Package Recipe 'r-seurat-disk'

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:

0.0.0.9021-2, 0.0.0.9021-1, 0.0.0.9021-0

Depends:

on r-base >=4.4,<4.5.0a0
on r-cli >=2.0.1
on r-crayon >=1.3.4
on r-hdf5r >=1.3.0
on r-matrix >=1.2.18
on r-r6 >=2.4.1
on r-rlang >=0.4.4
on r-seurat >=3.2.0
on r-seuratobject >=4.0.0
on r-stringi >=1.4.6
on r-withr >=2.1.2

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 r-seurat-disk

to add into an existing workspace instead, run:

pixi add r-seurat-disk

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 r-seurat-disk

Alternatively, to install into a new environment, run:

conda create -n envname r-seurat-disk

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/r-seurat-disk:<tag>

(see r-seurat-disk/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/r-seurat-disk/README.html)