User: roy.granit
roy.granit • 800
- Reputation:
- 800
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- Trusted
- Location:
- Israel/LabWorm
- Website:
- https://labworm.com/
- Twitter:
- rgranit
- Scholar ID:
- Google Scholar Page
- Last seen:
- 3 months, 3 weeks ago
- Joined:
- 4 years, 9 months ago
- Email:
- r*********@gmail.com
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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C: Interpreting DEseq2 results
... Thanks everyone. I'm not applying any cutoffs other than FDR < 0.05.
As for the details, this is 3' RNAseq lib which I have aligned to the genome/transcriptome using STAR and counted the reads with Salmon.
My main concern was that this is caused by some mistake in the analysis pram, but since ...
written 4 months ago by
roy.granit • 800
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C: Interpreting DEseq2 results
... Looks pretty equal.. ...
written 4 months ago by
roy.granit • 800
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... I ran an mRNA seq analysis with three groups: control, treated1, treated2 - each with two replicates.
When I look at the comparison of 'treated2 vs control' I notice that most of the genes that hit statistical adjusted p-value are 'log2FoldChange' positive - meaning they are up-regulated in treated ...
written 4 months ago by
roy.granit • 800
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... I also ask my self this question.. what is the meaning of mutation.count? are we talking about all mutations or only non-synonymous? does this relate only to gene regions or whole genome mutations? ...
written 4 months ago by
roy.granit • 800
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... Thanks. I suppose DESeq2 will turn to TPM while doing the statistics..? ...
written 4 months ago by
roy.granit • 800
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... I have a 3-prime RNA seq library which I have analyzed using STAR aligner followed by Salmon counter and currently analyzing the data using DEseq2.
It appears that I am getting many counts for some genes.. and I assume this is since I have used a 3' lib in which most reads are concentrated in a sm ...
written 4 months ago by
roy.granit • 800
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... I've searched around and could not find (possibly missed) advice on which transcript quantification tool is well suited for 3' prime RNA-seq lib?
I've considered using Salmon, but I'm not sure if it will correct for transcript length which is expected to be only a small part of the transcript
Wou ...
written 5 months ago by
roy.granit • 800
• updated
5 months ago by
WouterDeCoster ♦ 39k
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Comment:
C: GSEA on single-cell cluster data
... Thanks, not sure about these suggestions, I believe they are correct for pathway over-representation but not for hyper-geometric/GSEA analysis. I was seeking some tool that would take the individual GSEA scores for each cell in a certain cluster and conduct a statistical comparison of these to the s ...
written 8 months ago by
roy.granit • 800
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Comment:
C: IGV empty tracks render in blue
... Yes, these are segmented CNVs detected using QDNAseq, I know there are no CNVs on the blue tracks by looking at the raw SEG files ...
written 8 months ago by
roy.granit • 800
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... Hello Biostars,
I have 10x SC expression data which I have processed using Seurat, and now I wish to test the association of several gene-sets with certain clusters. What approach/R package would you recommend?
I suppose I can run GSEA on the expression of individual cells, but next how do I summar ...
written 8 months ago by
roy.granit • 800
• updated
3 months ago by
marcovicari3 • 0
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