recipe bioconductor-demixt

Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/DeMixT.html

License:

GPL-3.0-only

Recipe:

/bioconductor-demixt/meta.yaml

Links:

biotools: DeMixT

DeMixT is a software package that performs deconvolution on transcriptome data from a mixture of two or three components.

package bioconductor-demixt

versions:

1.16.0-1,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.10.0-2,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-1, 

1.16.0-1,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.10.0-2,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.4.0-0,  1.2.0-0,  1.0.2-0

depends bioconductor-dss:

>=2.48.0,<2.49.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0a0

depends bioconductor-sva:

>=3.50.0,<3.51.0

depends bioconductor-sva:

>=3.50.0,<3.51.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-base64enc:

depends r-dendextend:

depends r-ggplot2:

depends r-kernsmooth:

depends r-knitr:

depends r-matrixcalc:

depends r-matrixstats:

depends r-psych:

depends r-rcpp:

>=1.0.0

depends r-rmarkdown:

depends r-truncdist:

requirements:

additional platforms:

linux-aarch64

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-demixt

and update with::

   mamba update bioconductor-demixt

To create a new environment, run:

mamba create --name myenvname bioconductor-demixt

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-demixt:<tag>

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

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