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Understanding how to analyse VEP files and understand the impact of mutations on biological pathways
REACTOMEPA SNV VEP GO
7 weeks ago by namg • 0
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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…
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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…
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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…
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I'd consider making a [block annotation](https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#block-annotation…
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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…
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The DESeq2 manual tells us that the object class of vst() output is a subclass of RangedSummarizedExperiment. I suspect the methods applica…
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The WGCNA implementation by Langfelder and Horvath provides various correlation methods to create the initial correlation matrix. I don't t…
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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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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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