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User: Vladimir Kiselev

Reputation:
130
Status:
Trusted
Location:
Sanger Institute, Cambridge, UK
Website:
http://www.genat.uk/
Twitter:
wikiselev
Scholar ID:
Google Scholar Page
Last seen:
2 days, 11 hours ago
Joined:
3 years, 2 months ago
Email:
v******************@gmail.com

Posts by Vladimir Kiselev

<prev • 32 results • page 1 of 4 • next >
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Answer: A: error running sc3_plot_de_genes in SC3 R package
... I've replied on GitHub: https://github.com/hemberg-lab/SC3/issues/88#issuecomment-465484299 ...
written 2 days ago by Vladimir Kiselev130
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Answer: A: SC3 how to customize plots ?
... Hi, sorry for the late reply. For heatmap plots SC3 is using the pheatmap package (https://cran.r-project.org/web/packages/pheatmap/index.html). It looks like it's still not possible to control the colour palettes in that package, but please have a better look there and if there is could you please ...
written 9 weeks ago by Vladimir Kiselev130
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Answer: A: Failure to cluster SC3
... Hi James, I am afraid I will need your data to be able to reproduce. If you are happy to share it, could you please send it to vk6@sanger.ac.uk in addition with your script and sessionInfo()? ...
written 4 months ago by Vladimir Kiselev130
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Answer: A: How can I show certain gene's expression in clusters by sc3
... I don't think this is related to SC3. You can use the pheatmap package to visualise any genes you like. The heatmap will look similar to SC3, since it's also using pheatmap. ...
written 9 months ago by Vladimir Kiselev130
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Answer: A: Is there a way to pull out the stability index matrix from the SC3 object?
... Please refer to this GitHub issue: https://github.com/hemberg-lab/SC3/issues/60 ...
written 12 months ago by Vladimir Kiselev130
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Comment: C: SC3_estimate_k formatting error?
... I am afraid I need to look at your dataset, could you please share it with me again? ...
written 12 months ago by Vladimir Kiselev130
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Answer: A: SC3 Package: marker genes and normal genes obtained from featureData
... Hi, I would recommend you to read more about receiver operating characteristic (https://en.wikipedia.org/wiki/Receiver_operating_characteristic). Genes in which area under the ROC curve is less than the threshold are closer to completely random guess than the ones above the threshold. If you reduce ...
written 13 months ago by Vladimir Kiselev130
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Answer: A: Batch effect removal before SC3?
... Hi, what does removeBatchEffect return? If it remove zeros from your matrix this is not good for SC3 gene filter, which removes genes that have either very high or very low number of zeros. So, if there are no zeros in your data after batch correction, please switch the gene filter off by setting ge ...
written 14 months ago by Vladimir Kiselev130
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Answer: A: SC3_estimate_k formatting error?
... Hi!  I looked at your data and found that it is very shallowly sequenced. In fact there were about 40 cells with all zeros in your matrix. When estimating k SC3 scales the data and if all values are zeros they will become NA after scaling and that is exactly what it was complaining about. Therefore ...
written 14 months ago by Vladimir Kiselev130
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Comment: C: SC3_estimate_k formatting error?
... Very sorry, have been busy resubmitting a paper, will get back to this issue this week. Hope it's ok for you. Sorry again. ...
written 15 months ago by Vladimir Kiselev130

Latest awards to Vladimir Kiselev

Scholar 20 months ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts
Scholar 20 months ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts
Scholar 21 months ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts
Scholar 2.9 years ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts

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