Implementation of some functions that may come handy in analysing microbiome data.
The microbiomics package is developed at GitHub (https://github.com/tvatanen/microbiomics/).
Following functions are included:
read_metaphlan_table
read a MetaPhlAn 2.0 output file as an R data frame
jaccard
compute Jaccard distance/index between given microbial profiles
read_taxon_table
read a summarize_taxa.py output file as an R data frame
pairwise_spearman
compute pairwise correlations between columns of two data sets
get_significant_values
get significant components among a matrix of measurements
Maaslin.wrapper
run MaAsLin (https://bitbucket.org/biobakery/maaslin/) given a set of taxa and metadata
Maaslin2.wrapper
run MaAsLin2 (https://bitbucket.org/biobakery/maaslin2/) given a set of taxa and metadata
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