tidySummarizedExperiment
This is the development version of tidySummarizedExperiment; for the stable release version, see tidySummarizedExperiment.
Brings SummarizedExperiment to the Tidyverse
Bioconductor version: Development (3.24)
The tidySummarizedExperiment package provides a set of tools for creating and manipulating tidy data representations of SummarizedExperiment objects. SummarizedExperiment is a widely used data structure in bioinformatics for storing high-throughput genomic data, such as gene expression or DNA sequencing data. The tidySummarizedExperiment package introduces a tidy framework for working with SummarizedExperiment objects. It allows users to convert their data into a tidy format, where each observation is a row and each variable is a column. This tidy representation simplifies data manipulation, integration with other tidyverse packages, and enables seamless integration with the broader ecosystem of tidy tools for data analysis.
Author: Stefano Mangiola [aut, cre] <mangiolastefano at gmail.com>
Maintainer: Stefano Mangiola <mangiolastefano at gmail.com>
citation("tidySummarizedExperiment")):
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("tidySummarizedExperiment")
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("tidySummarizedExperiment")| Overview of the tidySummarizedExperiment package | HTML | R Script |
| Reference Manual |
Details
| biocViews | AssayDomain, Clustering, DifferentialExpression, GeneExpression, Infrastructure, Normalization, QualityControl, RNASeq, Sequencing, Software, Transcription, Transcriptomics |
| Version | 1.23.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | GPL-3 |
| Depends | R (>= 4.3.0), SummarizedExperiment, ttservice (>= 0.5.0) |
| Imports | dplyr, tibble (>= 3.0.4), magrittr, tidyr, ggplot2, rlang, purrr, lifecycle, methods, utils, S4Vectors, tidyselect, ellipsis, vctrs, pillar, stringr, cli, fansi, stats, pkgconfig, plyxp |
| System Requirements | |
| URL | https://github.com/stemangiola/tidySummarizedExperiment |
| Bug Reports | https://github.com/stemangiola/tidySummarizedExperiment/issues |
See More
| Suggests | BiocStyle, testthat, knitr, markdown, rmarkdown, plotly, rbibutils, prettydoc, airway |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | tidyomics |
| Suggests Me | tidybulk, tidyCoverage, tidySpatialExperiment |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | tidySummarizedExperiment_1.23.0.tar.gz |
| Windows Binary (x86_64) | tidySummarizedExperiment_1.23.0.zip |
| macOS Binary (big-sur-x86_64) | tidySummarizedExperiment_1.23.0.tgz |
| macOS Binary (sonoma-arm64) | tidySummarizedExperiment_1.23.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/tidySummarizedExperiment |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/tidySummarizedExperiment |
| Bioc Package Browser | https://code.bioconductor.org/browse/tidySummarizedExperiment/ |
| Package Short Url | https://bioconductor.org/packages/tidySummarizedExperiment/ |
| Package Downloads Report | Download Stats |