recipe bioconductor-hsmmsinglecell

Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)

Homepage:

https://bioconductor.org/packages/3.20/data/experiment/html/HSMMSingleCell.html

License:

Artistic-2.0

Recipe:

/bioconductor-hsmmsinglecell/meta.yaml

Skeletal myoblasts undergo a well-characterized sequence of morphological and transcriptional changes during differentiation. In this experiment, primary human skeletal muscle myoblasts (HSMM) were expanded under high mitogen conditions (GM) and then differentiated by switching to low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several hundred cells taken over a time-course of serum-induced differentiation. Between 49 and 77 cells were captured at each of four time points (0, 24, 48, 72 hours) following serum switch using the Fluidigm C1 microfluidic system. RNA from each cell was isolated and used to construct mRNA-Seq libraries, which were then sequenced to a depth of ~4 million reads per library, resulting in a complete gene expression profile for each cell.

package bioconductor-hsmmsinglecell

(downloads) docker_bioconductor-hsmmsinglecell

Versions:
1.30.0-0,  1.26.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-0,  1.17.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0, 

1.30.0-0,  1.26.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-0,  1.17.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.9.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.2.0-0,  0.114.0-0,  0.112.0-1,  0.112.0-0,  0.110.0-1,  0.110.0-0

Depends:

  • on bioconductor-data-packages >=20260207

  • on curl

  • on r-base >=4.5,<4.6.0a0

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-hsmmsinglecell

to add into an existing workspace instead, run:

pixi add bioconductor-hsmmsinglecell

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-hsmmsinglecell

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-hsmmsinglecell

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-hsmmsinglecell:<tag>

(see bioconductor-hsmmsinglecell/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.

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