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Package: schtools 0.4.1.9000

schtools: Schloss Lab Tools for Reproducible Microbiome Research

A collection of useful functions and example code created and used by the Schloss Lab for reproducible microbiome research. Perform common tasks like read files created by mothur <https://mothur.org/>, tidy up your microbiome data, and format R Markdown documents for publication. See the website <http://www.schlosslab.org/schtools/> for more information, documentation, and examples.

Authors:Kelly Sovacool [aut, cre], Nicholas Lesniak [aut], Sarah Lucas [aut], Courtney Armour [aut], Patrick Schloss [aut], Jacqueline Moltzau [ctb], Andrew Hannah [ctb], Nielson Baxter [ctb], Alyxandria Schubert [ctb], Kathryn Iverson [ctb]

schtools_0.4.1.9000.tar.gz
schtools_0.4.1.9000.zip(r-4.7-any)schtools_0.4.1.9000.zip(r-4.6-any)schtools_0.4.1.9000.zip(r-4.5-any)
schtools_0.4.1.9000.tgz(r-4.6-any)schtools_0.4.1.9000.tgz(r-4.5-any)
schtools_0.4.1.9000.tar.gz(r-4.7-any)schtools_0.4.1.9000.tar.gz(r-4.6-any)
schtools_0.4.1.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
schtools/json (API)

# Install 'schtools' in R:

install.packages('schtools', repos = c('https://kelly-sovacool.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/schlosslab/schtools/issues

Pkgdown/docs site:https://www.schlosslab.org

On CRAN:

microbiome mothur

5.69 score 32 stars 38 scripts 66 downloads 19 exports 21 dependencies

Last updated from:b066acf96b. Checks:9 OK. Indexed: no.

Target	Result	Time
linux-devel	OK	153
source / vignettes	OK	221
linux-release	OK	144
macos-release	OK	160
macos-oldrel	OK	170
windows-devel	OK	100
windows-release	OK	81
windows-oldrel	OK	102
wasm-release	OK	116

Exports:.data %>%calc_relabun close_enough format_number get_wildcards_tbl inline_hook is_nearly_whole is_nondesc load_deps log_snakemake parse_tax paste_oxford_list pool_taxon_counts read_dist read_tax set_knitr_opts theme_lucas theme_sovacool

Dependencies:cli cpp11 dplyr formatR generics glue lifecycle magrittr pillar pkgconfig purrr R6 rlang stringi stringr tibble tidyr tidyselect utf8 vctrs withr

Introduction to schtools

Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2022-11-15
Started: 2020-09-04

Help page	Topics
Calculate OTU relative abundances from a shared file	calc_relabun
Check whether two numeric vectors are close enough	close_enough
Format human-readable numbers.	format_number
Get the Snakemake wildcards as a tibble	get_wildcards_tbl
Inline hook for knitr to paste human-readable numbers and nice lists.	inline_hook
Checks whether a number is near to a whole number	is_nearly_whole
Check whether all elements given are sorted in non-descending order	is_nondesc
Install & load packages	load_deps
Save output, messages, warnings, and errors to the Snakemake log file	log_snakemake
Convert taxonomy strings into dataframe of labels based on taxonomic classification	parse_tax
Create a prose string from a list or vector	paste_oxford_list
Pool OTU counts at a particular taxonomic level	pool_taxon_counts
Read in lower left triangular matrix from file	read_dist
Read in a taxonomy file and parse it to a wide dataframe	read_tax
Set knitr chunk options & inline hook	set_knitr_opts
Sarah's go-to theme for ggplot2	theme_lucas
Kelly's go-to theme for ggplot2	theme_sovacool

Package: schtools 0.4.1.9000

schtools: Schloss Lab Tools for Reproducible Microbiome Research

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)