HMP16SData
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see HMP16SData.
16S rRNA Sequencing Data from the Human Microbiome Project
Bioconductor version: 3.9
HMP16SData is a Bioconductor ExperimentData package of the Human Microbiome Project (HMP) 16S rRNA sequencing data for variable regions 1–3 and 3–5. Raw data files are provided in the package as downloaded from the HMP Data Analysis and Coordination Center. Processed data is provided as SummarizedExperiment class objects via ExperimentHub.
Author: Lucas Schiffer <schiffer.lucas at gmail.com>, Rimsha Azhar <rimsha_azhar at hotmail.com>, Marcel Ramos <marcel.ramos at roswellpark.org>, Ludwig Geistlinger <ludwig.geistlinger at sph.cuny.edu>, Levi Waldron <lwaldron.research at gmail.com>
Maintainer: Lucas Schiffer <schiffer.lucas at gmail.com>
citation("HMP16SData")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("HMP16SData")
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("HMP16SData")| HMP16SData | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ExperimentData, ExperimentHub, Homo_sapiens_Data, MicrobiomeData, ReproducibleResearch, SequencingData |
| Version | 1.4.1 |
| License | Artistic-2.0 |
| Depends | R (>= 3.6.0), SummarizedExperiment |
| Imports | AnnotationHub, assertthat, dplyr, ExperimentHub, kableExtra, knitr, magrittr, methods, readr, S4Vectors, tibble, utils |
| System Requirements | |
| URL | https://github.com/waldronlab/HMP16SData |
| Bug Reports | https://github.com/waldronlab/HMP16SData/issues |
See More
| Suggests | Biobase, BiocCheck, BiocManager, BiocStyle, circlize, covr, cowplot, curatedMetagenomicData, dendextend, devtools, ggplot2, gridExtra, haven, phyloseq, rmarkdown, roxygen2, stats, testthat |
| 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 | HMP16SData_1.4.1.tar.gz |
| Windows Binary | |
| Mac OS X 10.11 (El Capitan) | |
| Source Repository | git clone https://git.bioconductor.org/packages/HMP16SData |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HMP16SData |
| Package Short Url | https://bioconductor.org/packages/HMP16SData/ |
| Package Downloads Report | Download Stats |