AWAggregatorData
This is the released version of AWAggregatorData; for the devel version, see AWAggregatorData.
Attribute-Weighted Aggregation Data
Bioconductor version: Release (3.23)
The AWAggregatorData package contains the data associated with the AWAggregator R package. It includes two pre-trained random forest models, one incorporating the average coefficient of variation as a feature, and the other one not including it. It also contains the PSMs in Benchmark Set 1~3 derived from the psm.tsv output files generated by FragPipe, which are used to train the random forest models.
Author: Jiahua Tan [aut, cre]
, Gian L. Negri [aut]
, Gregg B. Morin [aut]
, David D. Y. Chen [aut]
Maintainer: Jiahua Tan <jiahuatan at chem.ubc.ca>
citation("AWAggregatorData")):
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")
BiocManager::install("AWAggregatorData")
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("AWAggregatorData")| AWAggregatorData vignette | HTML | R Script |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | ExperimentData, ExperimentHub, MassSpectrometryData, PackageTypeData, Proteome |
| Version | 1.2.0 |
| License | MIT + file LICENSE |
| Depends | ExperimentHub |
| Imports | |
| System Requirements | |
| URL | https://github.com/Tan-Jiahua/AWAggregatorData |
| Bug Reports | https://github.com/Tan-Jiahua/AWAggregatorData/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | AWAggregator |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | AWAggregatorData_1.2.0.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/AWAggregatorData |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/AWAggregatorData |
| Package Short Url | https://bioconductor.org/packages/AWAggregatorData/ |
| Package Downloads Report | Download Stats |