recipe bioconductor-deconvr

Simulation and Deconvolution of Omic Profiles

Homepage:

https://bioconductor.org/packages/3.18/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:

1.8.0-0,  1.6.0-0,  1.4.0-0,  1.0.1-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-methylkit:

>=1.28.0,<1.29.0

depends bioconductor-minfi:

>=1.48.0,<1.49.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends r-assertthat:

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

>=1.14.0

depends r-dplyr:

>=1.0.7

depends r-e1071:

>=1.7.9

depends r-foreach:

>=1.5.1

depends r-magrittr:

>=2.0.1

depends r-mass:

depends r-matrixstats:

>=0.61.0

depends r-nnls:

>=1.4

depends r-quadprog:

>=1.5.8

depends r-rsq:

>=2.2

depends r-tidyr:

>=1.1.3

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-deconvr

and update with::

   mamba update bioconductor-deconvr

To create a new environment, run:

mamba create --name myenvname bioconductor-deconvr

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-deconvr:<tag>

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

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