Moderator: geek_y

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geek_y10k
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Barcelona
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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

<prev • 1,434 results • page 1 of 144 • next >
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Comment: C: SC-RNA Seq Analysis tutorials
... very useful information. ...
written 3 months ago by geek_y10k
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Comment: C: How to calculate N in TWAS simulated data
... 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 3 months ago by geek_y10k
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Answer: C: Correlation analysis for low expressed genes
... 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 3 months ago by geek_y10k
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Comment: C: How to calculate N in TWAS simulated data
... What do you mean by N ? ...
written 3 months ago by geek_y10k
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Answer: A: Most recent tools for circadian gene expression analysis (in plants)
... I am aware only of [JTKCycle][1] for identifying cycling genes. [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3119870/ ...
written 3 months ago by geek_y10k
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Answer: A: exon-intron reads in neuron samples
... GTEx provides [exon-exon junction counts][1] if that helps. [1]: https://gtexportal.org/home/datasets#filesetFilesDiv13 ...
written 3 months ago by geek_y10k
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Answer: A: Current standards for batch correction and gene expression correction?
... 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 3 months ago by geek_y10k
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Answer: A: DiffBind to call differential binding of Super-enhancers from ROSE
... 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 3 months ago by geek_y10k
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Answer: A: SNP calling and SNP discovery
... https://software.broadinstitute.org/gatk/documentation/article.php?id=3891 ...
written 4 months ago by geek_y10k
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Comment: C: the analysis of multiple samples of 10X scRNA-seq
... 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 4 months ago by geek_y10k

Latest awards to geek_y

Great Question 8 days ago, created a question with more than 5,000 views. For Multisample VCF file to Structure file format ?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Scholar 9 weeks ago, created an answer that has been accepted. For A: pdb to gff?
Scholar 9 weeks ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Great Question 9 weeks ago, created a question with more than 5,000 views. For Multisample VCF file to Structure file format ?
Scholar 11 weeks ago, created an answer that has been accepted. For A: pdb to gff?
Scholar 11 weeks ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: How get intervals of low coverage from a genome sequence?
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: bioinformatics basic training
Scholar 3 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Scholar 3 months ago, created an answer that has been accepted. For A: pdb to gff?
Scholar 3 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Great Question 4 months ago, created a question with more than 5,000 views. For Multisample VCF file to Structure file format ?
Scholar 4 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Scholar 4 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
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Scholar 8 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise

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