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Bioconductor - tidySummarizedExperiment

tidySummarizedExperiment

This is the released version of tidySummarizedExperiment; for the devel version, see tidySummarizedExperiment.

Brings SummarizedExperiment to the Tidyverse

Bioconductor version: Release (3.21)

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]

Maintainer: Stefano Mangiola <mangiolastefano at gmail.com>

Citation (from within R, enter citation("tidySummarizedExperiment")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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 PDF Details biocViews AssayDomain, Clustering, DifferentialExpression, GeneExpression, Infrastructure, Normalization, QualityControl, RNASeq, Sequencing, Software, Transcription, Transcriptomics Version 1.18.1 In Bioconductor since BioC 3.12 (R-4.0) (4.5 years) License GPL-3 Depends R (>= 4.3.0), SummarizedExperiment, ttservice (>= 0.4.0) Imports dplyr, tibble (>= 3.0.4), magrittr, tidyr, ggplot2, rlang, purrr, lifecycle, methods, utils, S4Vectors, tidyselect, ellipsis, vctrs, pillar, stringr, cli, fansi, stats, pkgconfig System Requirements URL https://github.com/stemangiola/tidySummarizedExperiment Bug Reports https://github.com/stemangiola/tidySummarizedExperiment/issues See More Package Archives

Follow Installation instructions to use this package in your R session.


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