Package Recipe 'bioconductor-hca'

recipe bioconductor-hca

Exploring the Human Cell Atlas Data Coordinating Platform

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/hca.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-hca/meta.yaml

This package provides users with the ability to query the Human Cell Atlas data repository for single-cell experiment data. The `projects()`, `files()`, `samples()` and `bundles()` functions retrieve summary information on each of these indexes; corresponding `*_details()` are available for individual entries of each index. File-based resources can be downloaded using `files_download()`. Advanced use of the package allows the user to page through large result sets, and to flexibly query the 'list-of-lists' structure representing query responses.

package bioconductor-hca¶

Versions:

1.14.0-0, 1.10.0-0, 1.8.1-0, 1.6.0-0, 1.2.0-0, 1.0.0-0

Depends:

on bioconductor-biocfilecache >=2.14.0,<2.15.0
on r-base >=4.4,<4.5.0a0
on r-digest
on r-dplyr
on r-dt
on r-httr
on r-jsonlite
on r-miniui
on r-readr
on r-shiny
on r-tibble
on r-tidyr

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 bioconductor-hca

to add into an existing workspace instead, run:

pixi add bioconductor-hca

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 bioconductor-hca

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-hca

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/bioconductor-hca:<tag>

(see bioconductor-hca/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/bioconductor-hca/README.html)