User: rodrigo.duarte88

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Posts by rodrigo.duarte88

<prev • 13 results • page 1 of 2 • next >
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Answer: A: How to run the annotation tool for GARFIELD v2: garfield_annotate_uk10k.sh
... Just in case someone stumbles upon this in the future, too.... I had help from a colleague and created the required annotation for GARFIELD in R using the short script below: library(data.table) dbsnp<-fread("eQTL_positions.bed", skip = 1) for(chr in 1:22){ tmp<- ...
written 4 months ago by rodrigo.duarte8820
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How to run the annotation tool for GARFIELD v2: garfield_annotate_uk10k.sh
... Hi all, I think I may have an impossible question here, but if by any chance any of you has used the EMBL-EBI tool 'Garfield' (https://www.ebi.ac.uk/birney-srv/GARFIELD/), could you please advise? Garfield is available as a bunch of shell scripts or as an R package, but I am having an issue specifi ...
unix shell garfield awk embl-ebi written 5 months ago by rodrigo.duarte8820
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Comment: C: [sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
... I had the same error, and removing low count genes from counts table (as suggested in sva tutorial, https://bioconductor.org/packages/release/bioc/vignettes/sva/inst/doc/sva.pdf) worked for me. ...
written 6 months ago by rodrigo.duarte8820
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Comment: C: Using PEER to identify hidden confounders in RNA-seq data (not working)
... Oops, sorry about that! To be fair, I think am going to try "sva", looks like there's more documentation for that one. Thanks, Martin! ...
written 6 months ago by rodrigo.duarte8820
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Comment: C: How to calculate overlap between transposable elements differentially expressed
... Fantastic! Thanks, Michael! Just one more quick question (for peace of mind): I am using the "~1" design to create this dds object to extract the normalised counts, since I have no groups, right? ...
written 6 months ago by rodrigo.duarte8820
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Using PEER to identify hidden confounders in RNA-seq data (not working)
... Hi all, I am trying to use PEER in R (on conda) to identify hidden confounders in the raw counts of my RNA-seq experiment. I am following their tutorial ( https://github.com/PMBio/peer/wiki/Tutorial ), but without much luck, and there's not much help available unfortunately. Anyone used this tool b ...
differential expression rna-seq peer hidden confounders written 6 months ago by rodrigo.duarte8820 • updated 6 months ago by Martin Morgan ♦♦ 23k
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Comment: C: Handling missing data, DESeq2
... Looks like you have 3 time points, but how many samples for each time point do you have? I think that as long as you have at least 3 samples per time point, you should be fine? ...
written 7 months ago by rodrigo.duarte8820
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How to calculate overlap between transposable elements differentially expressed in one experiment, with those expressed in another set of samples?
... Dear all, I've got a naive question for you, and I would really appreciate your thoughts. I found some transposable elements (TE) that were differentially expressed in a certain tissue, based on a case-control analysis of RNA-seq data using DESeq2, and a custom-made annotation for TEs. Now, **I w ...
deseq2 enrichment rna-seq gene expression written 7 months ago by rodrigo.duarte8820 • updated 7 months ago by Michael Love24k
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Comment: C: Subsetting a tximport object
... Many thanks, Michael! This is super useful, as usual! ...
written 7 months ago by rodrigo.duarte8820
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Comment: C: Subsetting a tximport object
... Hi [James][1], I was wondering if you know how I could remove samples from the tximport object which are contained in a list of outliers? Thanks! [1]: https://support.bioconductor.org/u/5106/ ...
written 7 months ago by rodrigo.duarte8820

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