User: A. Domingues

gravatar for A. Domingues
A. Domingues2.2k
Reputation:
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Location:
Dresden, Germany
Website:
http://adomingues.gith...
Twitter:
keyboardpipette
Last seen:
11 hours ago
Joined:
7 years, 6 months ago
Email:
a***********@gmail.com

Biologist doing research in gene expression regulation with a background in neurobiology and entering the world of bioinformatics.

Posts by A. Domingues

<prev • 235 results • page 1 of 24 • next >
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Answer: A: name of the figure
... It looks like a fancy Sankey or alluvial diagram. This would be a more typical example: ![alluvial][1] And there is another in here: https://bioconductor.org/packages/release/bioc/vignettes/Director/inst/doc/vignette.pdf [1]: http://%20https://www.researchgate.net/publication/329372747/figure/fi ...
written 6 weeks ago by A. Domingues2.2k
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Comment: C: Compare expression (coverage) of a set of genomic regions vs background
... You are right. However, in my particular case, I am not looking at genes, but rather piRNA expression. These very peculiar small RNAs are not expressed in defined units like genes are (except in some species where the primary piRNAs are indeed produced from expression units). I will also test for ov ...
written 10 weeks ago by A. Domingues2.2k
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Compare expression (coverage) of a set of genomic regions vs background
... I have a set of large genomic regions (~200, ~50-500kb) for which we hypothesize that there is higher RNA expression than expected by chance. The expression pertains to small RNAs, but let's make it broader and just think about RNA-seq coverage. An similar experiment would be if one had a set of ChI ...
expression coverage rna-seq written 10 weeks ago by A. Domingues2.2k
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Answer: A: How to extract upstream and downstream sequence of a set of genes using python
... Edit: this answer presumes you will want to do this in `python` as suggested by the tags. `pybedtools`, which is a python implementation of `bedtools` should do the trick. You will need a combination of: 1. `flank` to get the up and downstram location in relation to the inut coordinates, https://d ...
written 11 weeks ago by A. Domingues2.2k
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Comment: C: How to use RIPSeeker?
... No modification at all, I simply did a IP / input comparison and it worked well - at least that is what my colleagues which did the experimental validation told me. ...
written 3 months ago by A. Domingues2.2k
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Comment: C: How to use RIPSeeker?
... Not an answer but unless you really need to use RIPseeker, I would advise to look for alternatives. As far as I can tell development as been stagnating fro a long time now, with the last commit in github being 2 years ago, and pull requests and issues going unanswered from around that time. I also r ...
written 3 months ago by A. Domingues2.2k
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Comment: C: Expression of transposons in transcriptomes
... No idea. I suggest asking the developers in github. They have been quite responsive whenever I had similar questions. ...
written 6 months ago by A. Domingues2.2k
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Answer: A: Expression of transposons in transcriptomes
... I have used [SalmonTE](https://github.com/LiuzLab/SalmonTE) in the past and had good experiences. It uses `salmon` the background but then aggregates the counts per element, family and class. The results tables are also ready to use with `DESeq2` ...
written 6 months ago by A. Domingues2.2k
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Comment: C: Middle author, but not first author projects. How would you approach this?
... This. It's a huge change in contractual terms. Had it been suggested to me I would have flat out refused it. If insisted upon I would start applying to other positions. ...
written 9 months ago by A. Domingues2.2k
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Comment: C: Middle author, but not first author projects. How would you approach this?
... > I was considering a staff scientist career, but I wouldn’t like to do it with postdoctoral contracts. And rightly so. Since your background is mathematics, you might need to be on a postdoctoral contract for a period of time to show that you can hack it in a biology setting (communication can ...
written 9 months ago by A. Domingues2.2k

Latest awards to A. Domingues

Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Popular Question 5 months ago, created a question with more than 1,000 views. For Project organization: make code public and keep notes private
Popular Question 7 months ago, created a question with more than 1,000 views. For Project organization: make code public and keep notes private
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Appreciated 9 months ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: MutSigCV output and coMut plots
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: MutSigCV output and coMut plots
Scholar 13 months ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Appreciated 14 months ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Scholar 14 months ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Great Question 14 months ago, created a question with more than 5,000 views. For Issue with naming convention in bedtools
Popular Question 15 months ago, created a question with more than 1,000 views. For rRNA quantification: which is the best way?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Great Question 16 months ago, created a question with more than 5,000 views. For problems with MAF for MutSigCV (vcf2maf)
Great Question 16 months ago, created a question with more than 5,000 views. For Heatmap Of Read Coverage Around Tsss
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For A: MutSigCV output and coMut plots
Popular Question 20 months ago, created a question with more than 1,000 views. For rRNA quantification: which is the best way?
Popular Question 21 months ago, created a question with more than 1,000 views. For How to identify consecutive (adjacent) genomic intervals
Popular Question 22 months ago, created a question with more than 1,000 views. For How to identify consecutive (adjacent) genomic intervals
Student 23 months ago, asked a question with at least 3 up-votes. For Issue with naming convention in bedtools

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