Hadza

<p>Subset of two bins (and the associated contigs and genes)
generated by running SqueezeMeta on two gut metagenomic samples
obtained from two hunter-gatherers of the Hadza ethnic group.</p>

datasets

'SqueezeMeta' is a versatile pipeline for the automated analysis of metagenomics/metatranscriptomics data (<https://github.com/jtamames/SqueezeMeta>). This package provides functions loading 'SqueezeMeta' results into R, filtering them based on different criteria, and visualizing the results using basic plots. The 'SqueezeMeta' project (and any subsets of it generated by the different filtering functions) is parsed into a single object, whose different components (e.g. tables with the taxonomic or functional composition across samples, contig/gene abundance profiles) can be easily analyzed using other R packages such as 'vegan' or 'DESeq2'. The methods in this package are further described in Puente-Sánchez et al., (2020) <doi:10.1186/s12859-020-03703-2>.

Fernando Puente-Sánchez

SQMtools

Analyze Results Generated by the 'SqueezeMeta' Pipeline

Natalia García-García

Hadza function

<p>A SQM object; see <code>loadSQM</code>.</p>

Hadza: Hadza hunter-gatherer gut metagenomes

Description

Usage

Arguments

Format

References

Examples