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 bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-crayon:

depends r-digest:

depends r-dplyr:

depends r-ggplot2:

depends r-mclust:

depends r-rlang:

depends r-sessioninfo:

depends r-stringr:

depends r-tibble:

depends r-tidyr:

depends r-upsetr:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-summarizedbenchmark

and update with::

   mamba update bioconductor-summarizedbenchmark

To create a new environment, run:

mamba create --name myenvname bioconductor-summarizedbenchmark

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

(see `bioconductor-summarizedbenchmark/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

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