User: António Miguel de Jesus Domingues
- Reputation:
- 470
- Status:
- Trusted
- Location:
- Germany
- Website:
- http://adomingues.gith...
- Last seen:
- 4 days, 18 hours ago
- Joined:
- 7 years, 8 months ago
- Email:
- a***********@gmail.com
Posts by António Miguel de Jesus Domingues
<prev
• 65 results •
page 1 of 7 •
next >
0
votes
1
answer
110
views
1
answers
... 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 Domingues • 470
0
votes
1
answer
110
views
1
answers
... > 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 Domingues • 470
3
votes
1
answer
110
views
1
answer
... 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:
(not s ...
written 12 weeks ago by
António Miguel de Jesus Domingues • 470
• updated
12 weeks ago by
Leonardo Collado Torres • 710
3
votes
2
answers
177
views
2
answers
... 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 ...
written 4 months ago by
António Miguel de Jesus Domingues • 470
• updated
4 months ago by
arne.smits • 60
0
votes
1
answer
229
views
1
answers
... 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 Domingues • 470
0
votes
1
answer
229
views
1
answers
... 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 Domingues • 470
1
vote
2
answers
343
views
2
answers
... See my answer here: https://www.biostars.org/p/351612/#352575
...
written 12 months ago by
António Miguel de Jesus Domingues • 470
0
votes
1
answer
229
views
1
answer
... 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 ...
written 12 months ago by
António Miguel de Jesus Domingues • 470
2
votes
2
answers
343
views
2
answers
... 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 Domingues • 470
0
votes
1
answer
306
views
1
answers
... 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 Domingues • 470
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
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 16.09
Traffic: 174 users visited in the last hour