recipe bioconductor-spsimseq

Semi-parametric simulation tool for bulk and single-cell RNA sequencing data

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-spsimseq/meta.yaml

SPsimSeq uses a specially designed exponential family for density estimation to constructs the distribution of gene expression levels from a given real RNA sequencing data (single-cell or bulk), and subsequently simulates a new dataset from the estimated marginal distributions using Gaussian-copulas to retain the dependence between genes. It allows simulation of multiple groups and batches with any required sample size and library size.

package bioconductor-spsimseq

versions:

1.12.0-0,  1.10.0-0,  1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1,  1.0.0-0

depends bioconductor-edger:

>=4.0.0,<4.1.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-phyloseq:

>=1.46.0,<1.47.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends r-base:

>=4.3,<4.4.0a0

depends r-fitdistrplus:

depends r-hmisc:

depends r-mvtnorm:

depends r-wgcna:

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-spsimseq

and update with::

   mamba update bioconductor-spsimseq

To create a new environment, run:

mamba create --name myenvname bioconductor-spsimseq

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-spsimseq:<tag>

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

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Link to this page

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