R/Alldata.R

In HuaZou/MicrobiomeAnalysis: Data analysis toolkits in metagenomics

#' 16S rRNA data from "Moving pictures of the human microbiome"
#'
#' 16S read counts and phylogenetic tree file of 34 Illumina samples derived
#' from Moving Pictures of the Human Microbiome (Caporaso et al.) Group label:
#' gut, left palm, right palm, and tongue - indicating different sampled body
#' sites.
#'
#' @format a [phyloseq::phyloseq] object
#' @references
#' Caporaso, et al. Moving pictures of the human microbiome. Genome Biol 12,
#' R50 (2011).
#'
#' \url{https://doi.org/10.1186/gb-2011-12-5-r50}
#'
#' @source Data was downloaded from https://www.microbiomeanalyst.ca
#'
#'
#' @name data-caporaso
#' @aliases caporaso
#' @docType data
#' @author Yang Cao
NA


#' Enterotypes data of 39 samples
#'
#' The data contains 22 European metagenomes from Danish, French, Italian,
#' and Spanish individuals, and 13 Japanese and 4 American.
#'
#' @format a [`phyloseq::phyloseq-class`] object
#' @references
#' Arumugam, Manimozhiyan, et al. Enterotypes of the human gut microbiome.
#' nature 473.7346 (2011): 174-180.
#' @name data-enterotypes_arumugam
#' @aliases enterotypes_arumugam
#' @docType data
#' @author Yang Cao
NA


#' Data from Early Childhood Antibiotics and the Microbiome (ECAM) study
#'
#' The data from a subset of the Early Childhood Antibiotics and the
#' Microbiome (ECAM) study, which tracked the microbiome composition and
#' development of 43 infants in the United States from birth to 2 years of age,
#' identifying microbiome associations with antibiotic exposure, delivery mode,
#' and diet.
#'
#' @format a [`phyloseq::phyloseq-class`] object
#'
#' @references
#' Bokulich, Nicholas A., et al. "Antibiotics, birth mode, and diet shape
#' microbiome maturation during early life." Science translational medicine
#' 8.343 (2016): 343ra82-343ra82.
#'
#' \url{https://github.com/FrederickHuangLin/ANCOM/tree/master/data}
#' @name data-ecam
#' @aliases ecam
#' @docType data
NA

#' gut microbiota from Zeybel et al. - 2022 paper
#'
#' The data from Zeybel et al. - 2022 paper, which investigated the
#' microbiome composition and development of 56 MAFLD,
#' identifying gut microbiome associations with oral microbiome.
#'
#' @format a [`phyloseq::phyloseq-class`] object
#'
#' @references
#' Zeybel, Mujdat, et al. "Multiomics analysis reveals the impact of microbiota
#' on host metabolism in hepatic steatosis."
#' Advanced Science 9.11 (2022): 2104373.
#'
#' @name data-Zeybel_2022_gut
#' @aliases Zeybel_2022_gut
#' @docType data
NA

#' oral microbiota from Zeybel et al. - 2022 paper
#'
#' The data from Zeybel et al. - 2022 paper, which investigated the
#' microbiome composition and development of 56 MAFLD,
#' identifying gut microbiome associations with oral microbiome.
#'
#' @format a [`phyloseq::phyloseq-class`] object
#'
#' @references
#' Zeybel, Mujdat, et al. "Multiomics analysis reveals the impact of microbiota
#' on host metabolism in hepatic steatosis."
#' Advanced Science 9.11 (2022): 2104373.
#'
#' @name data-Zeybel_2022_oral
#' @aliases Zeybel_2022_oral
#' @docType data
NA

#' fecal metabolites from Zeybel et al. - 2022 paper
#'
#' The data from Zeybel et al. - 2022 paper, which investigated the
#' microbiome composition and development of 56 MAFLD,
#' identifying gut microbiome associations with oral microbiome.
#'
#' @format a [`SummarizedExperiment::SummarizedExperiment`] object
#'
#' @references
#' Zeybel, Mujdat, et al. "Multiomics analysis reveals the impact of microbiota
#' on host metabolism in hepatic steatosis."
#' Advanced Science 9.11 (2022): 2104373.
#'
#' @name data-Zeybel_2022_metabolite
#' @aliases Zeybel_2022_metabolite
#' @docType data
NA

#' serum protein from Zeybel et al. - 2022 paper
#'
#' The data from Zeybel et al. - 2022 paper, which investigated the
#' microbiome composition and development of 56 MAFLD,
#' identifying gut microbiome associations with oral microbiome.
#'
#' @format a [`SummarizedExperiment::SummarizedExperiment`] object
#'
#' @references
#' Zeybel, Mujdat, et al. "Multiomics analysis reveals the impact of microbiota
#' on host metabolism in hepatic steatosis."
#' Advanced Science 9.11 (2022): 2104373.
#'
#' @name data-Zeybel_2022_protein
#' @aliases Zeybel_2022_protein
#' @docType data
NA


#' Paired gut microbiota from Zeybel et al. - 2022 paper
#'
#' The data from Zeybel et al. - 2022 paper, which investigated the
#' microbiome composition and development of 56 MAFLD,
#' identifying gut microbiome associations with oral microbiome.
#'
#' @format a [`phyloseq::phyloseq-class`] object
#'
#' @references
#' Zeybel, Mujdat, et al. "Multiomics analysis reveals the impact of microbiota
#' on host metabolism in hepatic steatosis."
#' Advanced Science 9.11 (2022): 2104373.
#'
#' @name data-Zeybel_2022_gut_paired
#' @aliases Zeybel_2022_gut_paired
#' @docType data
NA

#' Paired oral microbiota from Zeybel et al. - 2022 paper
#'
#' The data from Zeybel et al. - 2022 paper, which investigated the
#' microbiome composition and development of 56 MAFLD,
#' identifying gut microbiome associations with oral microbiome.
#'
#' @format a [`phyloseq::phyloseq-class`] object
#'
#' @references
#' Zeybel, Mujdat, et al. "Multiomics analysis reveals the impact of microbiota
#' on host metabolism in hepatic steatosis."
#' Advanced Science 9.11 (2022): 2104373.
#'
#' @name data-Zeybel_2022_oral_paired
#' @aliases Zeybel_2022_oral_paired
#' @docType data
NA

#' Paired fecal metabolites from Zeybel et al. - 2022 paper
#'
#' The data from Zeybel et al. - 2022 paper, which investigated the
#' microbiome composition and development of 56 MAFLD,
#' identifying gut microbiome associations with oral microbiome.
#'
#' @format a [`SummarizedExperiment::SummarizedExperiment`] object
#'
#' @references
#' Zeybel, Mujdat, et al. "Multiomics analysis reveals the impact of microbiota
#' on host metabolism in hepatic steatosis."
#' Advanced Science 9.11 (2022): 2104373.
#'
#' @name data-Zeybel_2022_metabolite_paired
#' @aliases Zeybel_2022_metabolite_paired
#' @docType data
NA

#' Paired serum protein from Zeybel et al. - 2022 paper
#'
#' The data from Zeybel et al. - 2022 paper, which investigated the
#' microbiome composition and development of 56 MAFLD,
#' identifying gut microbiome associations with oral microbiome.
#'
#' @format a [`SummarizedExperiment::SummarizedExperiment`] object
#'
#' @references
#' Zeybel, Mujdat, et al. "Multiomics analysis reveals the impact of microbiota
#' on host metabolism in hepatic steatosis."
#' Advanced Science 9.11 (2022): 2104373.
#'
#' @name data-Zeybel_2022_protein_paired
#' @aliases Zeybel_2022_protein_paired
#' @docType data
NA