recipe bioconductor-tidysinglecellexperiment

Brings SingleCellExperiment to the Tidyverse

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/tidySingleCellExperiment.html

License:

GPL-3

Recipe:

/bioconductor-tidysinglecellexperiment/meta.yaml

'tidySingleCellExperiment' is an adapter that abstracts the 'SingleCellExperiment' container in the form of a 'tibble'. This allows *tidy* data manipulation, nesting, and plotting. For example, a 'tidySingleCellExperiment' is directly compatible with functions from 'tidyverse' packages `dplyr` and `tidyr`, as well as plotting with `ggplot2` and `plotly`. In addition, the package provides various utility functions specific to single-cell omics data analysis (e.g., aggregation of cell-level data to pseudobulks).

package bioconductor-tidysinglecellexperiment

versions:

1.12.0-0,  1.10.0-0,  1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1,  1.0.0-0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-cli:

depends r-dplyr:

depends r-ellipsis:

depends r-fansi:

depends r-ggplot2:

depends r-lifecycle:

depends r-magrittr:

depends r-matrix:

depends r-pillar:

depends r-pkgconfig:

depends r-plotly:

depends r-purrr:

depends r-rlang:

depends r-stringr:

depends r-tibble:

depends r-tidyr:

depends r-tidyselect:

depends r-ttservice:

>=0.3.8

depends r-vctrs:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-tidysinglecellexperiment

and update with::

   mamba update bioconductor-tidysinglecellexperiment

To create a new environment, run:

mamba create --name myenvname bioconductor-tidysinglecellexperiment

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

(see `bioconductor-tidysinglecellexperiment/tags`_ for valid values for ``<tag>``)

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