User: Vladimir Kiselev

Reputation:
150
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Trusted
Location:
Sanger Institute, Cambridge, UK
Website:
http://www.genat.uk/
Twitter:
wikiselev
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Google Scholar Page
Last seen:
2 months, 1 week ago
Joined:
3 years, 6 months ago
Email:
v******************@gmail.com

Posts by Vladimir Kiselev

<prev • 34 results • page 1 of 4 • next >
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Comment: C: Using SC3 with batch corrected MNN values
... There are lots of batch correction methods at the moment. Not all of them correct the expression matrix though. But for those that don't you could use other clustering methods such as louvain clustering on knn graph (default in scanpy package). Here we cover some of the batch correction methods: R - ...
written 10 weeks ago by Vladimir Kiselev150
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Answer: A: Using SC3 with batch corrected MNN values
... Hi, you can always copy your corrected matrix to logcounts, so no need to create a new object. Or if you care about logcounts, then yes, it would be a good idea to create a separate object. However, I think SC3 won't work well with negative values (as majority of other scRNAseq methods), so cannot ...
written 10 weeks ago by Vladimir Kiselev150
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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 3 months ago by Vladimir Kiselev150
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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 6 months ago by Vladimir Kiselev150
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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 8 months ago by Vladimir Kiselev150
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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 13 months ago by Vladimir Kiselev150
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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 16 months ago by Vladimir Kiselev150
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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 16 months ago by Vladimir Kiselev150
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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 17 months ago by Vladimir Kiselev150
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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 18 months ago by Vladimir Kiselev150

Latest awards to Vladimir Kiselev

Scholar 24 months ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts
Scholar 2.0 years ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts
Scholar 2.1 years ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts
Scholar 3.2 years ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts

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