recipe bioconductor-spsimseq

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

Homepage

https://bioconductor.org/packages/3.14/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

1.4.0-0,  1.2.0-0,  1.0.0-1,  1.0.0-0

Depends

• bioconductor-edger >=3.36.0,<3.37.0

• bioconductor-limma >=3.50.0,<3.51.0

• bioconductor-phyloseq >=1.38.0,<1.39.0

• bioconductor-singlecellexperiment >=1.16.0,<1.17.0

• r-base >=4.1,<4.2.0a0

• r-fitdistrplus

• r-hmisc

• r-mvtnorm

• r-wgcna

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-spsimseq

and update with:

conda update bioconductor-spsimseq

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-spsimseq:<tag>

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

Download stats

Link to this page

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