Package Recipe 'bioconductor-tidysummarizedexperiment'

recipe bioconductor-tidysummarizedexperiment

Brings SummarizedExperiment to the Tidyverse

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/tidySummarizedExperiment.html
License:: GPL-3
Recipe:: /bioconductor-tidysummarizedexperiment/meta.yaml

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.

package bioconductor-tidysummarizedexperiment¶

Versions:

1.20.1-0, 1.16.0-0, 1.12.0-0, 1.10.0-0, 1.8.0-0, 1.4.1-0, 1.2.0-0, 1.0.0-1, 1.0.0-0

Depends:

on bioconductor-plyxp >=1.4.0,<1.5.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-cli
on r-dplyr
on r-ellipsis
on r-fansi
on r-generics
on r-ggplot2
on r-lifecycle
on r-magrittr
on r-pillar
on r-pkgconfig
on r-purrr
on r-rlang
on r-stringr
on r-tibble >=3.0.4
on r-tidyr
on r-tidyselect
on r-ttservice >=0.5.0
on r-vctrs

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-tidysummarizedexperiment

to add into an existing workspace instead, run:

pixi add bioconductor-tidysummarizedexperiment

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-tidysummarizedexperiment

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-tidysummarizedexperiment

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-tidysummarizedexperiment:<tag>

(see bioconductor-tidysummarizedexperiment/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-tidysummarizedexperiment/README.html)