User: Lluís R

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

I am the author and maintainer of the BioCor package

Posts by Lluís R

<prev • 174 results • page 1 of 18 • next >
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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 3 days 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 6 days 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 17 days ago by Lluís R310
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Comment: C: Error topGO printGenes
... you don't pass a function to geneSel, do you? Could you paste the output of `print(GOdata)`? ...
written 18 days ago by Lluís R310
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Comment: C: Error topGO printGenes
... Could you provide how did you create your GOdata? This way the example is reproducible and I can check how to solve it. Thanks ...
written 19 days ago by Lluís R310
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Comment: C: What is the impact of using GOSeq to voom-adjusted RNA-seq Expressions ?
... Is cqn normalization method not desirable (it takes into account gene length and GC content) then? Thanks ...
written 25 days ago by Lluís R310
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Comment: C: custom background list for ReactomePA
... That means that you are filtering by size of the gene sets and that they are smaller than 10 genes. Without knowing the specific format I can't provide advice. Could you ask a new question with the file (or part of it) describing the format and what have you tried to import it? ...
written 6 weeks ago by Lluís R310
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Comment: C: custom background list for ReactomePA
... The universe is the genes of the background so you can pass a vector like c("G1", "G2", "G3", ...) enrichPathway will use it. ...
written 6 weeks ago by Lluís R310
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Comment: C: How to create the colData for a complex experiment
... Hi Levi, I didn't explain myself well, sorry.  I have some samples linked to a location (biopsies from 5 regions) and some that aren't (stools) [or that they are are always from the same region]. I have two essays for the biopsies (RNA-seq and 16S-seq) and one assay for the stools (16S-seq). My ma ...
written 11 weeks ago by Lluís R310
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How to create the colData for a complex experiment
... I have a dataset where for the same patient and time we have extracted different samples from different locations. What would be the best way to encode this in MAE? Patient Time Region State of the region A 0 A Healthy   A 0 B Injured ...
multiassayexperiment coldata written 11 weeks ago by Lluís R310 • updated 11 weeks ago by Levi Waldron390

Latest awards to Lluís R

Scholar 8 months ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?
Teacher 8 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 9 months ago, voted more than 100 times.
Centurion 11 months ago, created 100 posts.
Scholar 3.1 years ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?
Supporter 3.1 years ago, voted at least 25 times.

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