User: António Miguel de Jesus Domingues

Reputation:
390
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Trusted
Location:
Germany
Website:
http://adomingues.gith...
Last seen:
1 day, 14 hours ago
Joined:
6 years, 7 months ago
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Posts by António Miguel de Jesus Domingues

<prev • 55 results • page 1 of 6 • next >
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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 25 days ago by António Miguel de Jesus Domingues390 • updated 24 days ago by Martin Morgan ♦♦ 22k
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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 10 months ago by António Miguel de Jesus Domingues390
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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 10 months ago by António Miguel de Jesus Domingues390
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Comment: C: biomaRt: drerio_gene_ensembl dataset missing
... Good tip. In my case it was a little lazy because I am also using the script to run some C. elegans data analysis and this will work for both - RIPSeeker needs biomaRt/ensembl so I need an archive version before the move to Wormbase. Another hack. ...
written 10 months ago by António Miguel de Jesus Domingues390
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Comment: C: biomaRt: drerio_gene_ensembl dataset missing
... @moderators: I could not format the post properly due to an error: Language "fr" is not one of the supported languages ['en']! Post was copy-pasted from a markdown document generated via knitr, so no idea.   ...
written 10 months ago by António Miguel de Jesus Domingues390
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biomaRt: drerio_gene_ensembl dataset missing
... Whilst running a `RIPSeeper` analysis, I noticed that the dataset `drerio_gene_ensembl` which used to be available via `biomaRt` is not longer listed or accessible. To test this I first upgraded my `bioC` to make sure I am working with the latest version of `biomaRt` (2.34.0). ```r biocLite("BiocU ...
biomart ripseeker ensembl written 10 months ago by António Miguel de Jesus Domingues390 • updated 10 months ago by Mike Smith3.0k
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Comment: C: derfinder: how to merge regions and counts from individual chromosomes
... It worked, thanks! I wonder if this could be something to add to the vignette? In any case, it is now here for those struggling with the same issue. ...
written 10 months ago by António Miguel de Jesus Domingues390
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derfinder: how to merge regions and counts from individual chromosomes
... tldr: using derfinder for individual chromosomes works, but merging them using do.call(c) or do.call(rbind) leads to errors. How to perform DRE with all chromosomes? I have been following the tutorials for derfinder running the analysis for an individual chromosome: fullCov <- fullCoverage(fil ...
derfinder recount written 10 months ago by António Miguel de Jesus Domingues390 • updated 10 months ago by Leonardo Collado Torres610
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derfinder mean Expressed Region cutoff
... I am running derfinder to ultimately find DER in a time course but despite the very good documentation I have some doubts about how set the cutoff to find expressed regions. In the 2017 NAR paper, it is stated that an average across all regions and samples is used as a cut-off (Finding ERs): Here, ...
derfinder written 11 months ago by António Miguel de Jesus Domingues390 • updated 11 months ago by Leonardo Collado Torres610
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Comment: C: DESeq2 design formula: single control for multiple conditions [RIP-seq]
... > You can see from re-arrangement of terms that your desired ratio is mathematically equal to RFK679 / Tyr101 *faceslap* Of course. way simpler than I thought. I probably missed those other posts because I was looking specifically at RIP-seq (and ChIP-seq) posts. It turns out I was over-thinkin ...
written 12 months ago by António Miguel de Jesus Domingues390

Latest awards to António Miguel de Jesus Domingues

Popular Question 17 months ago, created a question with more than 1,000 views. For ChIPseeker: Error in annotatePeak
Supporter 17 months ago, voted at least 25 times.
Popular Question 17 months ago, created a question with more than 1,000 views. For problems generating a gene2GOlist in topGO
Popular Question 21 months ago, created a question with more than 1,000 views. For Gviz - show plus and minus strand from a bam
Appreciated 2.6 years ago, created a post with more than 5 votes. For A: Plot ggplot2 and ggbio Images Together
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Extend GRanges start/end
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Plot ggplot2 and ggbio Images Together
Scholar 3.4 years ago, created an answer that has been accepted. For A: Plot ggplot2 and ggbio Images Together

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