HMP2Data
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see HMP2Data.
16s rRNA sequencing data from the Human Microbiome Project 2
Bioconductor version: 3.16
HMP2Data is a Bioconductor package of the Human Microbiome Project 2 (HMP2) 16S rRNA sequencing data. Processed data is provided as phyloseq, SummarizedExperiment, and MultiAssayExperiment class objects. Individual matrices and data.frames used for building these S4 class objects are also provided in the package.
Author: John Stansfield <stansfieldjc at vcu.edu>, Ekaterina Smirnova <ekaterina.smirnova at vcuhealth.org>, Ni Zhao <nzhao10 at jhu.edu>, Jennifer Fettweis <jennifer.fettweis at vcuhealth.org>, Levi Waldron <levi.waldron at sph.cuny.edu>, Mikhail Dozmorov <mikhail.dozmorov at vcuhealth.org>
Maintainer: John Stansfield <stansfieldjc at vcu.edu>, Ekaterina Smirnova <ekaterina.smirnova at vcuhealth.org>
citation("HMP2Data")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("HMP2Data")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("HMP2Data")| HMP2Data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ExperimentData, Homo_sapiens_Data, MicrobiomeData, ReproducibleResearch, SequencingData |
| Version | 1.12.0 |
| License | Artistic-2.0 |
| Depends | R (>= 3.6.0) |
| Imports | AnnotationHub, assertthat, dplyr, ExperimentHub, kableExtra, knitr, magrittr, methods, readr, S4Vectors, SummarizedExperiment, phyloseq, MultiAssayExperiment, data.table |
| System Requirements | |
| URL | https://github.com/jstansfield0/HMP2Data |
| Bug Reports | https://github.com/jstansfield0/HMP2Data/issues |
See More
| Suggests | Biobase, BiocCheck, BiocManager, BiocStyle, cowplot, devtools, ggplot2, gridExtra, haven, rmarkdown, roxygen2, stats, testthat, tibble, UpSetR |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | HMP2Data_1.12.0.tar.gz |
| Windows Binary | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/HMP2Data |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HMP2Data |
| Package Short Url | https://bioconductor.org/packages/HMP2Data/ |
| Package Downloads Report | Download Stats |