Moderator: mikhail.shugay

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mikhail.shugay3.2k
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Location:
Czech Republic, Brno, CEITEC
Website:
https://github.com/mik...
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@antigenomics
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Last seen:
2 months, 3 weeks ago
Joined:
4 years, 6 months ago
Email:
m********************@gmail.com

Bioinformatician/software developer. Currently I focus on developing software for processing and analysis of T- and B-cell receptor repertoire data (aka Rep-Seq). I'm also a big fan of unique molecular identifier (UMI) technology, i.e. tagging individual DNA and cDNA molecules (and even entire cell genomes) with short degenerate nucleotide tags to track them in high-throughput sequencing experiments.

Posts by mikhail.shugay

<prev • 364 results • page 1 of 37 • next >
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Answer: A: Modeling paratope and epitope interaction
... Have you looked at the pipeline suggested at IEDB: http://tools.iedb.org/main/bcell/modeling-docking/? The **Web servers for modeling 3D structure of antibody-protein complexes** seems to be what you need, or at least can serve as a starting point. ...
written 6 months ago by mikhail.shugay3.2k
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Tool: MAGERI: a software tool for calling rare variants and detecting circulating tumor DNA from UMI-tagged high-throughput sequencing data
... Dear Colleagues, I would like to announce our recently published software tool called [MAGERI](https://github.com/mikessh/mageri) that is designed to facilitate the detection of ultra-rare variants from various kinds of high-throughput sequencing datasets prepared using the molecular barcoding tech ...
rare variant umi resequencing ctdna tool written 6 months ago by mikhail.shugay3.2k
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Comment: C: Mitcr: A Software Tool For Analyzing T-Cell Receptor Sequencing Data
... Indeed the CDR3 amino acid sequence is mostly meaningless here. However when looking at your data tables manually it can sometimes help to see sequencing errors, frameshift hypermutations in case of antibody data, etc. So consider this as an aesthetic for CDR3aa column. ...
written 9 months ago by mikhail.shugay3.2k
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Comment: C: Mitcr: A Software Tool For Analyzing T-Cell Receptor Sequencing Data
... ``~`` indicates a frameshift. In case of a frameshift the V -> J and J -> V translations are performed, the central incomplete codon is marked as ``~`` ...
written 9 months ago by mikhail.shugay3.2k
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Answer: C: How to convincingly illustrate and discuss negative results in NGS.
... I think the most straightforward way is the Volcano plot. Regarding the multiple testing, you can try to illustrate the fact that there are no significant differences by plotting the distribution of P-values and computing the false discovery rate (e.g. with this [package](https://cran.r-project.org/ ...
written 10 months ago by mikhail.shugay3.2k
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Answer: A: Making a data table more comprehensive
... Here you go: df <- data.frame(cond_1=c('a', 'b', NA), cond_2=c('a', 'b', 'c'), cond_3=c('b', 'c', 'd'), cond_4=c('e', 'f', 'g')) library(reshape2) df <- subset(dcast(melt(df, id.vars = c()), value~variable), !is.n ...
written 12 months ago by mikhail.shugay3.2k
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Answer: A: Why can't we downvote on this forum?
... Here are a couple of reasons: 1. Ask yourself if you want this forum to turn in a sort of stackoverflow. Count the number of downvotes you'll get for this post from SO perspective, assuming this question was already asked and core users are too conservative to change the voting system. 2. We work ...
written 12 months ago by mikhail.shugay3.2k
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Answer: A: Adaptive T cell receptor productive clone missing
... This is a productive sequence, just load it to IgBlast and see for yourself: ![enter image description here][1] ' TRBV14 is productive and in frame with J I think the situation can probably be explained as follows: the mapping software checks for conserved ``FGXG`` motif of Joining segment to ens ...
written 12 months ago by mikhail.shugay3.2k
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Comment: C: Visualize Gene Fusions
... If you are asking for visualization of the **evidence** then the answer of Malachi Griffith in the thread mentioned by @Amitm is what you need. ...
written 12 months ago by mikhail.shugay3.2k
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Answer: A: TCR RNAseq Single Cell Data Analysis
... Software for T/B-cell receptor repertoire analysis using non-amplicon samples: 1. [TraCeR](https://github.com/Teichlab/tracer) T-cell receptors, single-cell RNA-Seq 2. [VDjer](https://github.com/mozack/vdjer) B-cell receptors, RNA-Seq P.S. Check out [T cell fate and clonality inference from sing ...
written 12 months ago by mikhail.shugay3.2k

Latest awards to mikhail.shugay

Prophet 5 months ago, created a post with more than 20 followers. For Software For Hla Typing Using Ngs?
Popular Question 11 months ago, created a question with more than 1,000 views. For Functional Annotation Of Variant Calls (Vcf Files)
Teacher 12 months ago, created an answer with at least 3 up-votes. For C: Microarray | RNA Seq | Methylation Arrays - Correlations?
Great Question 12 months ago, created a question with more than 5,000 views. For Software For Hla Typing Using Ngs?
Teacher 12 months ago, created an answer with at least 3 up-votes. For C: Microarray | RNA Seq | Methylation Arrays - Correlations?
Scholar 12 months ago, created an answer that has been accepted. For C: Microarray | RNA Seq | Methylation Arrays - Correlations?
Scholar 12 months ago, created an answer that has been accepted. For C: Microarray | RNA Seq | Methylation Arrays - Correlations?
Teacher 12 months ago, created an answer with at least 3 up-votes. For C: Microarray | RNA Seq | Methylation Arrays - Correlations?
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: A new perspective needed for a newbie
Popular Question 13 months ago, created a question with more than 1,000 views. For MIGEC: towards error-free profiling of immune repertoires
Scholar 17 months ago, created an answer that has been accepted. For C: Microarray | RNA Seq | Methylation Arrays - Correlations?
Scholar 17 months ago, created an answer that has been accepted. For C: ANOVA TEST in R
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Great Question 19 months ago, created a question with more than 5,000 views. For Software For Hla Typing Using Ngs?
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Teacher 2.6 years ago, created an answer with at least 3 up-votes. For C: Microarray | RNA Seq | Methylation Arrays - Correlations?
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Teacher 2.6 years ago, created an answer with at least 3 up-votes. For C: Microarray | RNA Seq | Methylation Arrays - Correlations?

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