User: A. Domingues

gravatar for A. Domingues
A. Domingues1.6k
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Location:
Mainz, Germany
Website:
http://adomingues.gith...
Twitter:
keyboardpipette
Last seen:
10 hours ago
Joined:
6 years, 3 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 • 202 results • page 1 of 21 • next >
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Comment: C: R code to plot heatmap/average line plots from Deeptools computeMatrix
... Apropos, the json parsing is very easy (not base `R`): ```R library("jsonlite") h <- scan(mat_file, n=1, sep="\n", what=character()) params <- fromJSON(txt=gsub("@", "", h)) ``` ...
written 5 weeks ago by A. Domingues1.6k
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Comment: C: R code to plot heatmap/average line plots from Deeptools computeMatrix
... Quick note: shouldn't `skip=2` be `skip=1`? As far as I can tell from my data, the second line contains the first genomic region and thus should be included. ...
written 5 weeks ago by A. Domingues1.6k
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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 8 months ago by A. Domingues1.6k
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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 8 months ago by A. Domingues1.6k
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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 I think this table is little outdated in relation to `bpipe` - which I use daily.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 10 months ago by A. Domingues1.6k
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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 11 months ago by A. Domingues1.6k
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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 11 months ago by A. Domingues1.6k
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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 11 months ago by A. Domingues1.6k
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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 11 months ago by A. Domingues1.6k
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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 15 months ago by A. Domingues1.6k

Latest awards to A. Domingues

Popular Question 12 days ago, created a question with more than 1,000 views. For rRNA quantification: which is the best way?
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Great Question 24 days ago, created a question with more than 5,000 views. For problems with MAF for MutSigCV (vcf2maf)
Great Question 27 days ago, created a question with more than 5,000 views. For Heatmap Of Read Coverage Around Tsss
Good Answer 8 weeks ago, created an answer that was upvoted at least 5 times. For A: MutSigCV output and coMut plots
Popular Question 4 months ago, created a question with more than 1,000 views. For rRNA quantification: which is the best way?
Popular Question 5 months ago, created a question with more than 1,000 views. For How to identify consecutive (adjacent) genomic intervals
Popular Question 6 months ago, created a question with more than 1,000 views. For How to identify consecutive (adjacent) genomic intervals
Student 8 months ago, asked a question with at least 3 up-votes. For Issue with naming convention in bedtools
Popular Question 8 months ago, created a question with more than 1,000 views. For How to identify consecutive (adjacent) genomic intervals
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Popular Question 15 months ago, created a question with more than 1,000 views. For How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Appreciated 17 months ago, created a post with more than 5 votes. For A: from txt to bed
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For A: MutSigCV output and coMut plots
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Appreciated 17 months ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Appreciated 17 months ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Commentator 18 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Commentator 18 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Appreciated 19 months ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Scholar 19 months ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Appreciated 21 months ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots

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