User: roy.granit
roy.granit • 830
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- 830
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- Israel/LabWorm
- Website:
- http://roygranit.me/
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- rgranit
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- Google Scholar Page
- Last seen:
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- Joined:
- 6 years, 4 months ago
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- 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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... For now I've exported the plots to png files and loaded them into subplots:
plt.figure(figsize=(30, 15))
plt.suptitle("title", fontsize=22)
plt.subplot(133)
plt.imshow(mpimg.imread('./figures/heatmap_2.png',format="png"))
plt.title("expression")
plt.grid ...
written 10 weeks ago by
roy.granit • 830
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... Thanks, I'm actually using a specific type of clustermap (https://scvelo.readthedocs.io/scvelo.pl.heatmap.html) and when I try to add 'ax' to it I get an error: `TypeError: heatmap() got multiple values for keyword argument 'ax'`
...
written 10 weeks ago by
roy.granit • 830
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... Hi All,
Is there a way to plot several [clustermaps][1] in a single matplotlib figure.
Edit: I'm specifically using [https://scvelo.readthedocs.io/scvelo.pl.heatmap.html][2] to generate the heatmap. This returns an object of type `seaborn.matrix.ClusterGrid`
Thanks!
[1]: https://seaborn.pyda ...
written 10 weeks ago by
roy.granit • 830
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Comment:
C: Interpreting DEseq2 output
... Thanks, using `counts(dds, normalized=TRUE)` I was indeed able to obtain the normalized counts and obtain a better understanding of the data.. ...
written 5 months ago by
roy.granit • 830
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Comment:
C: Interpreting DEseq2 output
... The lib is 3' based, so I believe that the transcript length is not relevant in this case ...
written 5 months ago by
roy.granit • 830
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... I have been using DEseq2 for quite a while, but today I was looking a certain transcript and compared that to the raw counts, and found little login in the results. These are the output values:
log2FoldChange: 0.3434941483
pvalue: 2.16740140052804e-06
padj: 5.65192536063831e-06
...
written 5 months ago by
roy.granit • 830
• updated
5 months ago by
rpolicastro ♦ 3.3k
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... Thanks, how reliable is bbmap? never heard of it.. ...
written 7 months ago by
roy.granit • 830
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... I did not mention that some of these genes do not exist in the genome.. ...
written 7 months ago by
roy.granit • 830
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... I have 3 amplicons that I have sequenced and now I wish to align them to the sequences of these three genes so I can quantify how many reads mapped to each gene.
In order to use STAR must I go through the steps of genome indexing or is there a way to align stright with the fasta file containing the ...
written 7 months ago by
roy.granit • 830
2
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... I have a human DNA sequence and I wish to check how variable this sequence is.. is there a way to check how many SNPs are found at the given location?
Thanks! ...
written 8 months ago by
roy.granit • 830
• updated
8 months ago by
Pierre Lindenbaum ♦ 133k
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