User: roy.granit
roy.granit • 810
- Reputation:
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- Israel/LabWorm
- Website:
- https://labworm.com/
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- rgranit
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- Last seen:
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- Joined:
- 5 years, 4 months ago
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I'm a co-founder & CTO at LabWorm a crowd voting platform that enables scientists to discover the best & newest online research tools. Previously I explored pathways that determine intratumoral heterogeneity using high-throughput molecular biology & bioinformatics. My personal website.
Posts by roy.granit
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... The goal is to check how heterogeneous each cluster is.. one could take the correlation between all cells but that would not be very interesting since most genes do not change or are not expressed. ...
written 8 weeks ago by
roy.granit • 810
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... Thanks that was my thinking as well. Is there another way of showing a measure of how cells in a given cluster are similar to each other?
I initially took the distances of all cells from the center of the cluster.. but I guess this is just another view of the clustering ...
written 8 weeks ago by
roy.granit • 810
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... I'm working on single cell expression data using Seurat and have generated a umap and performed clustering of the data.
Now I was asked if there is a way to plot / calculate the distance between all cells in a given cluster, and was suggested to take the vector of each cell and run a formula like t ...
written 8 weeks ago by
roy.granit • 810
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Comment:
C: What does "Quadratic sum" mean?
... Thanks, but the problem that the forum is not that active so I could not find an answer there.. ...
written 3 months ago by
roy.granit • 810
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... I've used inferCNV to predict CNVs based on single cell expression data, and now I wish to calculate the "CNV score" as conducted in [this][1] publication.
It says:
"The CNV score of each cell was calculated as quadratic sum of CNVregion"
The possible values are 0.5, 1.5, 2 - but what does "Quadr ...
written 3 months ago by
roy.granit • 810
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... Hi All,
I suspect that my sample might have dna contamination. Is there a way of telling the fraction of reads mapped to the transcriptome vs genome when using the STAR aligner?
I have used the --quantMode TranscriptomeSAM flag so I guess that can use samtools to count the number of reads mapped t ...
written 3 months ago by
roy.granit • 810
• updated
3 months ago by
grant.hovhannisyan • 1.8k
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... Thanks. Ended up using this code after converting my .mate1 files into bam using picardtools ...
written 4 months ago by
roy.granit • 810
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... After adaptor cleaning I have about 30% of unaligned reads therefore I wish to inspect these reads and see what is the source, ideally it would be great to blast these sequences since I have no clue if these originate due to bacterial or viral contamination. ...
written 4 months ago by
roy.granit • 810
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... But how do I find the most common reads to blast them? ...
written 4 months ago by
roy.granit • 810
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... Indeed, I'm aware that I cannot align these sequences to the transcriptome/genome, but these reads are derived from a certain cell line which might express some 'external' genes that were transfected and I wish to know how many of the reads map to these genes (before I generate a hybrid genome) ...
written 4 months ago by
roy.granit • 810
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