OTUtable-package: OTU table analysis functions

In OTUtable: North Temperate Lakes - Microbial Observatory 16S Time Series Data and Functions

Description

Contains functions for the analysis of an OTU table generated from 16S rRNA amplicon sequencing. It also includes the data from the North Temperate Lakes-Microbial Observatory used in the paper Linz, et al. (2017) "Bacterial community composition and dynamics spanning five years in freshwater bog lakes." Please cite this paper if you use OTUtable. The data and code used in this paper are available at <https://github.com/McMahonLab/North_Temperate_Lakes-Microbial_Observatory>. Three data files are included: otu_table, taxonomy, and metadata. Access these by calling them with data(). There is also a fasta file associated with this dataset that is not included in this package - it can be found on our GitHub page in Data/16S_data. This package does not include functionality for fasta files; if you need this for analyses such as calculating UniFrac distance, please see the R package "phyloseq".

Details

Package:	OTUtable
Type:	Package
Version:	1.1.2
Date:	2018-05-26
License:	GPL-3

Functions include: bog_subset
chao1
clean_shared
clean_mothur_taxonomy
clean_TaxAss_taxonomy
combine_otus
extract_date
filter_taxa
grab_group
make_do_matrix
make_temp_matrix
obs_richness
pielou
plot_column
reduce_names
remove_reps
rotate
shannon
strat_metric
year_subset
zscore

Author(s)

Alexandra Linz <[e-mail]>

References

Alexandra M. Linz, Benjamin C. Crary, Ashley Shade, Sarah Owens, Jack A. Gilbert, Rob Knight, Katherine D. McMahon. Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes. mSphere Jun 2017, 2 (3) e00169-17; DOI: 10.1128/mSphere.00169-17

OTUtable documentation built on May 1, 2019, 10:51 p.m.