recipe bioconductor-singlecellexperiment

Defines a S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries.

Homepage

https://bioconductor.org/packages/3.8/bioc/html/SingleCellExperiment.html

License

GPL-3

Recipe

/bioconductor-singlecellexperiment/meta.yaml

package bioconductor-singlecellexperiment

Versions

1.4.0-0, 1.2.0-0, 1.0.0-1, 1.0.0-0

Depends

• bioconductor-biocgenerics >=0.28.0,<0.29.0

• bioconductor-s4vectors >=0.20.0,<0.21.0

• bioconductor-summarizedexperiment >=1.12.0,<1.13.0

• r-base >=3.5.1,<3.5.2.0a0

Required By

• bioconductor-scmap

• bioconductor-isee

• bioconductor-cydar

• bioconductor-scran

• bioconductor-scfind

• bioconductor-bearscc

• bioconductor-slingshot

• bioconductor-singlecelltk

• bioconductor-baynorm

• bioconductor-scruff

• bioconductor-zinbwave

• bioconductor-basics

• bioconductor-lineagepulse

• bioconductor-switchde

• bioconductor-singlecellexperiment-scripts

• bioconductor-tenxbraindata

• bioconductor-cogaps

• bioconductor-sc3

• r-brio

• bioconductor-dropletutils

• bioconductor-slalom

• bioconductor-tenxpbmcdata

• bioconductor-allenpvc

• bioconductor-clusterexperiment

• bioconductor-scater

• bioconductor-scpipe

• bioconductor-scnorm

• bioconductor-ccfindr

• bioconductor-scdd

• bioconductor-celltrails

• bioconductor-loomexperiment

• bioconductor-netsmooth

• dropletutils-scripts

• bioconductor-mast

• bioconductor-splatter

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-singlecellexperiment

and update with:

conda update bioconductor-singlecellexperiment

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-singlecellexperiment:<tag>

(see bioconductor-singlecellexperiment/tags for valid values for <tag>)

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-singlecellexperiment/README.html)