User: Lila M

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Lila M 820
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820
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UK
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8 months ago
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4 years, 11 months ago
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Posts by Lila M

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How to identify confunders covariates in metagenomic analysis
... Dear all, I'm working with metagenomic data (OTUs). I've alreade have the zero inflated matrix and an aditional matrix with more than 80 covariates. By using MaAsLin (https://github.com/biobakery/Maaslin2) I would like to identify the significant metagenomic species associated with clinical covarie ...
confunding maaslin metagenomic multivariate written 10 months ago by Lila M 820
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Comment: C: re sampling for unbalanced samples
... Is the third time that I got this answer. I explained why I want to do that. Please, add I comment if you could give any new feedback ...
written 11 months ago by Lila M 820
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Comment: A: re sampling for unbalanced samples
... Sorry, the "add comment" button doesn't work for me, it gives me an error all time, so this is why I used the "add comment". Lets say I have a data frame like this ID group gene1 gene2 gene3... s1 health 0.1 0.07 0.2 s2 cancer0.5 0.05 0.4 and I have 20 healthy samples and 40 cancer sa ...
written 11 months ago by Lila M 820
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Comment: A: re sampling for unbalanced samples
... Hi, I know how to do that in limma. The point is, that I want to create a function to apply it to a gene table, OTU table... in other words to extrapolate to different approach. Any clue? Thanks! ...
written 11 months ago by Lila M 820
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re sampling for unbalanced samples
... Dear all, I have a data set for two condition (before and after treatment). The patients are in rows and the gen expression in levels. I want to compare if there is any different in treatment, but the main problem that I have is the unbalanced samples (control 30:case 60). I would like to re-sampl ...
resamplig unbalanced samples written 11 months ago by Lila M 820
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best way to do a boxplot for abundnace matrix (microbiome data)
... I'm trying to find the best way to represent some microbiome data. First of all I've created a model using [ZIBR][1] so I can catch the abundance differences in my species regarding different condition. The "problem" that I have now is that I am trying to do a boxplot for different condition and as ...
boxplot microbiome zibr abundance written 13 months ago by Lila M 820
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Comment: C: How to analyze aCGH data in R?
... Hi Kevin, and thank you for your feed back. Yes I've checked it and found something related with `Agilent4x44K Arrays` however, this experiment is `CGH array (4X180K)` so I could not find something related with CGH arrays, any clue about how to start with it? Thanks! ...
written 13 months ago by Lila M 820
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How to analyze aCGH data in R?
... Dear all, I've tried to analyze this [data][1] that is a aCGH data in R. But I couldn't find any tutorial that can help me to import data and everything. Any idea? Thank you [1]: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36864 ...
acgh microarray written 13 months ago by Lila M 820
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How to sumarize longotudinal data by patients and plot it?
... Hi all, I'm trying to summarize some longitudinal data that looks like this: ID Time_point treatment 20 4 Treated 20 7 Treated 20 9 Treated 20 12 Treated 20 21 Treated 28 4 No Treated 28 7 No Treated ...
summary longitudinal data plot written 13 months ago by Lila M 820
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how to Dirichlet-multinomial mixture model over Bracken ssp abundance?
... Hi all, I'm trying to apply `Dirichlet-multinomial mixture model` over some `Bracken`(ayesian Reestimation of Abundance with KrakEN) specie abundance in two different condition: treated and not treated in two different data frames (rows as patient ID and cols as ssp). What I did first is to remove ...
microbiome bracken metagenomics dirichlet model written 14 months ago by Lila M 820

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Appreciated 11 months ago, created a post with more than 5 votes. For should I merge fastq files for different lanes before do QC?
Popular Question 11 months ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Popular Question 11 months ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Popular Question 13 months ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Popular Question 13 months ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: error while reading bigwig files in computeMatrix (deeptools)
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: error while reading bigwig files in computeMatrix (deeptools)
Popular Question 16 months ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Great Question 17 months ago, created a question with more than 5,000 views. For How to convert bedgraph to bigwig?
Popular Question 17 months ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Popular Question 17 months ago, created a question with more than 1,000 views. For problems with macs2 installation
Popular Question 17 months ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Popular Question 18 months ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Popular Question 18 months ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Popular Question 18 months ago, created a question with more than 1,000 views. For How to convert bedgraph to bigwig?
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Popular Question 19 months ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Popular Question 19 months ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Popular Question 19 months ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Popular Question 19 months ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Popular Question 19 months ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Student 19 months ago, asked a question with at least 3 up-votes. For should I merge fastq files for different lanes before do QC?
Popular Question 19 months ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Popular Question 20 months ago, created a question with more than 1,000 views. For how to create a minimun spanning tree with R
Great Question 22 months ago, created a question with more than 5,000 views. For How to convert bedgraph to bigwig?

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