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:
1 month, 3 weeks ago
Joined:
2 years, 7 months ago
Email:
v******************@gmail.com

Posts by Vladimir Kiselev

<prev • 29 results • page 1 of 3 • next >
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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 8 weeks 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 5 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 5 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 6 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 7 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 7 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 7 months ago by Vladimir Kiselev130
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Answer: A: SC3_estimate_k formatting error?
... Could you please share your dataset with me, so that I can reproduce your error? Please share it with vk6@sanger.ac.uk. ...
written 8 months ago by Vladimir Kiselev130
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Answer: A: Raw count data for SC3 and SingleCellExperiment set problem
... In addition to Aaron's answer, please note that SC3 operates on logcounts slot of the SingleCellExperiment object. So if you would like to cluster raw counts you need to write them directly to the logcounts slot when creating a SingleCellExperiment object (this step is also shown in the SC3 vignette ...
written 8 months ago by Vladimir Kiselev130
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Comment: C: SC3 gene clusters
... Hi Ahmed, Oh sorry, now I see what confused you. Clustering of genes on all heatmaps is done by default functionality of the `pheatmap` package (it has nothing to do with SC3): ?pheatmap::pheatmap() kmeans_k - the number of kmeans clusters to make, if we want to agggregate the rows before drawin ...
written 9 months ago by Vladimir Kiselev130

Latest awards to Vladimir Kiselev

Scholar 12 months ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts
Scholar 13 months ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts
Scholar 14 months ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts
Scholar 2.3 years ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts

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