User: António Miguel de Jesus Domingues

Reputation:
460
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Germany
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http://adomingues.gith...
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2 hours ago
Joined:
7 years, 5 months ago
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Posts by António Miguel de Jesus Domingues

<prev • 62 results • page 1 of 7 • next >
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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 weeks ago by António Miguel de Jesus Domingues460 • updated 19 days 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 8 months ago by António Miguel de Jesus Domingues460
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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 8 months ago by António Miguel de Jesus Domingues460
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Comment: C: Normalization for small non-coding RNA
... See my answer here: https://www.biostars.org/p/351612/#352575 ...
written 8 months ago by António Miguel de Jesus Domingues460
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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 8 months ago by António Miguel de Jesus Domingues460
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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 8 months ago by António Miguel de Jesus Domingues460
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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 9 months ago by António Miguel de Jesus Domingues460
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Speed and memory of custom function using scanBam
... Dear BioC team, I am trying to leverage the power of Rsamtools to summarize reads in a number of ways. For instance, read length (seq) of reads mapping to certain genes. Here is simplified version of one my functions: library("Rsamtools") get_seq_lengths <- function(bamPath, coordinates = NULL){ ...
rsamtools bam scanbamparam written 10 months ago by António Miguel de Jesus Domingues460 • updated 10 months ago by Martin Morgan ♦♦ 23k
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ExpressionAtlas: download RPKM/TPM
... I downloaded data for an RNA-seq experiment using the ExpressionAtlas package - very very straightforward by the way. Sadly the data contains only the  raw counts from said experiment, whereas my expectation was that one would also get access to the pre-calculated RPKM/TPM since these are available ...
embl tpm expressionatlas written 20 months ago by António Miguel de Jesus Domingues460
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Comment: C: biomaRt: drerio_gene_ensembl dataset missing
... > library(biomaRt) > packageVersion("biomaRt") [1] ‘2.35.2’ ## [1] 97 3 ## [1] "Is drerio present? TRUE" All systems are go :) Thank you for the fix. ...
written 20 months ago by António Miguel de Jesus Domingues460

Latest awards to António Miguel de Jesus Domingues

Popular Question 18 days ago, created a question with more than 1,000 views. For ChIPseeker: Error in annotatePeak
Popular Question 7 months ago, created a question with more than 1,000 views. For Gviz - show plus and minus strand from a bam
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Plot ggplot2 and ggbio Images Together
Popular Question 7 months ago, created a question with more than 1,000 views. For ChIPseeker: Error in annotatePeak
Popular Question 2.3 years ago, created a question with more than 1,000 views. For problems generating a gene2GOlist in topGO
Popular Question 2.3 years ago, created a question with more than 1,000 views. For ChIPseeker: Error in annotatePeak
Supporter 2.3 years ago, voted at least 25 times.
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Gviz - show plus and minus strand from a bam
Appreciated 3.4 years ago, created a post with more than 5 votes. For A: Plot ggplot2 and ggbio Images Together
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Extend GRanges start/end
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Plot ggplot2 and ggbio Images Together
Scholar 4.2 years ago, created an answer that has been accepted. For A: Plot ggplot2 and ggbio Images Together

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