HuMMANet
This is the development version of HuMMANet; to use it, please install the devel version of Bioconductor.
Curated Paired Human Microbiome-Metabolome Study Data
Bioconductor version: Development (3.24)
Provides access to curated paired human microbiome-metabolome study bundles available through Bioconductor ExperimentHub. The package organizes matched sample metadata, species abundance profiles, original and harmonized metabolite profiles, and study-specific annotation resources including metabolite identifier mappings, microbial producer annotations, disease associations, pathway annotations, and drug similarity matches. The resource is designed to support consistent and reproducible cross-study microbiome-metabolome analyses.
Author: Shivangi Verma [aut, fnd]
, Nalin Arora [aut, cre]
, Himel Mallick [aut]
, Tarini Shankar Ghosh [aut, fnd]
Maintainer: Nalin Arora <naa4050 at med.cornell.edu>
citation("HuMMANet")):
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("HuMMANet")
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("HuMMANet")| HuMMANet | HTML | R Script |
| Reference Manual |
Details
| biocViews | ExperimentData, ExperimentHub, Homo_sapiens_Data, MicrobiomeData |
| Version | 0.99.3 |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0) |
| Imports | ExperimentHub, MultiAssayExperiment, S4Vectors, SummarizedExperiment, stats, utils |
| System Requirements | |
| URL | https://github.com/ShivangiV-IIITD/HuMMANet |
| Bug Reports | https://github.com/ShivangiV-IIITD/HuMMANet/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) |
| 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 | HuMMANet_0.99.3.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/HuMMANet |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HuMMANet |
| Package Short Url | https://bioconductor.org/packages/HuMMANet/ |
| Package Downloads Report | Download Stats |