curatedMetagenomicDataTerminal

The curatedMetagenomicData command-line interface provides standardized, curated human microbiome data for novel analyses. It includes gene families, marker abundance, marker presence, pathway abundance, pathway coverage, and relative abundance for samples collected from different body sites. The bacterial, fungal, and archaeal taxonomic abundances for each sample were calculated with MetaPhlAn3, and metabolic functional potential was calculated with HUMAnN3. The manually curated sample metadata and standardized metagenomic data are available through this command-line interface.

Prerequisite

R is required; visit https://cran.r-project.org/ for installation instructions.

Installation

The curatedMetagenomicData command-line interface, curatedMetagenomicDataTerminal, is simply an R package with a symlinked R script that uses the curatedMetagenomicData R package to return data for use in other languages (python, etc.). You can install it the easier way (one command) or the harder way (three commands); neither way is difficult.

Easier Way

The easier way pipes the results of curl to bash, and that is always met with some controversy. If you don’t like it, don’t do it; the harder way is right there for you and is identical to the easier way, only it doesn’t check for R first. Follow the link to the install script (https://tinyurl.com/cMDTerminal) if you need to prove this to yourself before executing the one line install.

curl -sSL https://tinyurl.com/cMDTerminal | bash

Harder Way

As stated, the harder way is identical to the easier way, it just assumes you already have R installed. To install curatedMetagenomicDataTerminal the harder way, execute the following three commands from your terminal.

Rscript -e 'utils::install.packages("BiocManager", repos = "https://cloud.r-project.org/")'
Rscript -e 'BiocManager::install("waldronlab/curatedMetagenomicDataTerminal")'
Rscript -e 'curatedMetagenomicDataTerminal::install()'

MS Windows

Do you have Windows and want to use curatedMetagenomicDataTerminal? The steps above won’t work for you, see WINDOWS.md instead.

Introduction

curatedMetagenomicData - Curated Metagenomic Data of the Human Microbiome

The curatedMetagenomicData command-line interface provides standardized, curated
human microbiome data for novel analyses. It includes gene families, marker
abundance, marker presence, pathway abundance, pathway coverage, and relative
abundance for samples collected from different body sites. The bacterial,
fungal, and archaeal taxonomic abundances for each sample were calculated with
MetaPhlAn3, and metabolic functional potential was calculated with HUMAnN3. The
manually curated sample metadata and standardized metagenomic data are available
through this command-line interface.

Usage:
    curatedMetagenomicData <pattern>
    curatedMetagenomicData <pattern> --dryrun
    curatedMetagenomicData <pattern> --counts
    curatedMetagenomicData <pattern> --metadata

Arguments:
    <pattern> a regular expression pattern to look for in the titles of
              resources available in curatedMetagenomicData; "." will return all

Options:
    --dryrun    return only names of resources
    --counts    return taxa abundances as counts
    --metadata  return only subject metadata

Return Value:
    A table of tab-seperated values will be sent to stdout. Where multiple
    studies of the same data type are requested, they will be merged into a
    single table. Where the metadata option (--metadata) is specified, the
    returned table will contain only metadata.

Examples:
    To return the names of all resources matching "AsnicarF_20.+", the following
    command is used and will return all data types for both "AsnicarF" studies.

        # curatedMetagenomicData "AsnicarF_20.+" --dryrun

    To return the relative abundance table for the "AsnicarF_2017" study, the
    following command is used and will return a tab-seperated table to stdout.

        # curatedMetagenomicData "AsnicarF_2017.relative_abundance"

    To return a relative abundance table for both "AsnicarF" studies converted
    to read counts (i.e. relative abundance * read depth), the following command
    is used and will return a tab-seperated table to stdout.

        # curatedMetagenomicData "AsnicarF_20.+.relative_abundance" --counts

    To return a table containing only metadata for both "AsnicarF" studies, the
    metadata option (--metadata) is specified and will return a tab-seperated
    table to stdout.

        # curatedMetagenomicData "AsnicarF_20.+.relative_abundance" --metadata

Code of Conduct

Please note that the curatedMetagenomicDataTerminal package is released with a code of conduct. By contributing, you agree to abide by its terms.