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tidySummarizedExperiment

This is the development version of tidySummarizedExperiment; for the stable release version, see tidySummarizedExperiment.

Brings SummarizedExperiment to the Tidyverse


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
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 PDF

Details

biocViews AssayDomain, Clustering, DifferentialExpression, GeneExpression, Infrastructure, Normalization, QualityControl, RNASeq, Sequencing, Software, Transcription, Transcriptomics
Version 1.13.1
In Bioconductor since BioC 3.12 (R-4.0) (3.5 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
Suggests BiocStyle, testthat, knitr, markdown, plotly
Linking To
Enhances
Depends On Me
Imports Me tidyomics
Suggests Me nullranges, 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_1.13.1.tar.gz
Windows Binary tidySummarizedExperiment_1.13.1.zip (64-bit only)
macOS Binary (x86_64) tidySummarizedExperiment_1.13.1.tgz
macOS Binary (arm64) tidySummarizedExperiment_1.13.1.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