Biostar Bayesian-Inference

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Multispecies-Coalescent-Model Bayesian-Inference Phylogenomics Divergence-Time Maximum-Likelihood

updated 9 weeks ago by Ram 44k • written 9 weeks ago by carlopecoraro2 ★ 2.6k

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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 • 0

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 • 0

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.

Answer: Using NumReads column of quants.genes.sf file to build DESeq2 input by i.sudbery 20k

One of the improvements that the using the `salmon` -> `tximport` -> `DESeq2` pipeline, over just a `counts`->`DESeq2` pipeline is the abil…

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