User: A. Domingues

gravatar for A. Domingues
A. Domingues1.5k
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Location:
Mainz, Germany
Website:
http://adomingues.gith...
Twitter:
keyboardpipette
Last seen:
13 hours ago
Joined:
5 years, 9 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 • 200 results • page 1 of 20 • next >
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Answer: A: maSigPro edesign and error message
... Hi had the **exact** same problem and eventually found the solution: When creating the `design` object it needs a variable column which is not `Time`. My guess is that `maSigPro` was designed with multi-factorial experiments in mind, as seen in the vignette, and expects another (mock) condition oth ...
written 11 weeks ago by A. Domingues1.5k
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Comment: C: maSigPro edesign and error message
... Hi Simon, did you eventually found a solution for this problem? I am running into the same issue and would appreciate some help. ...
written 11 weeks ago by A. Domingues1.5k
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Comment: C: Snakemake vs. Nextflow: strengths and weaknesses
... I think this table is little outdated in relation to `bpipe` - which I use daily. SLURM support exists (at least we are using it in-house), and I am pretty sure that stages in R can be run natively without wrapping in an Rscript. ...
written 4 months ago by A. Domingues1.5k
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Comment: C: Detecting expression in intergenic regions
... > Yes, that makes sense. It would be great to follow-up the work with a ChIP experiment in order to see if markers of active transcription overlap with your regions. ChIP-seq is very very difficult because we are dealing with small number of cells (~1000), sub-population of cells during early em ...
written 5 months ago by A. Domingues1.5k
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Comment: C: Detecting expression in intergenic regions
... It just might. A bit more evolved than what I had in mind, but could give out extra useful information. I look into it, cheers. ...
written 5 months ago by A. Domingues1.5k
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Comment: C: Detecting expression in intergenic regions
... Thank you for the insightful comments/suggestions Kevin. Most of the questions about functionality were already in my follow-up list (and then some) and the ones that aren't is because they are not relevant to our model (non-human or mammalian). We also have a pretty good biological hypothesis, in f ...
written 5 months ago by A. Domingues1.5k
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Detecting expression in intergenic regions
... **Background** We observed some RNA-seq coverage in regions without annotated genes - let's called them intergenic. This expression appears to be more pronounced, or unique, to a particular condition. **Goal** Find those genomic regions that have higher coverage than expected by random noise alon ...
bedtools genome rna-seq written 5 months ago by A. Domingues1.5k
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Comment: C: Filtering Fasta Sequences By Chromosomes Names From A Big Fasta File
... `$fasta` is a variable that represents the input fasta. It should be defined before the loop as `fasta=my_fancy.fasta` ...
written 9 months ago by A. Domingues1.5k
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Comment: C: small RNA-seq reads grouping by adjacency
... If I read the question correctly I think the OP is looking for something like piRNA clusters - regions enriched for certain types of smRNA. Slightlym different approach because the regions/clusters would have variable lengths, and most of the genome would be free of these. More like a aggregation op ...
written 11 months ago by A. Domingues1.5k
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Answer: A: small RNA-seq reads grouping by adjacency
... I suggests a combination of `bedtools` [merge][1] or [cluster][2], depending on what is the final goal. For instance, using `merge`: ``` ## code untested bamToBed -i my.bam \ # converts bam to bed. Ensures that read ID is kept which will be useful for counting | mergeBed -i stdin -c 4 -o count \ ...
written 11 months ago by A. Domingues1.5k

Latest awards to A. Domingues

Popular Question 4 weeks ago, created a question with more than 1,000 views. For How to identify consecutive (adjacent) genomic intervals
Student 11 weeks ago, asked a question with at least 3 up-votes. For Issue with naming convention in bedtools
Popular Question 11 weeks ago, created a question with more than 1,000 views. For How to identify consecutive (adjacent) genomic intervals
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Popular Question 10 months ago, created a question with more than 1,000 views. For How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Appreciated 11 months ago, created a post with more than 5 votes. For A: from txt to bed
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: MutSigCV output and coMut plots
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Appreciated 11 months ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Appreciated 12 months ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Scholar 13 months ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Appreciated 13 months ago, created a post with more than 5 votes. 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
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Appreciated 15 months ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Student 15 months ago, asked a question with at least 3 up-votes. For MutSigCV output and coMut plots
Popular Question 17 months ago, created a question with more than 1,000 views. For problems with MAF for MutSigCV (vcf2maf)
Guru 17 months ago, received more than 100 upvotes.
Popular Question 17 months ago, created a question with more than 1,000 views. For problems with MAF for MutSigCV (vcf2maf)
Popular Question 18 months ago, created a question with more than 1,000 views. For problems with MAF for MutSigCV (vcf2maf)
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data

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