recipe bioconductor-treg

Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/TREG.html

License:

Artistic-2.0

Recipe:

/bioconductor-treg/meta.yaml

RNA abundance and cell size parameters could improve RNA-seq deconvolution algorithms to more accurately estimate cell type proportions given the different cell type transcription activity levels. A Total RNA Expression Gene (TREG) can facilitate estimating total RNA content using single molecule fluorescent in situ hybridization (smFISH). We developed a data-driven approach using a measure of expression invariance to find candidate TREGs in postmortem human brain single nucleus RNA-seq. This R package implements the method for identifying candidate TREGs from snRNA-seq data.

package bioconductor-treg

(downloads) docker_bioconductor-treg

versions:

1.6.0-0,  1.4.0-0,  1.2.0-0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-matrix:

depends r-purrr:

depends r-rafalib:

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-treg

and update with::

   mamba update bioconductor-treg

To create a new environment, run:

mamba create --name myenvname bioconductor-treg

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-treg:<tag>

(see `bioconductor-treg/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-treg/README.html)