recipe bioconductor-pipecomp

pipeComp pipeline benchmarking framework

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/pipeComp.html

License:

GPL

Recipe:

/bioconductor-pipecomp/meta.yaml

A simple framework to facilitate the comparison of pipelines involving various steps and parameters. The `pipelineDefinition` class represents pipelines as, minimally, a set of functions consecutively executed on the output of the previous one, and optionally accompanied by step-wise evaluation and aggregation functions. Given such an object, a set of alternative parameters/methods, and benchmark datasets, the `runPipeline` function then proceeds through all combinations arguments, avoiding recomputing the same step twice and compiling evaluations on the fly to avoid storing potentially large intermediate data.

package bioconductor-pipecomp

versions:

1.12.0-0,  1.10.0-0,  1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1,  1.0.0-0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-complexheatmap:

>=2.18.0,<2.19.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-scater:

>=1.30.0,<1.31.0

depends bioconductor-scran:

>=1.30.0,<1.31.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-aricode:

depends r-base:

>=4.3,<4.4.0a0

depends r-circlize:

depends r-clue:

depends r-cluster:

depends r-cowplot:

depends r-dplyr:

depends r-ggplot2:

depends r-intrinsicdimension:

depends r-knitr:

depends r-matrix:

depends r-matrixstats:

depends r-randomcolor:

depends r-rcolorbrewer:

depends r-reshape2:

depends r-rtsne:

depends r-scales:

depends r-seurat:

depends r-uwot:

depends r-viridislite:

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-pipecomp

and update with::

   mamba update bioconductor-pipecomp

To create a new environment, run:

mamba create --name myenvname bioconductor-pipecomp

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-pipecomp:<tag>

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

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