recipe bioconductor-lute

Framework for cell size scale factor normalized bulk transcriptomics deconvolution experiments

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/lute.html

License:

Artistic-2.0

Recipe:

/bioconductor-lute/meta.yaml

Provides a framework for adjustment on cell type size when performing bulk transcripomics deconvolution. The main framework function provides a means of reference normalization using cell size scale factors. It allows for marker selection and deconvolution using non-negative least squares (NNLS) by default. The framework is extensible for other marker selection and deconvolution algorithms, and users may reuse the generics, methods, and classes for these when developing new algorithms.

package bioconductor-lute

versions:

1.2.0-0

depends bioconductor-biobase:

>=2.66.0,<2.67.0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-scran:

>=1.34.0,<1.35.0

depends bioconductor-singlecellexperiment:

>=1.28.0,<1.29.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-dplyr:

depends r-ggplot2:

requirements:

additional platforms:

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-lute

and update with::

   mamba update bioconductor-lute

To create a new environment, run:

mamba create --name myenvname bioconductor-lute

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-lute:<tag>

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

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