Moderator: mikhail.shugay

gravatar for mikhail.shugay
mikhail.shugay3.4k
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Location:
Czech Republic, Brno, CEITEC
Website:
https://github.com/mik...
Twitter:
@antigenomics
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Google Scholar Page
Last seen:
10 months, 1 week ago
Joined:
6 years, 7 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 • 365 results • page 1 of 37 • next >
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Comment: C: MAGERI: a software tool for calling rare variants and detecting circulating tumo
... Dear Alon, The fact is that MAGERI is loading all reads into memory for consensus assembly, so we've tested it on a 64GB RAM servers for HiSeq analysis. The answer basically depends on the structure of your dataset: the number of reads, the number of unique UMI tags and reads-per-UMI distribution ( ...
written 10 months ago by mikhail.shugay3.4k
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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 2.6 years ago by mikhail.shugay3.4k
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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 2.6 years ago by mikhail.shugay3.4k • updated 10 months ago by alons270
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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 2.8 years ago by mikhail.shugay3.4k
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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 2.9 years ago by mikhail.shugay3.4k
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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 2.9 years ago by mikhail.shugay3.4k
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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 3.1 years ago by mikhail.shugay3.4k
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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 3.1 years ago by mikhail.shugay3.4k
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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 3.1 years ago by mikhail.shugay3.4k
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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 3.1 years ago by mikhail.shugay3.4k

Latest awards to mikhail.shugay

Popular Question 24 months ago, created a question with more than 1,000 views. For Author affiliation and for-profit licensing of published software
Popular Question 24 months ago, created a question with more than 1,000 views. For Mitcr: A Software Tool For Analyzing T-Cell Receptor Sequencing Data
Epic Question 24 months ago, created a question with more than 10,000 views. For Software For Hla Typing Using Ngs?
Teacher 24 months ago, created an answer with at least 3 up-votes. For C: Microarray | RNA Seq | Methylation Arrays - Correlations?
Appreciated 24 months ago, created a post with more than 5 votes. For A: Why can't we downvote on this forum?
Popular Question 24 months ago, created a question with more than 1,000 views. For MIGEC: towards error-free profiling of immune repertoires
Popular Question 24 months ago, created a question with more than 1,000 views. For VDJtools: a software for post-analysis of immune repertoire sequencing data
Popular Question 24 months ago, created a question with more than 1,000 views. For RepSeq-2016 Workshop on Immune Repertoire Sequencing
Great Question 2.3 years ago, created a question with more than 5,000 views. For Mitcr: A Software Tool For Analyzing T-Cell Receptor Sequencing Data
Prophet 2.5 years ago, created a post with more than 20 followers. For Software For Hla Typing Using Ngs?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Functional Annotation Of Variant Calls (Vcf Files)
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For C: Microarray | RNA Seq | Methylation Arrays - Correlations?
Great Question 3.1 years ago, created a question with more than 5,000 views. For Software For Hla Typing Using Ngs?
Scholar 3.1 years ago, created an answer that has been accepted. For C: Microarray | RNA Seq | Methylation Arrays - Correlations?
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For C: Microarray | RNA Seq | Methylation Arrays - Correlations?
Scholar 3.1 years ago, created an answer that has been accepted. For C: Microarray | RNA Seq | Methylation Arrays - Correlations?
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For C: Microarray | RNA Seq | Methylation Arrays - Correlations?
Commentator 3.1 years ago, created a comment with at least 3 up-votes. For C: A new perspective needed for a newbie
Popular Question 3.1 years ago, created a question with more than 1,000 views. For MIGEC: towards error-free profiling of immune repertoires
Scholar 3.5 years ago, created an answer that has been accepted. For C: ANOVA TEST in R
Scholar 3.5 years ago, created an answer that has been accepted. For C: Microarray | RNA Seq | Methylation Arrays - Correlations?
Good Answer 3.5 years ago, created an answer that was upvoted at least 5 times. For C: Genomics is not Special. Computational Biologist are reinventing the wheel for b

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