Package Recipe 'bioconductor-pipecomp'

recipe bioconductor-pipecomp

pipeComp pipeline benchmarking framework

Homepage:: https://bioconductor.org/packages/3.20/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:

1.20.0-0, 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:

on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-complexheatmap >=2.26.0,<2.27.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-scater >=1.38.0,<1.39.0
on bioconductor-scran >=1.38.0,<1.39.0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-aricode
on r-base >=4.5,<4.6.0a0
on r-circlize
on r-clue
on r-cluster
on r-cowplot
on r-dplyr
on r-ggplot2
on r-intrinsicdimension
on r-knitr
on r-matrix
on r-matrixstats
on r-randomcolor
on r-rcolorbrewer
on r-reshape2
on r-rtsne
on r-scales
on r-seurat
on r-uwot
on r-viridislite

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-pipecomp

to add into an existing workspace instead, run:

pixi add bioconductor-pipecomp

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-pipecomp

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-pipecomp

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-pipecomp:<tag>

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