User: Vladimir Kiselev

Reputation:
110
Status:
Trusted
Location:
Sanger Institute, Cambridge, UK
Website:
http://www.genat.uk/
Twitter:
wikiselev
Scholar ID:
Google Scholar Page
Last seen:
9 hours ago
Joined:
1 year, 10 months ago
Email:
v******************@gmail.com

Posts by Vladimir Kiselev

<prev • 20 results • page 1 of 2 • next >
0
votes
1
answers
39
views
1
answers
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 10 hours ago by Vladimir Kiselev110
0
votes
1
answers
39
views
1
answers
Answer: A: SC3 gene clusters
... Hi Ahmed, SC3 does not perform gene clustering. It only clusters cells. Therefore there is no column in `fData` for that. `sc3_N_markers_clusts` column defines which cell cluster each gene is a marker for. Hope this helps, Cheers, Vlad ...
written 11 hours ago by Vladimir Kiselev110
0
votes
1
answers
172
views
1
answers
Answer: A: counts method is not exported
... Found an answer here: https://github.com/drisso/SingleCellExperiment/issues/1 ...
written 6 weeks ago by Vladimir Kiselev110
1
vote
1
answer
172
views
1
answer
counts method is not exported
... Hi! Is there any reason why `counts()` method is not exported from the SingleCellExperiment package? The same applies to `assay()` method? Thanks you! ...
singlecellexperiment written 6 weeks ago by Vladimir Kiselev110
0
votes
1
answers
407
views
1
answers
Answer: A: Does SC3 correct counts for gene length?
... Hi, 1. SC3 does not correct for gene length, please use other tools for that. 2. Yes, you can use any units with SC3, it will always find some structure in your data. The thing is that if you don't normalise your data, or normalise it in a wrong way you will either get a wrong result or pick up a ...
written 7 weeks ago by Vladimir Kiselev110
0
votes
2
answers
581
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 3 months ago by Vladimir Kiselev110
0
votes
1
answers
167
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 4 months ago by Vladimir Kiselev110
0
votes
1
answers
141
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 4 months ago by Vladimir Kiselev110
0
votes
1
answers
169
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 5 months ago by Vladimir Kiselev110
0
votes
1
answers
169
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 5 months ago by Vladimir Kiselev110

Latest awards to Vladimir Kiselev

Scholar 4 months ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts
Scholar 5 months ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts
Scholar 19 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: 323 users visited in the last hour