recipe bioconductor-toast

Tools for the analysis of heterogeneous tissues

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/TOAST.html

License:

GPL-2

Recipe:

/bioconductor-toast/meta.yaml

This package is devoted to analyzing high-throughput data (e.g. gene expression microarray, DNA methylation microarray, RNA-seq) from complex tissues. Current functionalities include 1. detect cell-type specific or cross-cell type differential signals 2. tree-based differential analysis 3. improve variable selection in reference-free deconvolution 4. partial reference-free deconvolution with prior knowledge.

package bioconductor-toast

versions:

1.16.0-0,  1.14.0-0,  1.12.0-0,  1.7.1-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-epidish:

>=2.18.0,<2.19.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-corpcor:

depends r-doparallel:

depends r-ggally:

depends r-ggplot2:

depends r-nnls:

depends r-quadprog:

depends r-tidyr:

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-toast

and update with::

   mamba update bioconductor-toast

To create a new environment, run:

mamba create --name myenvname bioconductor-toast

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-toast:<tag>

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

Download stats

Link to this page

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