matrices correction before integrating single-cell RNA-seq datasets
... Hi Friederike, thank you for your reply. I only have access to CellRanger outputs unfortunately. ...
written 6 weeks ago by berry • 30
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Count matrices correction before integrating single-cell RNA-seq datasets
... Hi, I have 3 single-cell RNA-seq datasets from the same platform (10X), same type of sample, same condition, but from different labs to integrate. When I check the genes.tsv or features.tsv files, even though the high majority of the IDs match, I see some differences. For example here "ENSG0000024 ...
single-cell rna-seq count matrix integration written 6 weeks ago by berry • 30
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Comment: C: What's best way to perform sub-clustering in seurat integrate pipeline?
... Hi Wei, Have you find an answer for this question? ...
written 5 months ago by berry • 30
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Comment: C: Integrating TPM and raw count Seurat objects
... Can you share your email address please? ...
written 6 months ago by berry • 30
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Comment: C: Integrating TPM and raw count Seurat objects
... Sorry Antonio I was confused. So I got `760257.6` for the columns. And I guess this means it is already TPM? This was a public data and it was very hard to get a clear answer from the authors. Thank you for your help :) ...
written 6 months ago by berry • 30
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Comment: C: Integrating TPM and raw count Seurat objects
... Hi António, Thank you very much for your reply. When I sum up the columns, I got this : 760257.6 So I tried transforming with 2^(log(TPM+1)) and then summing up the columns I got this : 157130.48 Do you have any idea why this could be happening? ...
written 6 months ago by berry • 30
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Integrating TPM and raw count Seurat objects
... Hi, I have been given a normalised count matrix (single-cell) as following : Cell1 Cell2 Cell3 ..................... Gene1 0.0000 0 0.0000 Gene2 0.0000 0 0.0000 Gene3 155.8516 0 0. ...
single-cell sc-rnaseq seurat written 6 months ago by berry • 30 • updated 6 months ago by antonioggsousa • 2.0k
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Comment: C: TCGAbiolinks problem downloading ASCAT2 data
... Thank you very much, I appreciate it. ...
written 9 months ago by berry • 30
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Comment: C: TCGAbiolinks problem downloading ASCAT2 data
... Thank you for your reply. My version is 2.17.1 and that doesn't accept sample.type = "Primary solid Tumor". It works with "Primary Tumor". With your code, I'm only able to download "hg19.seg" file. However, I want to download a different type of segment data that is processed with ASCAT2 and fil ...
written 9 months ago by berry • 30

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