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User: A. Domingues

gravatar for A. Domingues
A. Domingues • 2.4k
Reputation:
2,440
Status:
Trusted
Location:
Dresden, Germany
Website:
http://adomingues.gith...
Twitter:
keyboardpipette
Last seen:
16 hours ago
Joined:
8 years, 8 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 • 280 results • page 1 of 28 • next >
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Comment: C: Annotating reads with the name of the feature to which they map
... No problem. If you think this solves the original question, please accept my answer or up-vote the relevant messages :) ...
written 16 hours ago by A. Domingues • 2.4k
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Comment: C: Annotating reads with the name of the feature to which they map
... I am not familiar with mpileup, but you could possible do (i) convert mpileup to bed, (ii) intersect with genomic features, (iii) use cut to removed the superfluous columns. This should give the results you are hoping for. ...
written 1 day ago by A. Domingues • 2.4k
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Answer: A: Annotating reads with the name of the feature to which they map
... If I understood teh goal correctly, I have use two different strategies in the past: **bedtools interesect** `bamToBed -i sample.bam | bedtools intersect -a - -b features.bed -s -wa -wb -bed -f 1.0 > $output1` You can play with the flags to make the intersections, unstranded/same/opposite stra ...
written 3 days ago by A. Domingues • 2.4k
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Comment: C: NGS Data storage solutions for small organisations or big labs
... That was pretty much my low-tech solution, but I was just wondering of there was better way of going about it. (Meta)Data retrieved from SRA/GEO can also go into lims. Thank you. ...
written 6 days ago by A. Domingues • 2.4k
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Comment: C: NGS Data storage solutions for small organisations or big labs
... Good points. We are using cloud storage (AWS), and we would have some support for setting this up, either internal expertise or contractors (I work for a private company). The basic policy is that the data is for internal usage only. At the moment we only have a couple of sequencing experiments, a c ...
written 9 days ago by A. Domingues • 2.4k
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Comment: C: NGS Data storage solutions for small organisations or big labs
... I am also interested in this subject, but on a different angle: how are you keeping track of the raw data + metadata? Custom DB with path to cloud location? iRODS? ELN? We don't actually generate the data, but rather get it from CROs or public repositories. Cheers. ...
written 10 days ago by A. Domingues • 2.4k
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Job: Scientist/Senior Scientist, Statistical Geneticist
... Dewpoint therapeutics is hiring computational biologists (senior scientist and group leader) and a statistical geneticist for their Boston office. Dewpoint Therapeutics is the first company founded to apply the emerging discipline of biomolecular condensates to drug discovery. Dewpoint believes tha ...
ngs genetics job statistics written 7 weeks ago by A. Domingues • 2.4k • updated 7 weeks ago by rpolicastro ♦ 4.0k
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Job: Group Leader/Assoc. Director, Computational Biology
... Dewpoint therapeutics is hiring computational biologists (senior scientist and group leader) and a statistical geneticist for their Boston office. Dewpoint Therapeutics is the first company founded to apply the emerging discipline of biomolecular condensates to drug discovery. Dewpoint believes tha ...
bioinformatics ngs genetics job computacional biology written 7 weeks ago by A. Domingues • 2.4k
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Job: Senior computational biologist
... Dewpoint therapeutics is hiring computational biologists (senior scientist and group leader) and a statistical geneticist for their Boston office. Dewpoint Therapeutics is the first company founded to apply the emerging discipline of biomolecular condensates to drug discovery. Dewpoint believes tha ...
ngs genetics job computacional biology statistics written 7 weeks ago by A. Domingues • 2.4k
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Comment: C: How to construct an anova to test diferences bewteen conditions taking into acco
... > "are the ratios of genes for one strand usually higher/lower in the control samples vs the treatment samples" That is pretty much want I want to know :) And still don't think `limma` is the solution here because I will get a result per gene, not to the question above (unless I missing somethin ...
written 12 weeks ago by A. Domingues • 2.4k

Latest awards to A. Domingues

Scholar 12 weeks ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Scholar 12 weeks ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Scholar 3 months ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Scholar 4 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
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Scholar 9 months ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Epic Question 10 months ago, created a question with more than 10,000 views. For Heatmap Of Read Coverage Around Tsss
Scholar 11 months ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Student 11 months ago, asked a question with at least 3 up-votes. For Issue with naming convention in bedtools
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Popular Question 18 months ago, created a question with more than 1,000 views. For Project organization: make code public and keep notes private
Popular Question 20 months ago, created a question with more than 1,000 views. For Project organization: make code public and keep notes private
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Commentator 23 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Commentator 23 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Appreciated 23 months ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Good Answer 23 months ago, created an answer that was upvoted at least 5 times. For A: MutSigCV output and coMut plots
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Good Answer 23 months ago, created an answer that was upvoted at least 5 times. For A: MutSigCV output and coMut plots
Scholar 2.2 years ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Appreciated 2.3 years ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
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