User: roy.granit

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roy.granit800
Reputation:
800
Status:
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

<prev • 118 results • page 1 of 12 • next >
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Comment: 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.granit800
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Comment: C: Interpreting DEseq2 results
... Looks pretty equal.. ...
written 4 months ago by roy.granit800
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Interpreting DEseq2 results
... 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 ...
deseq2 written 4 months ago by roy.granit800
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Comment: C: How is Mutation.Count derived in TCGA?
... 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.granit800
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Comment: C: Analyzing 3' RNA seq library with DESeq2
... Thanks. I suppose DESeq2 will turn to TPM while doing the statistics..? ...
written 4 months ago by roy.granit800
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Analyzing 3' RNA seq library with DESeq2
... 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 ...
deseq2 rna-seq written 4 months ago by roy.granit800
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What transcript quantification tool would you recommend for 3' prime RNA-seq?
... 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 ...
transcript quantification salmon rna-seq written 5 months ago by roy.granit800 • updated 5 months ago by WouterDeCoster39k
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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.granit800
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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.granit800
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GSEA on single-cell cluster data
... 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 ...
single-cell R gsea written 8 months ago by roy.granit800 • updated 3 months ago by marcovicari30

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Popular Question 4 months ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
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Centurion 10 months ago, created 100 posts.
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Teacher 13 months ago, created an answer with at least 3 up-votes. For A: About gene id
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Popular Question 20 months ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
Scholar 21 months ago, created an answer that has been accepted. For A: Genes and respective pathways from FTP database
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: About gene id
Popular Question 2.5 years ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
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Scholar 4.0 years ago, created an answer that has been accepted. For A: Genes and respective pathways from FTP database
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