Package Recipe 'bioconductor-singlecellalleleexperiment'

recipe bioconductor-singlecellalleleexperiment

S4 Class for Single Cell Data with Allele and Functional Levels for Immune Genes

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/SingleCellAlleleExperiment.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-singlecellalleleexperiment/meta.yaml

Defines a S4 class that is based on SingleCellExperiment. In addition to the usual gene layer the object can also store data for immune genes such as HLAs, Igs and KIRs at allele and functional level. The package is part of a workflow named single-cell ImmunoGenomic Diversity (scIGD), that firstly incorporates allele-aware quantification data for immune genes. This new data can then be used with the here implemented data structure and functionalities for further data handling and data analysis.

package bioconductor-singlecellalleleexperiment¶

Versions:

1.6.0-0, 1.2.0-0

Depends:

on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-delayedarray >=0.36.0,<0.37.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-matrix

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-singlecellalleleexperiment

to add into an existing workspace instead, run:

pixi add bioconductor-singlecellalleleexperiment

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-singlecellalleleexperiment

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-singlecellalleleexperiment

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-singlecellalleleexperiment:<tag>

(see bioconductor-singlecellalleleexperiment/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-singlecellalleleexperiment/README.html)