User: dpc

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dpc160
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India
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1 week ago
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11 months, 2 weeks ago
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Posts by dpc

<prev • 167 results • page 1 of 17 • next >
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What is the minimum LDA score I can take for LefSe analysis?
... Hi, I am doing differential abundance analysis and finding out biomarker from gut metagenomic sequences. For biomarker analysis, I am using the LefSe tool which has a default LDA score of 2.00. Can I lower this cut-off and still can consider significantly different taxa as a biomarker? If yes, which ...
sequencing written 7 weeks ago by dpc160
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Comment: C: What is the "Effect Size" in LefSe?
... Thanks zorbax. The default LDA value has kept as 2.00 in LefSe. Can you please suggest the minimum LDA score I can consider to find biomarker by LefSe analysis? ...
written 7 weeks ago by dpc160
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What is the "Effect Size" in LefSe?
... Hi - I have a basic question regarding the tool `LefSe` which is used for biomarker discovery. What I understand so far is, this tool at first does a Kruskal-Wallis test between groups followed by Wilcoxon rank-sum test among the subgroups. So far, so good. At last, it calculates the **` Effect Size ...
lefse statistics written 3 months ago by dpc160 • updated 11 weeks ago by zorbax250
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Change a column name according to the file name
... I have around 52 files named like: `ERR260147.genefamilies.tsv`, `ERR260158.genefamilies.tsv` `ERR275198.genefamilies.tsv`, etc and each file has two columns. I want to change the second column name of each file according to the name of the file. For example, the second column name for file `ERR2601 ...
bash written 4 months ago by dpc160 • updated 4 months ago by Ram32k
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Comment: C: problem in generating correlation heatmap with significance level
... Thanks Kevin for your suggestion and help. I will definitely take a look on it and let you know. Actually I want only the stars to be reflected inside the cells of the heatmap, not the values. I want this because I have a correlation heatmap of 150 microbes X 150 microbes it is quite large and the c ...
written 5 months ago by dpc160
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Comment: C: Can I use pseudocounts for differential abundance of OTUs?
... Thanks Antonio. I am deleting the question here. I have posted it as a new question [here][1] . I will like to draw your attention to the query. Thanks, dpc [1]: https://www.biostars.org/p/464247/ ...
written 5 months ago by dpc160
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problem in generating correlation heatmap with significance level
... Hi there!!! I want help regarding the correlation heatmap generation showing the significance level within the heatmap cells. I want to show the P-value <0.05 as "*" and P-value <0.001 as "**". For that, I am following the script from [here][1]. You can find the script under the header "Star ...
heatmap written 5 months ago by dpc160 • updated 5 months ago by Kevin Blighe71k
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How to show significance value (P value) in heatmap cells generated with pheatmap?
... Hi there!!! I am using pheatmap package to generate heatmap from correlation value. I want to show the significance level as '*' (P value < 0.05) and '**' (P value <0.01) within the cells. How can I do that? Can anyone please help? Thanks, DC7 ...
R pheatmap written 5 months ago by dpc160
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Comment: C: Can I use pseudocounts for differential abundance of OTUs?
... Thanks, Antonio. Yes, I have already used it. I asked just to have a cross-check my data with another method if available. ...
written 5 months ago by dpc160
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Comment: C: Can I use pseudocounts for differential abundance of OTUs?
... Do you have any idea how can I find out (statistically) the differentially abundant taxa from metaphlan output? ...
written 5 months ago by dpc160

Latest awards to dpc

Popular Question 5 weeks ago, created a question with more than 1,000 views. For Problem while downloading SRR file via **ASPERA CONNECT**
Popular Question 4 months ago, created a question with more than 1,000 views. For ERROR: "ascp: Failed to open TCP connection for SSH, exiting."
Supporter 7 months ago, voted at least 25 times.
Centurion 7 months ago, created 100 posts.
Popular Question 7 months ago, created a question with more than 1,000 views. For ERROR: "ascp: Failed to open TCP connection for SSH, exiting."
Rising Star 8 months ago, created 50 posts within first three months of joining.

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