User: Vladimir Kiselev

Reputation:
100
Status:
Trusted
Location:
Sanger Institute, Cambridge, UK
Website:
http://www.genat.uk/
Twitter:
wikiselev
Scholar ID:
Google Scholar Page
Last seen:
1 week, 6 days ago
Joined:
1 year, 8 months ago
Email:
v******************@gmail.com

Posts by Vladimir Kiselev

<prev • 15 results • page 1 of 2 • next >
0
votes
2
answers
527
views
2
answers
Comment: C: Monocle causes R session to crash
... Sorry, Martin, just noticed your question. We had this problem when running our course: http://hemberg-lab.github.io/scRNA.seq.course/pseudotime-analysis.html Namely, if I run this in RStudio (on any system): library(monocle) deng <- readRDS("deng.rds") cellLabels <- colnames(deng) d <- ...
written 4 weeks ago by Vladimir Kiselev100
0
votes
1
answers
110
views
1
answers
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 9 weeks ago by Vladimir Kiselev100
0
votes
1
answers
99
views
1
answers
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 10 weeks ago by Vladimir Kiselev100
0
votes
1
answers
138
views
1
answers
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 3 months ago by Vladimir Kiselev100
0
votes
1
answers
138
views
1
answers
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 3 months ago by Vladimir Kiselev100
0
votes
1
answers
383
views
1
answers
Comment: C: biomaRt error when connecting to host
... Looks like it works, indeed. Thanks! ...
written 4 months ago by Vladimir Kiselev100
0
votes
2
answers
527
views
2
answers
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 4 months ago by Vladimir Kiselev100
0
votes
1
answers
383
views
1
answers
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 4 months ago by Vladimir Kiselev100
0
votes
3
answers
235
views
3
answers
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 5 months ago by Vladimir Kiselev100
0
votes
1
answers
214
views
1
answers
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 6 months ago by Vladimir Kiselev100

Latest awards to Vladimir Kiselev

Scholar 10 weeks ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts
Scholar 3 months ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts
Scholar 17 months 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 2.2.0
Traffic: 136 users visited in the last hour