recipe bioconductor-simbu

Simulate Bulk RNA-seq Datasets from Single-Cell Datasets

Homepage:

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

License:

GPL-3 + file LICENSE

Recipe:

/bioconductor-simbu/meta.yaml

SimBu can be used to simulate bulk RNA-seq datasets with known cell type fractions. You can either use your own single-cell study for the simulation or the sfaira database. Different pre-defined simulation scenarios exist, as are options to run custom simulations. Additionally, expression values can be adapted by adding an mRNA bias, which produces more biologically relevant simulations.

package bioconductor-simbu

versions:

1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-basilisk:

>=1.14.0,<1.15.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-phyloseq:

>=1.46.0,<1.47.0

depends bioconductor-sparsematrixstats:

>=1.14.0,<1.15.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-dplyr:

depends r-ggplot2:

depends r-matrix:

>=1.3.3

depends r-proxyc:

depends r-rcolorbrewer:

depends r-rcurl:

depends r-reticulate:

depends r-tidyr:

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-simbu

and update with::

   mamba update bioconductor-simbu

To create a new environment, run:

mamba create --name myenvname bioconductor-simbu

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-simbu:<tag>

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

Download stats

Link to this page

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