ExperimentSubset
This is the development version of ExperimentSubset; for the stable release version, see ExperimentSubset.
Manages subsets of data with Bioconductor Experiment objects
Bioconductor version: Development (3.24)
Experiment objects such as the SummarizedExperiment or SingleCellExperiment are data containers for one or more matrix-like assays along with the associated row and column data. Often only a subset of the original data is needed for down-stream analysis. For example, filtering out poor quality samples will require excluding some columns before analysis. The ExperimentSubset object is a container to efficiently manage different subsets of the same data without having to make separate objects for each new subset.
Author: Irzam Sarfraz [aut, cre]
, Muhammad Asif [aut, ths]
, Joshua D. Campbell [aut]
Maintainer: Irzam Sarfraz <irzam9095 at gmail.com>
citation("ExperimentSubset")):
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("ExperimentSubset")
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("ExperimentSubset")| An introduction to ExperimentSubset class | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, DataRepresentation, Infrastructure, Software |
| Version | 1.23.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.0.0), SummarizedExperiment, SingleCellExperiment, SpatialExperiment, TreeSummarizedExperiment |
| Imports | methods, Matrix, S4Vectors |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat, covr, stats, scran, scater, scds, TENxPBMCData, airway |
| 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 | ExperimentSubset_1.23.0.tar.gz |
| Windows Binary (x86_64) | ExperimentSubset_1.23.0.zip |
| macOS Binary (big-sur-x86_64) | ExperimentSubset_1.23.0.tgz |
| macOS Binary (sonoma-arm64) | ExperimentSubset_1.23.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ExperimentSubset |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ExperimentSubset |
| Bioc Package Browser | https://code.bioconductor.org/browse/ExperimentSubset/ |
| Package Short Url | https://bioconductor.org/packages/ExperimentSubset/ |
| Package Downloads Report | Download Stats |