q2-breakaway

1.0
`breakaway` is the premier package for statistical analysis of microbial diversity. `breakaway` implements the latest and greatest estimates of richness, as well as the most commonly used estimates. The `breakaway` philosophy is to estimate diversity, to put error bars on diversity estimates, and to perform hypothesis tests for diversity that use those error bars.

source: https://github.com/statdivlab/q2-breakaway

install guide:

breakaway is based in R and requires installation of dependencies phyloseq, devtools, ggplot2,magrittr, tibble, dplyr,withr,testthat, and praise into your conda environment before installing breakaway. Please refer to the following instructions on how to install breakaway and its dependencies.

Activate your QIIME Environment

  • Here we activate our example version of QIIME, qiime2-2018.8. If you're not sure what your current version of QIIME is you can run conda env list in the command line to see a list of installed QIIME environments. Note: q2-breakaway is compatible only with version qiime2-2018.8 and on.
source activate qiime2-2018.8

Install breakaway dependencies

(Expected installation time ~3-5 minutes)

conda install -c bioconda -c conda-forge bioconductor-phyloseq r-devtools r-tibble r-magrittr r-dplyr r-withr r-testthat r-praise unzip
  • Note: When installing select y to proceed with installation when prompted.

Install breakaway and q2-breakaway

pip install git+https://github.com/statdivlab/q2-breakaway.git
qiime dev refresh-cache

Check that breakaway is installed

qiime breakaway --help

A link to the community tutorial for q2-breakaway can be found here: https://forum.qiime2.org/t/q2-breakaway-community-tutorial/5756

Citing breakaway

The R package breakaway implements a number of different richness estimates. Please cite the following if you use them:

  • breakaway(): Willis and Bunge (2015). Estimating diversity via frequency ratios. Biometrics.