Moderator: geek_y
geek_y ♦ 10.0k
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- geek_y
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I work with range of genomics data like transcriptome (RNA-Seq, scRNA-Seq, CAGE-Seq), open-chromatin/histone modifications/TF profiles, chromosome contact maps etc to understand tissue specific transcriptional regulation in human genome w.r.t to T2D.
I also work on small part of genetics (eQTLs, caQTLs, hQTLs etc) to understand role of common genetic variants in genome regulation.
Posts by geek_y
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Comment:
C: SC-RNA Seq Analysis tutorials
... very useful information. ...
written 6 days ago by
geek_y ♦ 10.0k
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... Are you talking about Transcriptome Wide Association Studies ? What softwares are you talking about ? No. of samples for each SNP ? Or the sample size required to perform TWAS ? ...
written 12 days ago by
geek_y ♦ 10.0k
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... One option is to use the samples with only non-zero expression values. Other option is to perform permutations and calculate a p-value. ...
written 13 days ago by
geek_y ♦ 10.0k
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... What do you mean by N ? ...
written 13 days ago by
geek_y ♦ 10.0k
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... I am aware only of [JTKCycle][1] for identifying cycling genes.
[1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3119870/ ...
written 13 days ago by
geek_y ♦ 10.0k
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... GTEx provides [exon-exon junction counts][1] if that helps.
[1]: https://gtexportal.org/home/datasets#filesetFilesDiv13 ...
written 14 days ago by
geek_y ♦ 10.0k
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... If you don't know batches, may be RUVSeq helps but it depends on non-differential gene expression to estimate surrogate variables. PCA regression performs well. Its included not in sva package as [sva_network][1] function. Plot the PCs and see how many PCs to regress out. sva also has function to es ...
written 14 days ago by
geek_y ♦ 10.0k
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... Super enhancer are nothing but collection of closely spaced individual "peaks" (less than 12.5kb I guess) in linear genomic space. So if you want to do a differential analysis, you could just perform a differential binding of all individual peaks and show an enrichment of differential peaks being a ...
written 14 days ago by
geek_y ♦ 10.0k
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Answer:
A: SNP calling and SNP discovery
... https://software.broadinstitute.org/gatk/documentation/article.php?id=3891 ...
written 27 days ago by
geek_y ♦ 10.0k
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... You can add your own answer what you think is the best for the question. I said it doesn't perform terrible. I did not say its the best.
Here is a plot which I generated using total count normalisation and the cells cluster by cell-types. Ofcourse, normalisation methods developed especially for sc ...
written 28 days ago by
geek_y ♦ 10.0k
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