microbiomeComputations is an R package which provides helper functions for performing common analyses on microbiome data. The results are available as json, or optionally in a data.table. This package is intended to be compliant with the API specified in VEuPathDB/service-eda-compute.
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Installation
Use the R package remotes to install microbiomeComputations. From the R command prompt:
remotes::install_github('microbiomeDB/microbiomeComputations')Usage
# df is a data frame of abundance values with samples as rows. One column should hold the sample id, all other columns are assumed to be taxa
# the 'recordIdColumn' is the name of the column that contains the sample ids.
# 'method' can be 'simpson', 'shannon', or 'evenness'.
dt <- alphaDiv(df, recordIdColumn="entity.SampleID", method='simpson')Contributing
Pull requests are welcome and should be made to the dev branch.
For major changes, please open an issue first to discuss what you would like to change.
Please make sure to update unit tests as appropriate.