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Recent Replies
Comment: Magnesium ion in a post-docking adjustment
by
dthorbur
★
2.5k
[`AlphaFold3`](https://alphafoldserver.com/) (assuming you're not at conflict with their terms of use) can handle both ligands and ions. An…
Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
by
ATpoint
85k
> But How could I know if the difference comes from sample instead of sequencing runs or cohort-driven batch effect?
You cannot. It's pe…
Comment: Comparing GSEA mutant data to wild type
by
conmul
•
0
Sorry that it was unclear in the post. The data is all CRISPR gene effect scores from DepMap. The 'significant genes' as mentioned in the p…
Comment: How to determine whether it is 10x data
by
king
•
0
Thank you for your answer, it's very inspiring.
Comment: Inquiry about depth of coverage and copy number variation
by
Chen
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Thanks Pierre, I was actually thinking about the duplicate PCR reads and didn't explain it properly. I have found a post mentioning that qu…
Comment: Can a read be aligned more than once?
by
GenoMax
146k
Yes a read can be aligned more than once (I don't specifically know about gam/gaf). It would be called a "multi-mapping" read. You could im…
Comment: Statistical test to be used for dataset
by
allingt
•
0
The choice of test depends on the types of variables involved and the hypothesis you have. But most importantly on the question you want am…
Comment: dittoHeatmap; adding column labels on the heatmap
by
jared.andrews07
★
18k
I'd consider making a [block annotation](https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#block-annotation…
Comment: Comparing GSEA mutant data to wild type
by
allingt
•
0
What do you mean by "significant gene"?
How did you perform GSEA and on how did you rank your genes for it?
From guesswork I might initiall…
Comment: Genes of Interest in a Multi-Tissue Analysis
by
allingt
•
0
The DESeq2 manual tells us that the object class of vst() output is a subclass of RangedSummarizedExperiment. I suspect the methods applica…
Comment: WGCNA: Why are my brown, yellow, and other modules not visible in the gene dendr
by
allingt
•
0
Did you perform blockwise module detection by any chance? Are your results object's contents sorted in blocks?
Comment: Why does WGCNA use weighted correlation instead of Pearson correlation?
by
allingt
•
0
The WGCNA implementation by Langfelder and Horvath provides various correlation methods to create the initial correlation matrix. I don't t…
Comment: dittoHeatmap; adding column labels on the heatmap
by
Varun Gupta
★
1.3k
any idea, how can I display the labels Pre and POst on the top of the heatmap? I am looking at complexheatmap package as to how they displa…
Comment: How can I determine the p-value of genes within each identified module in WGCNA?
by
allingt
•
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What p-value do you mean? When and how did you calculate it?
Answer: What is a genomic range that would almost always get decent WGS coverage but is
by
i.sudbery
20k
What about some of the well known enhancer regions, the globin locus LCR? Likely to be highly sequenceable, and yet not on exome panels.
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