User: António Miguel de Jesus Domingues

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470
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Germany
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http://adomingues.gith...
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Joined:
7 years, 8 months ago
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Posts by António Miguel de Jesus Domingues

<prev • 65 results • page 1 of 7 • next >
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Comment: C: Detection of large regions of expression
... Got it! For future reference, and in case someone else stumbles upon this, this is the final version of the commands I used: ```R fullCov <- fullCoverage( files = files, chrs = chrom, L = read_length, verbose = TRUE, totalMapped = total_mapped, targetSize = targetSize, filte ...
written 11 weeks ago by António Miguel de Jesus Domingues470
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Comment: C: Detection of large regions of expression
... > It seems that you are normalizing your data twice, no? That seems to have been the major issue. Once I remove filterring from the `fullCoverage` it all started to make sense. > The code you provided, is that the correct version? You should be getting an error when you run regionMatrix(fil ...
written 11 weeks ago by António Miguel de Jesus Domingues470
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Detection of large regions of expression
... I have been trying to leverage `definder`'s ability to detect expression without the need of an annotation to identify broad regions of expressions that we observe in certain conditions: ![](https://user-images.githubusercontent.com/2607577/64652309-d391c380-d423-11e9-91da-4b96d1c09626.png) (not s ...
derfinder intergenic expression written 12 weeks ago by António Miguel de Jesus Domingues470 • updated 12 weeks ago by Leonardo Collado Torres710
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Clarification of results tables in DEP
... I am starting to use the `DEP` [package][1] for analysis of differentially enriched proteins, and so far I am quite happy with it. The vignette is quite good and all the functions worked without issues. I am however confused about the meaning of the columns in the output results generated by `get_d ...
proteomics dep written 4 months ago by António Miguel de Jesus Domingues470 • updated 4 months ago by arne.smits60
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Comment: C: collapseReplicates changes order of factors
... I am also having problems replicating it so it is likely that at some I made a mistake. I will add a note at the top of the post. Apologies for the time lost but I was certain that something was going on.   ...
written 12 months ago by António Miguel de Jesus Domingues470
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Comment: C: collapseReplicates changes order of factors
... I actually tried to create a smaller example in the same way, and like you also failed. That is why I mention that this could be a localized issue. That said, I will try to replicate with a small subset of and get back to you.   ...
written 12 months ago by António Miguel de Jesus Domingues470
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Comment: C: Normalization for small non-coding RNA
... See my answer here: https://www.biostars.org/p/351612/#352575 ...
written 12 months ago by António Miguel de Jesus Domingues470
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collapseReplicates changes order of factors
... IGNORE this issue. It is likely that I did something wrong at some point since I am having problems reproducing the problem myself.   tldr: it seems that after `collapseReplicates` the levels of newly created factors are shifted affecting the results. **If** this observation is correct and not a d ...
deseq2 bug written 12 months ago by António Miguel de Jesus Domingues470
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Answer: A: Normalization for small non-coding RNA
... Hi konstatinos, The majority of reads multimap to different piRNAs, I took the sum of reads assigned to each piRNA (both unmatched/matched reads to the genome). Maybe I misunderstood, but does this mean that a read is counted more than once? Each read should be counted only once. If you want to u ...
written 12 months ago by António Miguel de Jesus Domingues470
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Comment: C: Speed and memory of custom function using scanBam
... Sorry for the belated reply, but working on other things got in the way. Thank your for the clarification regarding the separate call for each range - I had no idea it worked that way. For now I am sticking with  GenomicAlignments followed by GR. Memory might be an issue down the line, but having re ...
written 13 months ago by António Miguel de Jesus Domingues470

Latest awards to António Miguel de Jesus Domingues

Popular Question 4 months ago, created a question with more than 1,000 views. For ChIPseeker: Error in annotatePeak
Popular Question 11 months ago, created a question with more than 1,000 views. For Gviz - show plus and minus strand from a bam
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Plot ggplot2 and ggbio Images Together
Popular Question 11 months ago, created a question with more than 1,000 views. For ChIPseeker: Error in annotatePeak
Popular Question 2.6 years ago, created a question with more than 1,000 views. For problems generating a gene2GOlist in topGO
Popular Question 2.6 years ago, created a question with more than 1,000 views. For ChIPseeker: Error in annotatePeak
Supporter 2.6 years ago, voted at least 25 times.
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Gviz - show plus and minus strand from a bam
Appreciated 3.7 years ago, created a post with more than 5 votes. For A: Plot ggplot2 and ggbio Images Together
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Extend GRanges start/end
Teacher 4.4 years ago, created an answer with at least 3 up-votes. For A: Plot ggplot2 and ggbio Images Together
Scholar 4.5 years ago, created an answer that has been accepted. For A: Plot ggplot2 and ggbio Images Together

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