Package Recipe 'bioconductor-sccomp'

recipe bioconductor-sccomp

Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/sccomp.html
License:: GPL-3
Recipe:: /bioconductor-sccomp/meta.yaml

A robust and outlier-aware method for testing differential tissue composition from single-cell data. This model can infer changes in tissue composition and heterogeneity, and can produce realistic data simulations based on any existing dataset. This model can also transfer knowledge from a large set of integrated datasets to increase accuracy further.

package bioconductor-sccomp¶

Versions:

2.2.0-0, 1.4.0-0, 1.1.0-1, 1.1.0-0

Depends:

on bioconductor-singlecellexperiment >=1.32.0,<1.33.0
on r-base >=4.5,<4.6.0a0
on r-boot
on r-cli
on r-crayon
on r-dplyr
on r-fansi
on r-forcats
on r-ggplot2
on r-ggrepel
on r-glue
on r-instantiate >=0.2.3
on r-lifecycle
on r-magrittr
on r-patchwork
on r-purrr
on r-readr
on r-rlang
on r-scales
on r-stringr
on r-tibble
on r-tidyr
on r-tidyselect

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-sccomp

to add into an existing workspace instead, run:

pixi add bioconductor-sccomp

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-sccomp

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-sccomp

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-sccomp:<tag>

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