tidySummarizedExperiment

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

Brings SummarizedExperiment to the Tidyverse

Bioconductor version: Development (3.18)

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 "4.3") 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	1.11.1
In Bioconductor since	BioC 3.12 (R-4.0) (3 years)
License	GPL-3
Depends	R (>= 4.1.0), SummarizedExperiment, ttservice
Imports	tibble (>= 3.0.4), dplyr, magrittr, tidyr, ggplot2, rlang, purrr, lifecycle, methods, plotly, utils, S4Vectors, tidyselect, ellipsis, vctrs, pillar, stringr, cli, fansi, stats
Linking To
Suggests	BiocStyle, testthat, knitr, markdown
System Requirements
Enhances
URL	https://github.com/stemangiola/tidySummarizedExperiment
Bug Reports	https://github.com/stemangiola/tidySummarizedExperiment/issues

Depends On Me
Imports Me
Suggests Me	nullranges, tidybulk
Links To Me
Build Report

Package Archives

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

Source Package	tidySummarizedExperiment_1.11.1.tar.gz
Windows Binary	tidySummarizedExperiment_1.11.1.zip
macOS Binary (x86_64)	tidySummarizedExperiment_1.11.1.tgz
macOS Binary (arm64)	tidySummarizedExperiment_1.11.1.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