Package Recipe 'bioconductor-limpca'

recipe bioconductor-limpca

An R package for the linear modeling of high-dimensional designed data based on ASCA/APCA family of methods

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/limpca.html
License:: Artistic-2.0
Recipe:: /bioconductor-limpca/meta.yaml

This package has for objectives to provide a method to make Linear Models for high-dimensional designed data. limpca applies a GLM (General Linear Model) version of ASCA and APCA to analyse multivariate sample profiles generated by an experimental design. ASCA/APCA provide powerful visualization tools for multivariate structures in the space of each effect of the statistical model linked to the experimental design and contrarily to MANOVA, it can deal with mutlivariate datasets having more variables than observations. This method can handle unbalanced design.

package bioconductor-limpca¶

Versions:

1.6.0-0, 1.2.0-0

Depends:

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-doparallel
on r-dplyr
on r-ggplot2
on r-ggrepel
on r-ggsci
on r-plyr
on r-reshape2
on r-stringr
on r-tibble
on r-tidyr
on r-tidyverse

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-limpca

to add into an existing workspace instead, run:

pixi add bioconductor-limpca

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-limpca

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-limpca

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-limpca:<tag>

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