User: A. Domingues

gravatar for A. Domingues
A. Domingues2.3k
Reputation:
2,310
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Location:
Dresden, Germany
Website:
http://adomingues.gith...
Twitter:
keyboardpipette
Last seen:
1 day, 17 hours ago
Joined:
8 years, 2 months ago
Email:
a***********@gmail.com

I analyse -omics data and try to make sense of it. I used to work at the bench, but it has been long enough that I can consider myself a bioinformatician now.

Posts by A. Domingues

<prev • 245 results • page 1 of 25 • next >
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Comment: C: zScore conversion: zFPKM vs scale function
... I meant exactly what Kevin Blighe said: "zFPKM was initially developed to determine expressed | not expressed". The experimentally validated bit was referring to the original zFPKM publication in which they used chromatin state data to find a threshold for expressed | not expressed. I have no exper ...
written 7 weeks ago by A. Domingues2.3k
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Comment: C: zScore conversion: zFPKM vs scale function
... You can see how it was done in this paper and other from the same lab (Huttner): https://elifesciences.org/articles/32332 ...
written 7 weeks ago by A. Domingues2.3k
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Comment: C: zScore conversion: zFPKM vs scale function
... Since you are interested in differences in response to treatment, could you not use logFC (treatment / control) instead of FPKMs? That way the expression is normalized within dataset. ...
written 7 weeks ago by A. Domingues2.3k
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Comment: C: zScore conversion: zFPKM vs scale function
... I see that Kevin was quicker and has a more comprehensive answer :) ...
written 7 weeks ago by A. Domingues2.3k
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Answer: A: zScore conversion: zFPKM vs scale function
... As someone who briefly used the zFKPM package in the past, it's goal is not to do the sort of centering/scaling one usually does before a PCA. The goal is to generate a score to select expressed genes using a somewhat experimentally validated prior. If all you want to do is sample clustering (PCA) b ...
written 7 weeks ago by A. Domingues2.3k
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Comment: C: Bioinformatics Data Analyst
... Sorry for the late reply - thought I'd answered but somehow failed to press send. It is valid for anyone who could legally work in Germany. As far as I know this includes non-german German/EU residents. But you can send and email to bioinfojob@scionics.com and ask directly - we are relatively infor ...
written 10 weeks ago by A. Domingues2.3k
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Job: Bioinformatics Data Analyst
... ## Bioinformatics Data Analyst ### Job Description Scionics Computer Innovation seeks to recruit a highly motivated individual who will be integrated into an existing team dedicated to scientific computing and bioinformatics data analysis. This team provides services within an academic research in ...
R python job blast rna-seq written 3 months ago by A. Domingues2.3k
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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 3 months ago by A. Domingues2.3k
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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 6 months ago by A. Domingues2.3k
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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 6 months ago by A. Domingues2.3k

Latest awards to A. Domingues

Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Scholar 3 months ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Epic Question 4 months ago, created a question with more than 10,000 views. For Heatmap Of Read Coverage Around Tsss
Scholar 6 months ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Student 6 months ago, asked a question with at least 3 up-votes. For Issue with naming convention in bedtools
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Popular Question 13 months ago, created a question with more than 1,000 views. For Project organization: make code public and keep notes private
Popular Question 14 months ago, created a question with more than 1,000 views. For Project organization: make code public and keep notes private
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For A: MutSigCV output and coMut plots
Appreciated 17 months ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: MutSigCV output and coMut plots
Scholar 21 months ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Appreciated 22 months ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Scholar 22 months ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Great Question 22 months ago, created a question with more than 5,000 views. For Issue with naming convention in bedtools
Popular Question 23 months ago, created a question with more than 1,000 views. For rRNA quantification: which is the best way?
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data

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