recipe r-immunedeconv

collection of methods for immune cell deconvolution of bulk RNA-seq samples.

Homepage:

https://github.com/omnideconv/immunedeconv

License:

BSD / BSD_3_clause

Recipe:

/r-immunedeconv/meta.yaml

Links:

doi: 10.1101/463828

package r-immunedeconv

versions:

2.1.2-2,  2.1.2-1,  2.1.2-0,  2.1.1-1,  2.1.1-0,  2.1.0-1,  2.1.0-0,  2.0.3-2,  2.0.3-1, 

2.1.2-2,  2.1.2-1,  2.1.2-0,  2.1.1-1,  2.1.1-0,  2.1.0-1,  2.1.0-0,  2.0.3-2,  2.0.3-1,  2.0.3-0,  2.0.2-1,  2.0.2-0,  2.0.1-0,  2.0.0-0,  1.1.1-0

depends bioconductor-biobase:

depends bioconductor-biocparallel:

depends bioconductor-biomart:

depends bioconductor-preprocesscore:

depends bioconductor-quantiseqr:

depends bioconductor-sva:

depends r-base:

>=4.3,<4.4.0a0

depends r-comics:

depends r-consensustme:

depends r-data.tree:

>=0.7

depends r-dplyr:

>=0.7

depends r-e1071:

>=1.6

depends r-epic:

>=1.1

depends r-limsolve:

>=1.5.5.1

depends r-magrittr:

>=1.5

depends r-mcpcounter:

depends r-mmcpcounter:

depends r-readr:

>=1.1

depends r-readxl:

>=1.0

depends r-testit:

>=0.7

depends r-tibble:

>=1.4.2

depends r-xcell:

>=1.2

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 r-immunedeconv

and update with::

   mamba update r-immunedeconv

To create a new environment, run:

mamba create --name myenvname r-immunedeconv

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/r-immunedeconv:<tag>

(see `r-immunedeconv/tags`_ for valid values for ``<tag>``)

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