User: Vladimir Kiselev

Reputation:
80
Status:
Trusted
Location:
Sanger Institute, Cambridge, UK
Website:
http://www.genat.uk/
Twitter:
wikiselev
Scholar ID:
Google Scholar Page
Last seen:
1 day, 4 hours ago
Joined:
1 year, 5 months ago
Email:
v******************@gmail.com

Posts by Vladimir Kiselev

<prev • 12 results • page 1 of 2 • next >
0
votes
1
answers
78
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 7 days ago by Vladimir Kiselev80
0
votes
1
answers
78
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 10 days ago by Vladimir Kiselev80
0
votes
1
answers
205
views
1
answers
Comment: C: biomaRt error when connecting to host
... Looks like it works, indeed. Thanks! ...
written 5 weeks ago by Vladimir Kiselev80
0
votes
1
answers
425
views
1
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 5 weeks ago by Vladimir Kiselev80
0
votes
1
answers
205
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 6 weeks ago by Vladimir Kiselev80
0
votes
3
answers
157
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 10 weeks ago by Vladimir Kiselev80
0
votes
1
answers
149
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 3 months ago by Vladimir Kiselev80
0
votes
1
answers
149
views
1
answers
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 3 months ago by Vladimir Kiselev80
0
votes
1
answers
149
views
1
answers
Answer: A: sc3_prepare function error
... Hi, It looks like you have an old version of Bioconductor (both SC3 and scater versions are quite old). Could you please provide an output of this call? source("https://bioconductor.org/biocLite.R") If it offers you to upgrade, please do so and then update all the Bioconductor packages. This sho ...
written 3 months ago by Vladimir Kiselev80
0
votes
1
answers
187
views
1
answers
Answer: A: SC3 tutorial error
... Hi Jenn, Looks like you need to update the 'scater' package. Could you please check whether your 'scater' version is higher than 1.1.14? You can check it by looking at the output of sessionInfo(). Cheers, Vladimir ...
written 6 months ago by Vladimir Kiselev80

Latest awards to Vladimir Kiselev

Scholar 7 days 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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 285 users visited in the last hour