recipe r-seurat-disk

The h5Seurat file format is specifically designed for the storage and analysis of multi-modal single-cell and spatially-resolved expression experiments, for example, from CITE-seq or 10X Visium technologies. It holds all molecular information and associated metadata, including (for example) nearest-neighbor graphs, dimensional reduction information, spatial coordinates and image data, and cluster labels. We also support rapid and on-disk conversion between h5Seurat and AnnData objects, with the goal of enhancing interoperability between Seurat and Scanpy.

Homepage:

https://mojaveazure.github.io/seurat-disk/

Developer docs:

https://github.com/mojaveazure/seurat-disk

License:

GPL3 / GPL-3.0-only

Recipe:

/r-seurat-disk/meta.yaml

package r-seurat-disk

versions:

0.0.0.9021-0

depends r-base:

>=4.3,<4.4.0a0

depends r-cli:

>=2.0.1

depends r-crayon:

>=1.3.4

depends r-hdf5r:

>=1.3.0

depends r-matrix:

>=1.2.18

depends r-r6:

>=2.4.1

depends r-rlang:

>=0.4.4

depends r-seurat:

>=3.2.0

depends r-seuratobject:

>=4.0.0

depends r-stringi:

>=1.4.6

depends r-withr:

>=2.1.2

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 r-seurat-disk

and update with::

   mamba update r-seurat-disk

To create a new environment, run:

mamba create --name myenvname r-seurat-disk

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/r-seurat-disk:<tag>

(see `r-seurat-disk/tags`_ for valid values for ``<tag>``)

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