Package Recipe 'bioconductor-scmultisim'

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:

1.6.0-0, 1.2.0-0

Depends:

on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-ape
on r-assertthat
on r-base >=4.5,<4.6.0a0
on r-crayon
on r-dplyr
on r-foreach
on r-ggplot2
on r-gplots
on r-igraph
on r-kernelknn
on r-markdown
on r-mass
on r-matrixstats
on r-phytools
on r-rlang
on r-rtsne
on r-zeallot

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-scmultisim

to add into an existing workspace instead, run:

pixi add bioconductor-scmultisim

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-scmultisim

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-scmultisim

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-scmultisim/README.html)