recipe bioconductor-simbu

Simulate Bulk RNA-seq Datasets from Single-Cell Datasets

Homepage:

https://bioconductor.org/packages/3.16/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:

1.0.0-0

Depends:

• bioconductor-basilisk >=1.9.0,<1.10.0

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-phyloseq >=1.42.0,<1.43.0

• bioconductor-sparsematrixstats >=1.10.0,<1.11.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-data.table

• r-dplyr

• r-ggplot2

• r-matrix >=1.3.3

• r-proxyc

• r-rcolorbrewer

• r-rcurl

• r-reticulate

• r-tidyr

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-simbu

and update with:

conda update bioconductor-simbu

or 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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