recipe bioconductor-tmexplorer

A Collection of Tumour Microenvironment Single-cell RNA Sequencing Datasets and Corresponding Metadata

Homepage:

https://bioconductor.org/packages/3.17/data/experiment/html/TMExplorer.html

License:

Artistic-2.0

Recipe:

/bioconductor-tmexplorer/meta.yaml

This package provides a tool to search and download a collection of tumour microenvironment single-cell RNA sequencing datasets and their metadata. TMExplorer aims to act as a single point of entry for users looking to study the tumour microenvironment at the single cell level. Users can quickly search available datasets using the metadata table and then download the ones they are interested in for analysis.

package bioconductor-tmexplorer

(downloads) docker_bioconductor-tmexplorer

versions:

1.10.0-0,  1.8.0-0,  1.4.0-1,  1.4.0-0,  1.2.1-0,  1.0.1-0,  0.99.6-0

depends bioconductor-biocfilecache:

>=2.8.0,<2.9.0

depends bioconductor-data-packages:

>=20230706

depends bioconductor-singlecellexperiment:

>=1.22.0,<1.23.0

depends curl:

depends r-base:

>=4.3,<4.4.0a0

depends r-matrix:

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-tmexplorer

and update with::

   mamba update bioconductor-tmexplorer

To create a new environment, run:

mamba create --name myenvname bioconductor-tmexplorer

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-tmexplorer:<tag>

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

Download stats

Link to this page

Render an install-with-bioconda 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-tmexplorer/README.html)