In waldronlab/curatedMetagenomicData: Curated Metagenomic Data of the Human Microbiome

library(curatedMetagenomicData)

curatedMetagenomicData

The r BiocStyle::Biocpkg("curatedMetagenomicData") package 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 as (Tree)SummarizedExperiment objects.

Installation

To install r BiocStyle::Biocpkg("curatedMetagenomicData") from Bioconductor, use r BiocStyle::CRANpkg("BiocManager") as follows.

BiocManager::install("curatedMetagenomicData")

To install r BiocStyle::Biocpkg("curatedMetagenomicData") from GitHub, use r BiocStyle::CRANpkg("BiocManager") as follows.

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

Most users should simply install r BiocStyle::Biocpkg("curatedMetagenomicData") from Bioconductor.

Examples

To access curated metagenomic data, users will use the curatedMetagenomicData() method both to query and return resources. Multiple resources can be queried or returned with a single call to curatedMetagenomicData(), but only the titles of resources are returned by default.

curatedMetagenomicData("AsnicarF_20.+")

When the dryrun argument is set to FALSE, a list of SummarizedExperiment and/or TreeSummarizedExperiment objects is returned. The rownames argument determines the type of rownames to use for relative_abundance resources: either "long" (the default), "short" (species name), or "NCBI" (NCBI Taxonomy ID). When a single resource is requested, a single element list is returned.

curatedMetagenomicData("AsnicarF_2017.relative_abundance", dryrun = FALSE, rownames = "short")

When the counts argument is set to TRUE, relative abundance proportions are multiplied by read depth and rounded to the nearest integer prior to being returned. Also, when multiple resources are requested, the list will contain named elements corresponding to each SummarizedExperiment and/or TreeSummarizedExperiment object.

curatedMetagenomicData("AsnicarF_20.+.relative_abundance", dryrun = FALSE, counts = TRUE, rownames = "short")

Analyses

See curatedMetagenomicAnalyses for analyses in R and Python using r BiocStyle::Biocpkg("curatedMetagenomicData").

Contributing

To contribute to the r BiocStyle::Biocpkg("curatedMetagenomicData") R/Bioconductor package, first read the contributing guidelines and then open an issue. Also, note that in contributing you agree to abide by the code of conduct.

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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.

waldronlab/curatedMetagenomicData documentation built on Nov. 4, 2024, 7:57 a.m.