User: Konstantin Okonechnikov

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20
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New User
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Website:
http://okko73313.blogs...
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1 week, 3 days ago
Joined:
3 years, 3 months ago
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Posts by Konstantin Okonechnikov

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Integrating the computed spike-in coefficients for the normalisation before diff
... Thanks a lot for the reply! My further question: how to create the object with adjusted coefficients for further processing? Is there a specific way to set the reference? Here's my code example: # standard object creation dtCounts <- dba.count(dt) # retrieve peaks peaksRes < ...
written 17 days ago by Konstantin Okonechnikov20
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Integrating the computed spike-in coefficients for the normalisation before differential peaks analysis
... Hi! Have a question about using DiffBind for ChIP-seq data with drosophila spike-ins. I already have computed peaks from usage of control data and spike-in normalisation coefficients for a cohort of target samples across two conditions. The spike-in coefficients computation is based on drosophila a ...
chipseq diffbind spike-ins written 4 weeks ago by Konstantin Okonechnikov20 • updated 24 days ago by Rory Stark3.0k
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Comment: C: A/B compartments computation: control settings
... Thanks a lot for the detailed reply, it fully covers my questions! ...
written 5 months ago by Konstantin Okonechnikov20
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A/B compartments computation: control settings
... Hi! I am using HiTC on HiC-Pro results to compute the A/B compartments. The package documentation is detailed, but for this topic in the tutorial there is only one example command showing this procedure. Because of that I have some additional questions. My code is the following: conFile <- ...
hitc written 5 months ago by Konstantin Okonechnikov20 • updated 5 months ago by Nicolas Servant260
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Answer: A: InTAD: Sample Size and Statistical Power
... Actually the sample size definitely has specific effect. For example, we observed loss of associations based on subsampling of the dataset. It is described in the figure S1A (https://static-content.springer.com/esm/art%3A10.1186%2Fs12859-019-2655-2/MediaObjects/12859_2019_2655_MOESM1_ESM.pdf ). The ...
written 5 months ago by Konstantin Okonechnikov20
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Comment: C: Issues with DEXSeq: rows did not converge in beta
... Hi Alejandro, number of NAs was 68028 (~11%) for p-value and 70609 (~12%) for log2fold_conditon  (total number of exons 588569). Indeed, I did not perform any initial  filtering like excluding not-expressed genes. Is there a suitable strategy for the filtering before analysis? ...
written 2.8 years ago by Konstantin Okonechnikov20
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Issues with DEXSeq: rows did not converge in beta
... HI!  I am using DEXSeq to compare exons within two conditions. The applied strategy was the same as in tutorial. However, after running testForDEU(...) function the following messages were reported: using supplied model matrix 5 rows did not converge in beta, labelled in mcols(object)$fullBetaCo ...
rnaseq dexseq written 2.8 years ago by Konstantin Okonechnikov20
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Comment: C: DESeq2: one condition vs multiple combined
... Thanks a lot for quick and detailed reply! ...
written 3.3 years ago by Konstantin Okonechnikov20
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DESeq2: one condition vs multiple combined
... I have multiple RNA-seq samples from 6 conditions and have to compare each condition against all the others: find genes dominant only in a specific group. I tried two approaches. First approach: separate all samples in 2 conditions: samples from one group vs samples from other groups, then repeat ...
rnaseq deseq2 written 3.3 years ago by Konstantin Okonechnikov20 • updated 21 months ago by rammohanshukla10

Latest awards to Konstantin Okonechnikov

Scholar 5 months ago, created an answer that has been accepted. For A: InTAD: Sample Size and Statistical Power
Popular Question 2.8 years ago, created a question with more than 1,000 views. For DESeq2: one condition vs multiple combined

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