msd16s
This is the development version of msd16s; for the stable release version, see msd16s.
Healthy and moderate to severe diarrhea 16S expression data
Bioconductor version: Development (3.24)
Gut 16S sequencing expression data from 992 healthy and moderate-to-severe diarrhetic samples used in 'Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition'.
Author: Joseph N. Paulson, Hector Corrada Bravo, Mihai Pop
Maintainer: Joseph N. Paulson <jpaulson at umiacs.umd.edu>
citation("msd16s")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("msd16s")
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("msd16s")| msd16s | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ExperimentData, MicrobiomeData, SequencingData |
| Version | 1.33.0 |
| License | Artistic-2.0 |
| Depends | R (>= 2.10), Biobase, metagenomeSeq |
| Imports | |
| System Requirements | |
| URL | http://www.cbcb.umd.edu/research/projects/GEMS-pathogen-discovery |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | scTreeViz |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | msd16s_1.33.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/msd16s |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/msd16s |
| Package Short Url | https://bioconductor.org/packages/msd16s/ |
| Package Downloads Report | Download Stats |