Questions tagged [microbiome]
A microbiome is the community of microorganisms that usually coexist in any given habitat.
12 questions
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Interpretation of MVABUND results
I ran multivariate analysis using the mvabund package on R to see which factors were significant in influencing gut microbiota. When I was running it for just the factor "Line", my results ...
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How can I as a programmer help microbiome research through my programming skills without any specific biology know-how?
I am a chronically ill patient and currently reading 10% human by Alanna Collen. Over the past years, I have become more and more interested in the human microbiome. I am a skilled programmer, but don'...
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I want to know what are the main differences between two R Objects constructed for analysis of microbiome data: phyloseq and TreeSummarizedExperiment
I am looking for main differences between two R Objects constructed for analysis of microbiome data: phyloseq object and TreeSummarizedExperiment object
First, I will provide a little information ...
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Model optimization causes overfitting
I'm working on an ML model to predict colorectal cancer using data from the human microbiome (collected from fecal samples).
My dataset is made up of metadata (containing phenotypic information on the ...
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Feature-selection microbiome data to build a model to predict cancer
I want to build a machine learning model to predict colorectal cancer based on 16S rRNA microbiome data (stool samples).
I have filtered the data using filtering approach by Duvallet(removing samples ...
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Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome
Cross-posted on biostars: https://www.biostars.org/p/9572744/
I am trying to understand better what number to be used and how to put it in the function MRcoefs within the Metagenomeseq package in R ...
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Can files with different R1 and R2 lengths be trusted?
I received paired end amplicon sequence from a LAB with different lengths for R1 (320) and R2(280). Should I trust this lab to sequence other samples?
Also, I had to do a trimming over the R2 at 220(...
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WCGNA - Relate modules with Y features when the % of variance explained of each eigengen is low
I'm doing a WCGNA analysis (signed network) on microbiome 16S data.
I have transformed counts to centeres log-ratio transformed data (CLR) to address the compositional characteristics of the data and ...
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Simple template for calculating Shannon diversity index from FASTQ files with R
I have a bunch of files in FASTQ format and need to calculate the Shannon diversity index from all of them.
Is there a simple way to do that with R, some kind of step-by-step recipe?
My problem is not ...
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Co-occurrence networks in Metagenomics studies
I have recently acquired some 16S metagenomics data, and was wondering if anyone can speak of the potential limitations, challenges as well as advantages to conducting a network-based study on ...
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maxEE parameter from DADA2 package in R
I have just started the QC steps from the dada2 pipeline, and have failed to find a detailed explanation of what the maxEE argument entails.
I have surfed many forums, as well as the details given by ...
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How to plot a PCOA biplot with OTU loadings as arrows
I'm working on gut microbiota data. I want to perform a biplot showing my 2 enterotypes and the major OTU explaining the variance between my two enterotypes.
Something like : from https://doi.org/10....
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