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schtools

Schloss Lab Tools for Reproducible Microbiome Research

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Version

Install

install.packages('schtools')

Monthly Downloads

48

Version

0.4.1

License

MIT + file LICENSE

Issues

7

Pull Requests

1

Stars

31

Forks

11

Maintainer

Kelly Sovacool

Last Published

August 21st, 2023

Functions in schtools (0.4.1)

theme_lucas

Sarah's go-to theme for ggplot2
read_dist

Read in lower left triangular matrix from file
read_tax

Read in a taxonomy file and parse it to a wide dataframe
pool_taxon_counts

Pool OTU counts at a particular taxonomic level
paste_oxford_list

Create a prose string from a list or vector
schtools-package

schtools: Schloss Lab Tools for Reproducible Microbiome Research
format_number

Format human-readable numbers.
is_nearly_whole

Checks whether a number is near to a whole number
log_snakemake

Save output, messages, warnings, and errors to the Snakemake log file
close_enough

Check whether two numeric vectors are close enough
get_wildcards_tbl

Get the Snakemake wildcards as a tibble
parse_tax

Convert taxonomy strings into dataframe of labels based on taxonomic classification
calc_relabun

Calculate OTU relative abundances from a shared file
load_deps

Install & load packages
inline_hook

Inline hook for knitr to paste human-readable numbers and nice lists.
is_nondesc

Check whether all elements given are sorted in non-descending order
set_knitr_opts

Set knitr chunk options & inline hook
reexports

dplyr pipe
theme_sovacool

Kelly's go-to theme for ggplot2