Package Recipe 'bioconductor-debcam'

recipe bioconductor-debcam

Deconvolution by Convex Analysis of Mixtures

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/debCAM.html
License:: GPL-2
Recipe:: /bioconductor-debcam/meta.yaml

An R package for fully unsupervised deconvolution of complex tissues. It provides basic functions to perform unsupervised deconvolution on mixture expression profiles by Convex Analysis of Mixtures (CAM) and some auxiliary functions to help understand the subpopulation-specific results. It also implements functions to perform supervised deconvolution based on prior knowledge of molecular markers, S matrix or A matrix. Combining molecular markers from CAM and from prior knowledge can achieve semi-supervised deconvolution of mixtures.

package bioconductor-debcam¶

Versions:

1.24.0-0, 1.20.0-0, 1.18.0-0, 1.16.0-0, 1.12.0-0, 1.10.0-0, 1.8.0-1, 1.8.0-0, 1.4.0-0

Depends:

on bioconductor-biobase >=2.66.0,<2.67.0
on bioconductor-biocparallel >=1.40.0,<1.41.0
on bioconductor-summarizedexperiment >=1.36.0,<1.37.0
on openjdk
on r-apcluster
on r-base >=4.4,<4.5.0a0
on r-corpcor
on r-dmwr2
on r-geometry
on r-nmf
on r-nnls
on r-pcapp
on r-rjava

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-debcam

to add into an existing workspace instead, run:

pixi add bioconductor-debcam

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-debcam

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-debcam

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-debcam:<tag>

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