Package Recipe 'bioconductor-deconvr'

recipe bioconductor-deconvr

Simulation and Deconvolution of Omic Profiles

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

This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. Users are given the option to create or extend a reference atlas and,also simulate the desired size of the bulk signature profile of the reference cell types.The package includes the cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can be used in deconvolution. Additionally,we included BSmeth2Probe, to make mapping WGBS data to their probe IDs easier.

package bioconductor-deconvr¶

Versions:

1.16.0-0, 1.12.0-0, 1.8.0-0, 1.6.0-0, 1.4.0-0, 1.0.1-0

Depends:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-methylkit >=1.36.0,<1.37.0
on bioconductor-minfi >=1.56.0,<1.57.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on r-assertthat
on r-base >=4.5,<4.6.0a0
on r-data.table >=1.14.0
on r-dplyr >=1.0.7
on r-e1071 >=1.7.9
on r-foreach >=1.5.1
on r-magrittr >=2.0.1
on r-mass
on r-matrixstats >=0.61.0
on r-nnls >=1.4
on r-quadprog >=1.5.8
on r-rsq >=2.2
on r-tidyr >=1.1.3

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-deconvr

to add into an existing workspace instead, run:

pixi add bioconductor-deconvr

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-deconvr

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-deconvr

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-deconvr:<tag>

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