- recipe bioconductor-single.mtec.transcriptomes
Single Cell Transcriptome Data and Analysis of Mouse mTEC cells
- Homepage:
https://bioconductor.org/packages/3.20/data/experiment/html/Single.mTEC.Transcriptomes.html
- License:
LGPL
- Recipe:
This data package contains the code used to analyse the single-cell RNA-seq and the bulk ATAC-seq data from the manuscript titled: Single-cell transcriptome analysis reveals coordinated ectopic-gene expression patterns in medullary thymic epithelial cells. This paper was published in Nature Immunology 16,933-941(2015). The data objects provided in this package has been pre-processed: the raw data files can be downloaded from ArrayExpress under the accession identifiers E-MTAB-3346 and E-MTAB-3624. The vignette of this data package provides a documented and reproducible workflow that includes the code that was used to generate each statistic and figure from the manuscript.
- package bioconductor-single.mtec.transcriptomes¶
- Versions:
1.38.0-0,1.34.0-0,1.30.0-0,1.28.0-0,1.25.0-0,1.22.0-1,1.22.0-0,1.20.0-0,1.18.0-1,1.38.0-0,1.34.0-0,1.30.0-0,1.28.0-0,1.25.0-0,1.22.0-1,1.22.0-0,1.20.0-0,1.18.0-1,1.18.0-0,1.17.0-0,1.16.0-0,1.14.0-0,1.12.0-1,1.12.0-0,1.10.0-0- Depends:
on bioconductor-data-packages
>=20260207on 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-single.mtec.transcriptomes
to add into an existing workspace instead, run:
pixi add bioconductor-single.mtec.transcriptomes
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-single.mtec.transcriptomes
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-single.mtec.transcriptomes
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-single.mtec.transcriptomes:<tag>
(see bioconductor-single.mtec.transcriptomes/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:
[](http://bioconda.github.io/recipes/bioconductor-single.mtec.transcriptomes/README.html)
