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In order to run the QIIME command:
```
differential_abundance.py
```
We needed to install these additional dependencies:
```
bioconductor-biomformat
r-biom
bioconductor-metagenomeSeq
r-…
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# Full name
Dr Antoine Bichat
# Link to GitHub repo
https://github.com/abichat/thesis
https://abichat.github.io/thesis/
# Template
https://github.com/abichat/hadamardown
# Complet…
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Hi,
The grouping column I specified for doing the differential abundance analysis consists of three groups. I've learned that by using DESeq2 directly I can change the parameters to use LRT and ind…
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Hello,
I have a problem when I want to run this command:
daa_results_df
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## Request
I would like to propose support for sample-/gene-dependent normalization factors to enable the use length offset matrices from [pytximport](https://pytximport.readthedocs.io/en/latest/st…
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Dear Chi,
I am having some trouble interpreting the LEfSe results from my dataset, and was wondering if there could be a calculation error when obtaining the LDA scores. The distribution of certai…
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If using any example data, we'd likely want to use a blood cancer dataset.
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Hello!
I'm trying to use aldex.glm() to explore differential abundance for a complex design involving both Genotype (B6 vs. TCR) and stress condition (Stress vs. NoStress). My code is as follows (d…
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DIMet is a bioinformatics pipeline for differential analysis of targeted isotope-labelled data.
DIMet supports the analysis of full metabolite abundances and isotopologue contributions, and allows …
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Dear all,
I did use the package for differential abundance test and to determine the indicator taxa using LEfSe method. I created LDA barplot and abundance plot. I noticed that in some cases one o…