Package Recipe 'bioconductor-summarizedbenchmark'

recipe bioconductor-summarizedbenchmark

Classes and methods for performing benchmark comparisons

Homepage:: https://bioconductor.org/packages/3.18/bioc/html/SummarizedBenchmark.html
License:: GPL (>= 3)
Recipe:: /bioconductor-summarizedbenchmark/meta.yaml

This package defines the BenchDesign and SummarizedBenchmark classes for building, executing, and evaluating benchmark experiments of computational methods. The SummarizedBenchmark class extends the RangedSummarizedExperiment object, and is designed to provide infrastructure to store and compare the results of applying different methods to a shared data set. This class provides an integrated interface to store metadata such as method parameters and software versions as well as ground truths (when these are available) and evaluation metrics.

package bioconductor-summarizedbenchmark¶

Versions:

2.20.0-0, 2.18.0-0, 2.16.0-0, 2.12.0-0, 2.10.0-0, 2.8.0-1, 2.8.0-0, 2.6.0-0, 2.4.0-0,

2.20.0-0, 2.18.0-0, 2.16.0-0, 2.12.0-0, 2.10.0-0, 2.8.0-1, 2.8.0-0, 2.6.0-0, 2.4.0-0, 2.2.2-0, 2.0.0-0

Depends:

on bioconductor-biocgenerics >=0.48.0,<0.49.0
on bioconductor-biocparallel >=1.36.0,<1.37.0
on bioconductor-s4vectors >=0.40.0,<0.41.0
on bioconductor-summarizedexperiment >=1.32.0,<1.33.0
on r-base >=4.3,<4.4.0a0
on r-crayon
on r-digest
on r-dplyr
on r-ggplot2
on r-mclust
on r-rlang
on r-sessioninfo
on r-stringr
on r-tibble
on r-tidyr
on r-upsetr

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-summarizedbenchmark

to add into an existing workspace instead, run:

pixi add bioconductor-summarizedbenchmark

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-summarizedbenchmark

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-summarizedbenchmark

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-summarizedbenchmark:<tag>

(see bioconductor-summarizedbenchmark/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-summarizedbenchmark/README.html)