microbiomics-package: Microbiomics

In tvatanen/microbiomics: Microbiomics

Description

Implementation of some functions that may come handy in analysing microbiome data.

Details

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

tvatanen/microbiomics documentation built on Sept. 27, 2019, 7:29 a.m.