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:
6 months, 1 week ago
Joined:
3 years, 10 months ago
Email:
v******************@gmail.com

Posts by Vladimir Kiselev

<prev • 34 results • page 3 of 4 • next >
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Answer: A: Import .mtx file in R
... Hi, looks like this question is not related to SC3... Could you please change the tag of your question, so that proper people can answer it? ...
written 2.3 years ago by Vladimir Kiselev150
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Answer: A: sc3_plot_expression, colour labels
... Hi, Unfortunately, it is not possible through sc3_plot_expression itself. However, since all heatmaps in SC3 are based on the pheatmap package, you can use the source code of sc3_plot_expression and add some manual colour annotations to it via pheatmap arguments. So if object is your scater object ...
written 2.4 years ago by Vladimir Kiselev150
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Comment: C: Sharing SC3_interactive results
... Yes, it is right. And no, you can't share the results via a link, your collaborator needs to have R and SC3 installed to be able to run sc3_interactive(). Cheers, Vlad ...
written 2.4 years ago by Vladimir Kiselev150
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Answer: A: Sharing SC3_interactive results
... Hi Coral, In the newest version of SC3, if you share (for example save it in an ".rds" file) a scater object that you used to run the SC3 analysis on, it will contain all the data required for sc3_interactive(). So the person that you share it will only need to run sc3_interactive(YOUR_SCATER_OBJEC ...
written 2.4 years ago by Vladimir Kiselev150
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Comment: C: biomaRt error when connecting to host
... Looks like it works, indeed. Thanks! ...
written 2.5 years ago by Vladimir Kiselev150
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Comment: C: Monocle causes R session to crash
... Exactly the same problem with me and several other people I know. My session info: R Under development (unstable) (2016-10-20 r71540) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X Yosemite 10.10.5 locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attac ...
written 2.5 years ago by Vladimir Kiselev150
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Comment: C: biomaRt error when connecting to host
... Thanks Mike! So is it a temporary or permanent problem? Are you planning to update the release branch any time soon? ...
written 2.5 years ago by Vladimir Kiselev150
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Answer: A: using SC3 and scater for bulk-RNAseq
... Hi Assa, Regarding scater Davis and Aaron extensively replied above. Regarding SC3 I will second Davis - using SC3 in general should be OK. But keep in mind that we optimised the range of the eigenvectors used for clustering (4%-7% of N, where N is the number of cells, see paper for details - http ...
written 2.6 years ago by Vladimir Kiselev150
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Comment: C: sc3_prepare function error
... Note that in the course we used an old version of Seurat (1.3). Now there is a new one available, where the clustering algorithm is completely different. We will try to update the course with this new version when we run it next time (middle of March 2017). ...
written 2.7 years ago by Vladimir Kiselev150
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Comment: C: sc3_prepare function error
... Have you updated the scater package as well? You need the latest scater version (1.2.0) for SC3 to work. ...
written 2.7 years ago by Vladimir Kiselev150

Latest awards to Vladimir Kiselev

Scholar 2.3 years ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts
Scholar 2.4 years ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts
Scholar 2.4 years ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts
Scholar 3.6 years ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts

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