Questions tagged [microbiome]

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Combine different FASTQ belonging to different hypervariable 16s regions

I'm really newbie in 16s microbiome analyses, so sorry for this question. I would like to perform a meta-analysis using only Illumina Amplicons sequences from different studies that have different ...
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25 views

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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co-occurrence analysis and visualization for amplicon microbial data

I am trying to learn co-occurrence analysis for microbial data. I got relative abundance at the genera level for 50 genera in 19 samples. I understand that for network analysis first I need to do ...