User: roy.granit

gravatar for roy.granit
roy.granit750
Reputation:
750
Status:
Trusted
Location:
Israel/LabWorm
Website:
https://labworm.com/
Twitter:
rgranit
Scholar ID:
Google Scholar Page
Last seen:
1 month, 3 weeks ago
Joined:
4 years, 3 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 • 111 results • page 1 of 12 • next >
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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 9 weeks ago by roy.granit750
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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 9 weeks ago by roy.granit750
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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 9 weeks ago by roy.granit750 • updated 9 weeks ago by igor7.1k
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Comment: C: SNP matrix to a nice phylogenetic tree
... After creating Newick file ,I used [Dendroscope][1] to create the "radial" plot [1]: http://dendroscope.org/ ...
written 3 months ago by roy.granit750
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Comment: C: SNP matrix to a nice phylogenetic tree
... Thanks. I was able to use FastTree to convert the data into Newick format, now I need to find a way to plot it was nicely as in the figure.. would be happy to receive suggestions ...
written 4 months ago by roy.granit750
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SNP matrix to a nice phylogenetic tree
... Hi All, I have matrix with SNP calling for several positions in 6 bacterial genomes relative to a ref. sample. (generated using [snippy][1]) For example: gene position wt sample_1 sample_2 ... nm_1234 123 A C T nm_1234 129 G T ...
R phylogenetics snp written 4 months ago by roy.granit750
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Comment: C: Bioinformatics workshop or training courses
... Checkout the ["biostar handbook][1]" [1]: https://biostar.myshopify.com/ ...
written 4 months ago by roy.granit750
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Comment: C: How to make a survival plot for a gene between High expression and low expressio
... Yes, you can try a cutoff on 1 or 2 and see how it looks like ( for a two sided distribution the critical Z score values when using a 95% confidence level are -1.96 and +1.96). This task could be easily accomplished using [cbioportal.org][1] I would plot cancer and normal on different charts (not s ...
written 4 months ago by roy.granit750
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Comment: C: How to make a survival plot for a gene between High expression and low expressio
... You could plot the data and see how it spreads and use this do define the cutoff (e.g. if you notice there is clear separation into 2 groups). Another approach might be to use z-score and take +-1-2 score as high and low.. ...
written 4 months ago by roy.granit750
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Comment: C: IGV empty tracks render in blue
... Here is the image.. ![Image][1] [1]: https://u.cubeupload.com/rgranit/igvsnapshot.png ...
written 4 months ago by roy.granit750

Latest awards to roy.granit

Centurion 4 months ago, created 100 posts.
Popular Question 5 months ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: About gene id
Supporter 9 months ago, voted at least 25 times.
Popular Question 14 months ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
Scholar 14 months ago, created an answer that has been accepted. For A: Genes and respective pathways from FTP database
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: About gene id
Popular Question 24 months ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
Scholar 3.5 years ago, created an answer that has been accepted. For A: Genes and respective pathways from FTP database
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: About gene id
Autobiographer 3.6 years ago, has more than 80 characters in the information field of the user's profile.

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