Package Recipe 'r-loom'

recipe r-loom

An interface for the single-cell RNAseq-oriented loom format. Loom files are an HDF5-based format for storing and interacting with large single-cell RNAseq datasets. loomR provides an interface for working with loom files in a loom-specific way; we provide routines for validating loom files, iterating with chunks through data within the loom file, and provide a platform for other packages to build support for loom files.

Homepage:: https://github.com/mojaveazure/loomR
License:: GPL3 / GPL-3
Recipe:: /r-loom/meta.yaml

package r-loom¶

Versions:

0.2.0.2-7, 0.2.0.2-6, 0.2.0.2-5, 0.2.0.2-4, 0.2.0.2-3, 0.2.0.2-2, 0.2.0.2-1, 0.2.0.2-0, 0.2.0.1-0

Depends:

on icu >=64
on r-base >=4.4,<4.5.0a0
on r-hdf5r
on r-iterators
on r-itertools
on r-matrix
on r-pbapply
on r-stringr

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-loom

to add into an existing workspace instead, run:

pixi add r-loom

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-loom

Alternatively, to install into a new environment, run:

conda create -n envname r-loom

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-loom:<tag>

(see r-loom/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-loom/README.html)