AnnotatedBCGEData
This is the development version of AnnotatedBCGEData; to use it, please install the devel version of Bioconductor.
100+ Curated Breast Cancer Gene Expression Data sets
Bioconductor version: Development (3.24)
AnnotatedBCGEData is an R Bioconductor package that provides access to more than 100 gene-expression datasets generated using microarray and RNA- sequencing technologies. We collected these datsets from public repositories, including Gene Expression Omnibus, ArrayExpress, and The Cancer Genome Atlas. Where feasible, we obtained and reprocessed the raw data using computational pipelines and annotations that were standardized and more updated than those used to process the data originally. Additionally, we annotated the sample metadata using oncology terms from the National Cancer Institute Thesaurus. This was necessary because different data submitters used different terminology to describe breast-cancer patients and samples. Mapping the metadata to ontology terms makes it possible for users to search the data using these standardized terms.
Author: Heidi Steadman [aut], Shu-Fei Lo [aut], Stephen Piccolo [cre]
, BYU College Undergraduate Research Award [fnd]
Maintainer: Stephen Piccolo <stephen_piccolo at byu.edu>
citation("AnnotatedBCGEData")):
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("AnnotatedBCGEData")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | ArrayExpress, BreastCancerData, CancerData, ExperimentData, ExpressionData, GEO, Genome, Homo_sapiens_Data, MicroarrayData, SequencingData, Tissue, TissueMicroarrayData |
| Version | 0.99.11 |
| License | CC0 |
| Depends | R (>= 4.6) |
| Imports | SummarizedExperiment, stringr, readr, dplyr, tibble, tidyr, zen4R, BiocFileCache, cli, rlang |
| System Requirements | |
| URL | https://github.com/srp33/AnnotatedBCGEData |
| Bug Reports | https://github.com/srp33/AnnotatedBCGEData//issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, sessioninfo, ggplot2, 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 | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/AnnotatedBCGEData |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/AnnotatedBCGEData |
| Package Short Url | https://bioconductor.org/packages/AnnotatedBCGEData/ |
| Package Downloads Report | Download Stats |