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Recent Replies
Answer: How to find the adapter sequence of an RNAseq dataset?
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Looks like you are doing this analysis via Galaxy so the following may not help immediately. You can always post to Galaxy help forum for s…
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There are few ways, but you can't be 100% sure. 1st you can try to normilize with SCTransform (suppossed to remove some of the batch effect…
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v0.0.2 has full platform supported now :) !
[https://github.com/dwpeng/filterx/releases/tag/v0.0.2][1]
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Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
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> 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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Thank you for your answer, it's very inspiring.
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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…
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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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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…
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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"?
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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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