HMP2Data is a Bioconductor ExperimentData package of the Human Microbiome Project (iHMP) 16S rRNA sequencing data. Raw data files are provided in the package as downloaded from the iHMP Data Analysis and Coordination Center. See the package vignette for usage details. Please, review the publication moratorium when using this data.
HMP2Data can be installed using BiocManager as follows.
BiocManager::install("HMP2Data")If installation fails while compiling dependencies (for example, RcppArmadillo,
Matrix, nlme, mgcv, ape, phyloseq, or MultiAssayExperiment), this
usually indicates an R toolchain/environment problem rather than an issue in
HMP2Data itself. In that case:
- Confirm Bioconductor is configured for your current R version:
BiocManager::version()
BiocManager::valid()-
On macOS, install/update command line compilers and a Fortran toolchain required by several dependencies, then restart R and retry installation.
-
Reinstall dependencies and the package in one call:
BiocManager::install(c(
"RcppArmadillo", "Matrix", "nlme", "mgcv", "ape",
"phyloseq", "SummarizedExperiment", "MultiAssayExperiment", "HMP2Data"
))The vignettes can be browsed using browseVignettes("HMP2Data").
The development version can be installed from this repository https://github.com/jstansfield0/HMP2Data using r BiocStyle::CRANpkg("devtools"). Install the package using the command devtools::install_github("jstansfield0/HMP2Data").
The stable version is available at the dozmorovlab GitHub repository https://github.com/dozmorovlab/HMP2Data and can be installed using the command devtools::install_github("dozmorovlab/HMP2Data").
To load the MOMSPI16S data run the following commands. This will generate a phyloseq object with the 16S rRNA data.
library(HMP2Data)
MOMSPI16s <- momspi16S()The MOMSPI cytokines data can be accessed with this command.
cyto <- momspiCytokines()You may also load the Type 2 diabetes data and the Inflammatory bowel disease data as follows.
T2D <- T2D16S()
IBD <- IBD16S()Please see the vignette for more information about the usage of the package.
If you have questions, comments, or suggestions you feel free to contact John Stansfield (stansfieldjc[at]vcu[dot]edu) or Mikhail Dozmorov (mikhail.dozmorov[at]vcuhealth[dot]org).