User: Vladimir Kiselev

Reputation:
150
Status:
Trusted
Location:
Sanger Institute, Cambridge, UK
Website:
http://www.genat.uk/
Twitter:
wikiselev
Scholar ID:
Google Scholar Page
Last seen:
8 months ago
Joined:
4 years ago
Email:
v******************@gmail.com

Posts by Vladimir Kiselev

<prev • 34 results • page 1 of 4 • next >
1
vote
1
answer
291
views
1
answers
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 8 months ago by Vladimir Kiselev150
1
vote
1
answer
291
views
1
answers
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 8 months ago by Vladimir Kiselev150
0
votes
1
answer
185
views
1
answers
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 9 months ago by Vladimir Kiselev150
0
votes
1
answer
280
views
1
answers
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 11 months ago by Vladimir Kiselev150
0
votes
1
answer
268
views
1
answers
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 14 months ago by Vladimir Kiselev150
0
votes
1
answer
266
views
1
answers
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 18 months ago by Vladimir Kiselev150
0
votes
1
answer
312
views
1
answers
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 22 months ago by Vladimir Kiselev150
0
votes
2
answers
765
views
2
answers
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 22 months ago by Vladimir Kiselev150
0
votes
1
answer
470
views
1
answers
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 23 months ago by Vladimir Kiselev150
0
votes
1
answer
571
views
1
answers
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 2.0 years ago by Vladimir Kiselev150

Latest awards to Vladimir Kiselev

Scholar 2.5 years ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts
Scholar 2.5 years ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts
Scholar 2.6 years ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts
Scholar 3.7 years ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 229 users visited in the last hour