recipe bioconductor-scmultisim

Simulation of Multi-Modality Single Cell Data Guided By Gene Regulatory Networks and Cell-Cell Interactions

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-scmultisim/meta.yaml

scMultiSim simulates paired single cell RNA-seq, single cell ATAC-seq and RNA velocity data, while incorporating mechanisms of gene regulatory networks, chromatin accessibility and cell-cell interactions. It allows users to tune various parameters controlling the amount of each biological factor, variation of gene-expression levels, the influence of chromatin accessibility on RNA sequence data, and so on. It can be used to benchmark various computational methods for single cell multi-omics data, and to assist in experimental design of wet-lab experiments.

package bioconductor-scmultisim

versions:

1.2.0-0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-ape:

depends r-assertthat:

depends r-base:

>=4.4,<4.5.0a0

depends r-crayon:

depends r-dplyr:

depends r-foreach:

depends r-ggplot2:

depends r-gplots:

depends r-igraph:

depends r-kernelknn:

depends r-markdown:

depends r-mass:

depends r-matrixstats:

depends r-phytools:

depends r-rlang:

depends r-rtsne:

depends r-zeallot:

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-scmultisim

and update with::

   mamba update bioconductor-scmultisim

To create a new environment, run:

mamba create --name myenvname bioconductor-scmultisim

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-scmultisim:<tag>

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

Download stats

Link to this page

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