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schtools
- schtools: Schloss Lab Tools for Reproducible Microbiome Research
Microbiome
Handle microbiome-related data.
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read_dist()
- Read in lower left triangular matrix from file
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read_tax()
- Read in a taxonomy file and parse it to a wide dataframe
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parse_tax()
- Convert taxonomy strings into dataframe of labels based on taxonomic classification
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calc_relabun()
- Calculate OTU relative abundances from a shared file
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pool_taxon_counts()
- Pool OTU counts at a particular taxonomic level
R Markdown helpers
Format publication-quality documents.
ggplot2 helpers
Make your plots even prettier.
Everything else
Useful tools for miscellaneous tasks.
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close_enough()
- Check whether two numeric vectors are close enough for gov't work.
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is_nearly_whole()
- Checks whether a number is near to a whole number
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is_nondesc()
- Check whether all elements given are sorted in non-descending order
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load_deps()
- Install & load packages
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log_snakemake()
- Save output, messages, warnings, and errors to the Snakemake log file