User: Lluís R

gravatar for Lluís R
Lluís R310
Reputation:
310
Status:
Trusted
Location:
European Union
Last seen:
1 day, 4 hours ago
Joined:
3 years, 3 months ago
Email:
l************@gmail.com

I am the author and maintainer of the BioCor package

Posts by Lluís R

<prev • 181 results • page 1 of 19 • next >
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Comment: C: how to run GO enrichment analysis for non-model organisms (errors when using hyp
... are your genes in mygsc in the same fashion as in genes? How do you  map from your ids of genes to gene ontology terms ? ...
written 9 days ago by Lluís R310
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Comment: C: How to compare RNA-seq counts matrices from different aligners ?
... Are they in the same id name? Are they for the same sample? Then you can do a PCA for each matrix, and compare the results. Are the same samples near the same other samples? ...
written 4 weeks ago by Lluís R310
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Comment: C: Problems with the correct installation of GOseq
... The first error says: "installation path not writeable, unable to update package", you seem to need to update the packages to installl GOseq. Which version of R and Bioconductor are you using? Are they up to date? ...
written 6 weeks ago by Lluís R310
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Comment: C: Using topGO for GO Enrichment on methylation markers (Illumina 450k)
... Consider editing your original question with this new information and deleting this question. As it seems that the question is already answer that way. ...
written 7 weeks ago by Lluís R310
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Answer: A: choose between normalization techniques for OTU counts
... You should have a look to the metagenomeSeq package where there is a normalization procedure for this kind of data. There are a couple of papers worth mentioning: "Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible": About subsampling to the number of reads in 16S sequencing "Propor ...
written 7 weeks ago by Lluís R310
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Comment: C: how to get the last version of tximport
... Which version of R and Bioconductor are you running? You seem to be using the Bioconductor version 3.4 ...
written 8 weeks ago by Lluís R310
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Comment: C: topGO error : could not find function "annotationFun"
... Could you post your session info? Did you look at the manual page from page 8 and on? ...
written 8 weeks ago by Lluís R310
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Answer: A: Gene Set Enrichment based on gene presence/absence
... If I understood you correctly you want to compare if your organism has more genes or less in the same KO terms. You could use BioCor package using mpathSim to compare if between the same KO terms despite having different genes are still similar between them. It is not the same as you requested, but ...
written 9 weeks ago by Lluís R310
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Comment: C: GOenrichmentAnalysis of WGCNA mocules in Zea mays
... This package doesn't seem to exists. See this for creating it yourself. ...
written 9 weeks ago by Lluís R310
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Comment: C: Unannotated genes in TopGO
... How do you create the GOdata for topGO? As you show it seems like a list, but it is usually done from an annotation package. Have you checked it with the vignette? ...
written 10 weeks ago by Lluís R310

Latest awards to Lluís R

Scholar 10 months ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Does anyone need to install an R package which is used by another package as imp
Voter 11 months ago, voted more than 100 times.
Centurion 13 months ago, created 100 posts.
Scholar 3.3 years ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?
Supporter 3.3 years ago, voted at least 25 times.

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