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")):Stefano Mangiola. tidySummarizedExperiment: Brings SummarizedExperiment to the Tidyverse. doi:10.18129/B9.bioc.tidySummarizedExperiment, R package version 1.23.2, https://bioconductor.org/packages/tidySummarizedExperiment.
Generated from the package metadata; it may differ from the package's own citation.
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 | 1.23.2 |
| 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 | tidyprint, dplyr, tibble (>= 3.0.4), magrittr, tidyr, ggplot2, rlang, purrr, lifecycle, methods, utils, S4Vectors, tidyselect, ellipsis, vctrs, pillar, stringr, cli, fansi, stats, pkgconfig, plyxp, generics |
| System Requirements | |
| URL | https://github.com/stemangiola/tidySummarizedExperiment |
| Bug Reports | https://github.com/stemangiola/tidySummarizedExperiment/issues |
See More
| Suggests | AnnotationDbi, BiocStyle, microbenchmark, org.Hs.eg.db, testthat, knitr, markdown, rmarkdown, plotly, rbibutils, prettydoc, airway |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | growkar, tidyomics |
| Suggests Me | tidybulk, tidyCoverage, tidySpatialExperiment |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | tidySummarizedExperiment_1.23.2.tar.gz |
| Windows Binary (x86_64) | tidySummarizedExperiment_1.23.2.zip |
| macOS Binary (big-sur-x86_64) | tidySummarizedExperiment_1.23.2.tgz |
| macOS Binary (sonoma-arm64) | tidySummarizedExperiment_1.23.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/tidySummarizedExperiment |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/tidySummarizedExperiment |
| Package Short Url | https://bioconductor.org/packages/tidySummarizedExperiment/ |
| Package Downloads Report | Download Stats |