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:
9 hours ago
Joined:
7 years, 10 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 • 238 results • page 1 of 24 • next >
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Answer: A: Correlation Plot for bed files
... I think `intervene` might do the job. Look for the options in the module `intervene` pairwise: https://intervene.readthedocs.io/en/latest/examples.html#pairwise-module-examples > Intervene provides an easy and automated interface for effective > intersection and visualization of genomic regio ...
written 9 hours ago by A. Domingues2.2k
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Comment: C: Detecting expression in intergenic regions
... Will do. It took a while to get the problem sorted tbh. In those two years there was a lot more sequencing done, a number of other approaches tested, and even derfinder took a while to get to grips with. Not to mention all the other pesky parallel projects getting in the way :) ...
written 10 weeks ago by A. Domingues2.2k
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Answer: A: Detecting expression in intergenic regions
... To answer my own question, I ended using two complementary approaches: 1. was to simply count total intergenic reads per condition and compare those (normalizing to mapped reads). The picture as pretty obvious with some conditions showing a lot more intergenic expression than others. 2. I also us ...
written 10 weeks ago by A. Domingues2.2k
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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 5 months 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 6 months 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 6 months 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 6 months 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 7 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 8 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 10 months ago by A. Domingues2.2k

Latest awards to A. Domingues

Teacher 16 days ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Epic Question 27 days ago, created a question with more than 10,000 views. For Heatmap Of Read Coverage Around Tsss
Scholar 10 weeks ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Student 11 weeks ago, asked a question with at least 3 up-votes. For Issue with naming convention in bedtools
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Popular Question 9 months ago, created a question with more than 1,000 views. For Project organization: make code public and keep notes private
Popular Question 11 months ago, created a question with more than 1,000 views. For Project organization: make code public and keep notes private
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Appreciated 13 months ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: MutSigCV output and coMut plots
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: MutSigCV output and coMut plots
Scholar 17 months ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Appreciated 18 months ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Scholar 18 months ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Great Question 19 months ago, created a question with more than 5,000 views. For Issue with naming convention in bedtools
Popular Question 20 months ago, created a question with more than 1,000 views. For rRNA quantification: which is the best way?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Great Question 20 months ago, created a question with more than 5,000 views. For problems with MAF for MutSigCV (vcf2maf)
Great Question 20 months ago, created a question with more than 5,000 views. For Heatmap Of Read Coverage Around Tsss
Good Answer 21 months ago, created an answer that was upvoted at least 5 times. For A: MutSigCV output and coMut plots

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