The curatedMetagenomicData package provides microbial taxonomic, functional, and gene marker abundance for samples collected from different body sites.

Installation

You can install curatedMetagenomicData from Bioconductor with:

BiocManager::install("curatedMetagenomicData")

You can install curatedMetagenomicData from GitHub with:

BiocManager::install("waldronlab/curatedMetagenomicData", dependencies = TRUE, build_vignettes = TRUE)

You can install the last version of curatedMetagenomicData 1 (v1.20.0) from GitHub with:

BiocManager::install("waldronlab/curatedMetagenomicData", dependencies = TRUE, build_vignettes = TRUE, ref = "v1.20.0")

Command-line installation

You must first install the R package, see instructions above. Then you can place the command-line tool on your path as follows:

CMDLIB=$(R -e 'find.package("curatedMetagenomicData")' | grep -o -e "/.*\w")/exec
echo -e "export PATH=\$PATH:$CMDLIB" >> ~/.bashrc

Command-line usage

Usage:
  curatedMetagenomicData [--metadata] [--counts] [--dryrun] [<NAME>]...
  curatedMetagenomicData [-mcd] [<NAME>]...
  curatedMetagenomicData -l | --list
  curatedMetagenomicData -h | --help

Examples

See the package vignette for more detailed examples.

curatedMetagenomicData("AsnicarF_2017")
#> 2021-03-31.AsnicarF_2017.gene_families
#> 2021-03-31.AsnicarF_2017.marker_abundance
#> 2021-03-31.AsnicarF_2017.marker_presence
#> 2021-03-31.AsnicarF_2017.pathway_abundance
#> 2021-03-31.AsnicarF_2017.pathway_coverage
#> 2021-03-31.AsnicarF_2017.relative_abundance
curatedMetagenomicData("AsnicarF_2017.relative_abundance")
#> 2021-03-31.AsnicarF_2017.relative_abundance
curatedMetagenomicData("AsnicarF_2017.relative_abundance", dryrun = FALSE)
#> class: SummarizedExperiment 
#> dim: 550 24 
#> metadata(0):
#> assays(1): relative_abundance
#> rownames(550): k__Bacteria k__Bacteria|p__Proteobacteria ...
#>   k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus_gordonii
#>   k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia_sp_HMSC24B09
#> rowData names(0):
#> colnames(24): MV_FEI1_t1Q14 MV_FEI2_t1Q14 ... MV_MIM5_t2M14
#>   MV_MIM5_t3F15
#> colData names(20): studyName subjectID ... curator NCBI_accession

Contributing

All are welcome to contribute to the curatedMetagenomicData project provided contributions are appropriate. Please see the contributing guide.

Code of Conduct

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


Pasolli E, Schiffer L, Manghi P, Renson A, Obenchain V, Truong D, Beghini F, Malik F, Ramos M, Dowd J, Huttenhower C, Morgan M, Segata N, Waldron L (2017). Accessible, curated metagenomic data through ExperimentHub. Nat. Methods, 14(11), 1023-1024. ISSN 1548-7091, 1548-7105, doi: 10.1038/nmeth.4468.