Package Recipe 'bioconductor-scfeatures'

recipe bioconductor-scfeatures

scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction

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

scFeatures constructs multi-view representations of single-cell and spatial data. scFeatures is a tool that generates multi-view representations of single-cell and spatial data through the construction of a total of 17 feature types. These features can then be used for a variety of analyses using other software in Biocondutor.

package bioconductor-scfeatures¶

Versions:

1.6.0-0, 1.2.0-0, 1.0.0-0

Depends:

on bioconductor-aucell >=1.28.0,<1.29.0
on bioconductor-biocparallel >=1.40.0,<1.41.0
on bioconductor-delayedarray >=0.32.0,<0.33.0
on bioconductor-delayedmatrixstats >=1.28.0,<1.29.0
on bioconductor-ensdb.hsapiens.v79 >=2.99.0,<2.100.0
on bioconductor-ensdb.mmusculus.v79 >=2.99.0,<2.100.0
on bioconductor-ensembldb >=2.30.0,<2.31.0
on bioconductor-gsva >=2.0.0,<2.1.0
on bioconductor-matrixgenerics >=1.18.0,<1.19.0
on bioconductor-singlecellsignalr >=1.18.0,<1.19.0
on r-ape
on r-base >=4.4,<4.5.0a0
on r-cli
on r-dplyr
on r-dt
on r-glue
on r-gtools
on r-msigdbr
on r-proxyc
on r-reshape2
on r-rmarkdown
on r-seurat
on r-spatstat.explore
on r-spatstat.geom
on r-tidyr

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-scfeatures

to add into an existing workspace instead, run:

pixi add bioconductor-scfeatures

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-scfeatures

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-scfeatures

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-scfeatures:<tag>

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